release cand. 2

Dataset/LiveStudy/Patches

@@ -1,119 +0,0 @@
-BC_UNCONFIRMED_CAST
-BC_UNCONFIRMED_CAST_OF_RETURN_VALUE  Comments: no any useful common fix patterns.
-EI_EXPOSE_REP
-EI_EXPOSE_REP2
-IS2_INCONSISTENT_SYNC
-NM_METHOD_NAMING_CONVENTION
-
-DE_MIGHT_IGNORE        Compile failed.
-DLS_DEAD_LOCAL_STORE   Compile failed
-NP_LOAD_OF_KNOWN_NULL_VALUE
-
-DM_CONVERT_CASE    To be improved
-
-DM_BOXED_PRIMITIVE_FOR_PARSING
-DM_DEFAULT_ENCODING
-DM_FP_NUMBER_CTOR
-DM_NUMBER_CTOR
-ES_COMPARING_STRINGS_WITH_EQ   Comments: ignored
-
-MS_PKGPROTECT
-MS_SHOULD_BE_FINAL  Comments: failed to checkstyle.
-
-NP_NONNULL_RETURN_VIOLATION
-NP_NULL_ON_SOME_PATH
-NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE
-NP_PARAMETER_MUST_BE_NONNULL_BUT_MARKED_AS_NULLABLE
-OBL_UNSATISFIED_OBLIGATION
-OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE
-ODR_OPEN_DATABASE_RESOURCE
-OS_OPEN_STREAM
-OS_OPEN_STREAM_EXCEPTION_PATH
-PZLA_PREFER_ZERO_LENGTH_ARRAYS
-RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE
-RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE
-REC_CATCH_EXCEPTION
-RI_REDUNDANT_INTERFACES
-RV_RETURN_VALUE_IGNORED_BAD_PRACTICE
-RV_RETURN_VALUE_IGNORED_NO_SIDE_EFFECT
-SBSC_USE_STRINGBUFFER_CONCATENATION
-SE_NO_SERIALVERSIONID
-SF_SWITCH_NO_DEFAULT
-SIC_INNER_SHOULD_BE_STATIC
-SIC_INNER_SHOULD_BE_STATIC_ANON
-SQL_PREPARED_STATEMENT_GENERATED_FROM_NONCONSTANT_STRING
-ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD
-UC_USELESS_CONDITION
-UC_USELESS_OBJECT
-UCF_USELESS_CONTROL_FLOW
-UPM_UNCALLED_PRIVATE_METHOD
-URF_UNREAD_FIELD
-URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD
-UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR
-UWF_UNWRITTEN_FIELD
-VA_FORMAT_STRING_USES_NEWLINE
-WMI_WRONG_MAP_ITERATOR
-
-
-rejected 1 https://github.com/apache/commons-io/pull/47
-rejected 1 https://github.com/apache/commons-io/pull/45
-
-rejected 1 https://github.com/apache/commons-lang/pull/298
-         5 https://github.com/apache/commons-lang/pull/297
-improved 1 https://github.com/apache/commons-lang/pull/297   Comments: some patches failed to pass test cases, some patches led to compile failed, some patches led to checkstyle failed.
-
-         2 https://github.com/apache/commons-math/pull/69
-         1 https://github.com/apache/commons-math/pull/68    Comments: inner static class, there is no need to fix the violations in this kind of class.
-         2 https://github.com/apache/commons-math/pull/67    Comments: improve patches.
-         1 https://github.com/apache/commons-math/pull/66
-
-rejected 1 https://github.com/apache/ant/pull/47
-improved 1 https://github.com/apache/ant/pull/46
-merged   2 https://github.com/apache/ant/pull/46
-	     2 https://github.com/apache/ant/pull/45
-rejected 3 https://github.com/apache/ant/pull/44
-merged   1 https://github.com/apache/ant/pull/43
-merged   5 https://github.com/apache/ant/pull/42    Comments: need to import new packages, unless the fixed patches will fail to compile.
-merged   1 https://github.com/apache/ant/pull/41
-
-         1 https://github.com/apache/aries/pull/80
-         1 https://github.com/apache/aries/pull/79
-         1 https://github.com/apache/aries/pull/78
-         1 https://github.com/apache/aries/pull/77
-         1 https://github.com/apache/aries/pull/76
-
-rejected 1 https://github.com/apache/camel/pull/2031 ShouldBeFinal
-rejected 6 https://github.com/apache/camel/pull/2029 master5
-merged   1 https://github.com/apache/camel/pull/2035 master7
-merged   2 https://github.com/apache/camel/pull/2032 Useless
-merged   2 https://github.com/apache/camel/pull/2025 master6
-merged   1 https://github.com/apache/camel/pull/2024 master4
-merged   1 https://github.com/apache/camel/pull/2023 master2
-rejected 1 https://github.com/apache/camel/pull/2017 master3        Comments: compile failed, the return value of method invocation is not Boolean, it is a specific case.
-merged   1 https://github.com/apache/camel/pull/2016 master
-merged   6 https://github.com/apache/camel/pull/2038 boxedParsing
-
-
-         3 https://github.com/apache/cassandra/pull/165
-         4 https://github.com/apache/cassandra/pull/164
-         2 https://github.com/apache/cassandra/pull/163
-         
-Fixed    1 https://github.com/fangyidong/json-simple/pull/126    Comments: fixed in another version.          https://github.com/RalleYTN/SimpleJSON
-         1 https://github.com/fangyidong/json-simple/pull/125
-         
-On hold  1 https://github.com/apache/mahout/pull/346
-         1 https://github.com/apache/mahout/pull/345
-         1 https://github.com/apache/mahout/pull/344
-         
-merged   2 https://github.com/apache/poi/pull/77 5
-merged   4 https://github.com/apache/poi/pull/78 6
-merged   2 https://github.com/apache/poi/pull/79 t
-merged   1 https://github.com/apache/poi/pull/80 4
-merged   4 https://github.com/apache/poi/pull/76 2
-merged  30 https://github.com/apache/poi/pull/75 master
-merged   1 https://github.com/apache/poi/pull/74 3
-
-
-
-Some violations never happened in these projects: 
-

Dataset/Patterns/Fix-Patterns

@@ -1,131 +0,0 @@
-=====================================
-=========Useful Fix Patterns=========
-=====================================
-==============Detailed===============
-DM_CONVERT_CASE
-	(1) ADD a rule of Locale.ENGLISH into toLowerCase/toUpperCase. 
-RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE
-	(1) DEL Null-Check IfStatement, 
-	(2) DEL Null-Check Conditional Expression. 
-REC_CATCH_EXCEPTION
-	(1) Change Exception to a specific exception class.
-SE_NO_SERIALVERSIONID
-	(1) Insert a private static final field serialVersionUID.  
-VA_FORMAT_STRING_USES_NEWLINE
-	(1) DEL "$backslash$n", 
-	(2) Replace "$backslash$n" with "n" 
-MS_SHOULD_BE_FINAL
-	(1) ADD a ``final'' modifier. 
-WMI_WRONG_MAP_ITERATOR
-	(1) Replace the KeySet iterating ForStatement with an EntrySet iterating ForStatement. 
-DM_NUMBER_CTOR
-	(1) Replace the NumberType ClassInstanceCreation with a NumberType.valueOf() method invocation.
-SIC_INNER_SHOULD_BE_STATIC
-	(1) ADD a "static" modifier, 
-	(2) DEL the buggy statements. 
-DE_MIGHT_IGNORE
-    (1) Change Exception to a specific exception class.
-DM_BOXED_PRIMITIVE_FOR_PARSING
-	(1) Replace NumberType.valueOf() with NumberType.parseNumberType().
-DM_FP_NUMBER_CTOR  
-	(1) DEL the buggy statement, 
-	(2) Replace Double or Float ClassInstanceCreation with (Double or Float).valueOf(), 
-	(3) Remove the Double or Float ClassInstanceCreation from the buggy expression. 
-MS_PKGPROTECT
-	(1) DEL the buggy statement, 
-	(2) DEL the ``public'' or ``protected'' modifier 
-	(3) Replace the ``public'' or ``protected'' modifier with the ``private'' modifier. 
-	(4) DEL the initialization expression.
-ES_COMPARING_STRINGS_WITH_EQ   
-	(1) Replace the ``=='' InfixExpression with a stringVar.equals() method invocation. 
-
-
-===============Abstract==============  
-NP_NULL_ON_SOME_PATH
-    (1) ADD a Null-check statement or expression.  
-RI_REDUNDANT_INTERFACES
-	(1) DEL the implemented Interface type.  
-NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE
-	(1) ADD a Null-check statement or expression, 
-	(2) DEL the buggy statement. 
-UCF_USELESS_CONTROL_FLOW
-	(1) DEL the buggy statement, 
-	(2) DEL the useless ConditionalExpression. 
-UC_USELESS_CONDITION   
-	(1) UPD the operator of a ConditionalExpersion, 
-	(2) UPD an sub-expression of a ConditionExpression. 
-NP_LOAD_OF_KNOWN_NULL_VALUE
-	(1) DEL Null-check expression or statement,
-	(2) Replace the null-known variable with NULL.	
-SBSC_USE_STRINGBUFFER_CONCATENATION
-	(1) Replace String type with StringBuilder, and replace plus operator of StringVarialbe with the append method of StringBuilder.
-UC_USELESS_OBJECT
-    (1) DEL the buggy statement.  
-UPM_UNCALLED_PRIVATE_METHOD
-	(1) DEL the buggy statements. 
-NM_METHOD_NAMING_CONVENTION
-	(1) Update Method Name of MethodDeclaration.
-URF_UNREAD_FIELD
-	(1) DEL the buggy statement.
-=====================================
-NP_NONNULL_RETURN_VIOLATION
-	(1) DEL the null-returned ReturnStatement. 
-	(2) Replace NullLiteral with an Expression which returns an empty list. 
-PZLA_PREFER_ZERO_LENGTH_ARRAYS
-	(1) DEL the buggy statement, 
-  √ (2) Replace NullLiteral with an empty array. 
-SIC_INNER_SHOULD_BE_STATIC_ANON
-	(1) DEL a parameter of a ClassInstanceCreation in an AnonymousClassDeclaration, 
-	(2) DEL the statement contains an AnonymousClassDeclaration, 
-  √ (3) Replace the AnonymousClassDeclaration with an defined Static Object of this class.
-DLS_DEAD_LOCAL_STORE
-	(1) DEL the buggy statement. 
-DM_DEFAULT_ENCODING
-  √ (1) ADD a parameter (i.e., "UTF-8") into the ClassInstanceCreation of a Stream object. 
-	(2) Replace ClassInstanceCreation with a MethodInvocation. 
-	(3) DEL the buggy statement.
-BC_UNCONFIRMED_CAST
-	(1) DEL the buggy statement,
-	(2) DEL the Cast Type,
-	(3) Replace CastExpression with NullLiteral.
-URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD
-	(1) ADD a ``final'' modifier, 
-  √ (2) DEL the buggy statement.
-RV_RETURN_VALUE_IGNORED_BAD_PRACTICE
-	(1) Replace boolean-returned statement with a a new MethodInvocation. 
-  √ (2) ADD an IfStatement.
-EI_EXPOSE_REP
-	(1) DEL the buggy statement, 
-  * (2) Replace the being assigned Expression with a ConditionalExpression.
-  √ (3) Replace the Expression being assigned with other Expression
-EI_EXPOSE_REP2
-	(1) DEL the buggy statement, 
-  * (2) Replace the being assigned Expression with a ConditionalExpression. 
-  √ (3) Replace the being assigned Expression with other Expression.
-  
-=====================================
-==========Null Fix Patterns==========
-=====================================
-UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR                   null.   
-OBL_UNSATISFIED_OBLIGATION   							   null.
-OS_OPEN_STREAM_EXCEPTION_PATH   						   null. 
-SF_SWITCH_NO_DEFAULT   									   null.  
-UWF_UNWRITTEN_FIELD  									   null.  
-IS2_INCONSISTENT_SYNC  									   null.  
-ODR_OPEN_DATABASE_RESOURCE 								   null.  
-SQL_PREPARED_STATEMENT_GENERATED_FROM_NONCONSTANT_STRING   null. 
-OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE				   null.  
-OS_OPEN_STREAM   										   null. 
-NP_PARAMETER_MUST_BE_NONNULL_BUT_MARKED_AS_NULLABLE		   null. 
-
-=====================================
-========Useless Fix Patterns=========
-=====================================
-BC_UNCONFIRMED_CAST_OF_RETURN_VALUE
-	(1) UPD T1 v1 = (T1) method_invocation() with T2 v1 = method_invocation(), 
-	(2) DEL the buggy statement, 
-	(3) Replace the buggy CastExpresion with a MethodInvocation.
-ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD
-	(1) DEL the buggy statement.  
-RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE
-	(1) ADD a Null-check statement or expression. 

Dataset/Patterns/Source-Code-Patterns-Unfixed-Violations

@@ -1,107 +0,0 @@
-================================
-=========Single Pattern=========
-================================
-SIC_INNER_SHOULD_BE_STATIC_ANON:  new Type() { override some methods(...){...} }. Anonymous inner class declaration. 100%
-DE_MIGHT_IGNORE:  try{...} catch (Exception e) {...}, Exception is not any specified. 
-VA_FORMAT_STRING_USES_NEWLINE:  "\n", this new line symbol is in a StringLiteral of a format method.
-UCF_USELESS_CONTROL_FLOW:  if (conditional expression) {empty statements.}. 
-UC_USELESS_CONDITION:  if (conditional expressions) {...}. 
-UC_USELESS_OBJECT:  T1 v1 = new T1().
-PZLA_PREFER_ZERO_LENGTH_ARRAYS:  return null. 
-EI_EXPOSE_REP:  return variable;
-REC_CATCH_EXCEPTION:  try{...} catch (Exception e) {...}, Exception is not any specific exception.
-SF_SWITCH_NO_DEFAULT:  switch(exp) {case1:...case2:...}, without default statement.
-UWF_UNWRITTEN_FIELD:  return exp / variable. 
-SBSC_USE_STRINGBUFFER_CONCATENATION:  stringVariable += stringExp, 
-RV_RETURN_VALUE_IGNORED_NO_SIDE_EFFECT:  return method_invocation_exp. Method invocation statement returns a value, but does not assign the value to any variable. (High false positives.)  
-NP_NONNULL_RETURN_VIOLATION:  return null.     (High false positives.) 
-================================
-========Multiple Patterns=======
-================================
-NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE:  (1) for (File file : filesArray) {...} (2) for (int i =0; i < filesArray.length; i ++) {...}
-DM_CONVERT_CASE:  (1) stringExp.toLowerCase(), 24,897  
-				  (2)stringExp.toUpperCase(). 10,406
-MS_PKGPROTECT:  (1) public static final T1 v1 = initializationExp, 2442
-	 				(2) protected static final T1 v1 = initializationExp. 175
-	 				(3) protected static T1 v1 = initializationExp. 158
-	 				(4) public static T1 v1 = initializationExp. 262,      other 46
-SIC_INNER_SHOULD_BE_STATIC:  (1) this.v1 = v2; 590
- 							 (2) v1 = v2;  170
- 							 (3) super(...). 213
-BC_UNCONFIRMED_CAST:  (1) T1 v1 = (T(1) v2/exp, (2) v1 = (T(1) v2/exp, (3) ((T(1) v2).exp.
-ES_COMPARING_STRINGS_WITH_EQ:  (1) stringExp1 == stringExp2    IfStatement, ReturnStatement, WhileStatement.
-							   (2) stringExp1 != stringExp2
-RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE:  (1) if (exp == null ...) {...}, 
-										   (2) if (exp != null ...) {...}, 
-										   (3) exp == null ? exp1 : exp2, 
-										   (4) exp != null ? exp1 : exp2.
-DM_NUMBER_CTOR:  (1) new Long(...), (2)new Integer(...), (3)new Short(...), (4)new Byte(...), (5)new Char(...).
-DM_FP_NUMBER_CTOR:  (1) new Double(exp), (2)new Float(exp). 
-DM_BOXED_PRIMITIVE_FOR_PARSING:  (1) Integer.valueOf(str), (2)Long.valueOf(str).  Comments: it contains fewer patterns than findbugs.	
-EI_EXPOSE_REP2:  (1) this.v1 = v2,
-				 (2) v1 = v2. 3700												
-BC_UNCONFIRMED_CAST_OF_RETURN_VALUE:  (1) T1 v1 = (T) method_invocation(),
-									  (2) v1 = (T) method_invocation(), 
-									  (3) ((T) method_invocation()).exp. 
-ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD:  (1) static_v1 = instance_exp1.method_invocation(),
-										  (2) v1 = instance_exp1.method_invocation(), 
-										  (3) v1 = exp1, other variable assignment statement. 
-RV_RETURN_VALUE_IGNORED_BAD_PRACTICE:  (1) File.mkdirs(), 
-									   (2) File.mkdir(), 
-									   (3) File.delete(), 
-									   (4) File.createNewFile(), 
-									       (5) other exp.method_invoation() returns a value. 
-SQL_PREPARED_STATEMENT_GENERATED_FROM_NONCONSTANT_STRING:  (1) sqlExecutionStatement = StringLiteral1 + stringV1 + ... +  StringLiteral2 + stringV2. 
-														   (2) sqlRelatedVariable = sqlRelatedMethodInvocation();
-OS_OPEN_STREAM:  (1) StreamType v = new StreamType(...), 2) streamVariable = new StreamType(new StreamType2(...)), e.g., 1. FileOutputStream fos = new FileOutputStream(outFile); 
-DM_DEFAULT_ENCODING:  (1) new BufferedReader(new InputStreamReader(input)), 99+ 
-					  (2) new StreamWriter(output); 
-					  (3) stringExp.getBytes(), 
-					  (4) new String(byteExp), 
-					  (5) byteExp.toString().
-ODR_OPEN_DATABASE_RESOURCE:  (1) conn.createStatement(), 
-							 (2) conn.createStatement.execute(...), 
-							 (3) PreparedStatement st = conn.prepareStatement(), 
-							 (4) DataBaseConnection conn = exp.getConnection(...). 		
-NP_PARAMETER_MUST_BE_NONNULL_BUT_MARKED_AS_NULLABLE:  (1) return method_invocation(...), 2) return class_instance_creation(...). 	                  
-========================================
-==========Inefficient Patterns==========
-========================================
-OBL_UNSATISFIED_OBLIGATION:  (1) StreamType v = new StreamType(...), 
-							 (2) streamVariable = new StreamType(new StreamType2(...)), 
-							 (3) sqlStatementExp.executeMethod(). e.g., 1. FileOutputStream fos = new FileOutputStream(outFile); 2. ResultSet rs = sqlStmt.executeQuery().
-OS_OPEN_STREAM_EXCEPTION_PATH:  (1) StreamType v = new StreamType(...), 
-								(2) streamVariable = new StreamType(...).
-IS2_INCONSISTENT_SYNC:  (1) return v1, 
-						(2) if(conditionalExp) {...}, 
-						(3) sqlStmt = stringLiteral1 + stringExp + stringLiteral2.   not very consistent. 
-OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE:  (1) StreamType v = new StreamType(...), 
-											(2) streamVariable = new StreamType(new StreamType2(...)), 
-											(3) sqlStatementExp.executeMethod(). e.g., 1. FileOutputStream fos = new FileOutputStream(outFile); 2. ResultSet rs = sqlStmt.executeQuery(). 
-WMI_WRONG_MAP_ITERATOR:  for statement { ... MapVariable.get(keyExp) ... }.   or NULL.  Lack of enough information.
-========================================
-=====Redundant Inconsistent Pattern=====
-========================================
-MS_SHOULD_BE_FINAL:  (1) public (28,302) static T1 v1 = exp. e.g., public static int maxStringLength = 65535. 
-					 (2) protected (6,719) static T1 v1 = exp.
-URF_UNREAD_FIELD:  (1) this.v1 = v2, (2)this.v1 = new T(), (3)private Type v = exp.		Comments: it contains more patterns than findbugs.  only pattern 3 is consistent.
-URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD:  (1) this.v1 = v2,  
-									   (2) public/protected (static) T1 v1 = exp;       Comments: only 2 is consistent.
-									   (3) v1 = exp1.
-========================================
-=========Inconsistent Patterns=========
-========================================						
-RI_REDUNDANT_INTERFACES:  super(...). Comments: not very consistent. Locate on the position of super classes.
-========================================
-==============Null Pattern==============
-========================================	
-===========Inaccurate Position==========
-NM_METHOD_NAMING_CONVENTION:               null.   Comments: violate on title, but position locates on body.
-SE_NO_SERIALVERSIONID:                     null.  
-UPM_UNCALLED_PRIVATE_METHOD: 			   null.   (method body) 
-UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR:  null.   inaccurate positions.
-==========Specific Source Code==========
-DLS_DEAD_LOCAL_STORE:                      null.   Variable assignment statements.    Comments: specific source code.
-NP_NULL_ON_SOME_PATH:  					   null. 
-NP_LOAD_OF_KNOWN_NULL_VALUE:               null.
-RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE:  null. 

FixPatternMiner.iml

@@ -11,15 +11,6 @@
     <orderEntry type="inheritedJdk" />
     <orderEntry type="sourceFolder" forTests="false" />
     <orderEntry type="library" name="Maven: org.javatuples:javatuples:1.2" level="project" />
-    <orderEntry type="module" module-name="simple-utils" />
-    <orderEntry type="library" name="Maven: org.apache.poi:poi:3.12" level="project" />
-    <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.9" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml:3.12" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml-schemas:3.12" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlbeans:xmlbeans:2.6.0" level="project" />
-    <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
-    <orderEntry type="library" name="Maven: net.sourceforge.jexcelapi:jxl:2.6.12" level="project" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.14" level="project" />
     <orderEntry type="library" name="Maven: com.typesafe.akka:akka-actor_2.11:2.4.11" level="project" />
     <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.8" level="project" />
     <orderEntry type="library" name="Maven: com.typesafe:config:1.3.0" level="project" />
@@ -27,9 +18,18 @@
     <orderEntry type="module" module-name="core" />
     <orderEntry type="library" name="Maven: com.github.mpkorstanje:simmetrics-core:3.0.3" level="project" />
     <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
+    <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.10" level="project" />
     <orderEntry type="library" name="Maven: net.sf.trove4j:trove4j:3.0.3" level="project" />
     <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.3" level="project" />
     <orderEntry type="module" module-name="gen.jdt" />
+    <orderEntry type="library" name="Maven: edu.lu.uni:simple-utils:0.0.1-SNAPSHOT" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.poi:poi:3.12" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml:3.12" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml-schemas:3.12" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.xmlbeans:xmlbeans:2.6.0" level="project" />
+    <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
+    <orderEntry type="library" name="Maven: net.sourceforge.jexcelapi:jxl:2.6.12" level="project" />
+    <orderEntry type="library" name="Maven: log4j:log4j:1.2.14" level="project" />
     <orderEntry type="library" name="Maven: org.eclipse.core:runtime:3.10.0-v20140318-2214" level="project" />
     <orderEntry type="library" name="Maven: org.eclipse:osgi:3.10.0-v20140606-1445" level="project" />
     <orderEntry type="library" name="Maven: org.eclipse.equinox:common:3.6.200-v20130402-1505" level="project" />
@@ -43,20 +43,12 @@
     <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.7.7" level="project" />
     <orderEntry type="library" name="Maven: ch.qos.logback:logback-classic:1.1.2" level="project" />
     <orderEntry type="library" name="Maven: ch.qos.logback:logback-core:1.1.2" level="project" />
-    <orderEntry type="module" module-name="GitTraveller" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.7" level="project" />
-    <orderEntry type="library" name="Maven: org.jsoup:jsoup:1.11.2" level="project" />
-    <orderEntry type="library" name="Maven: org.eclipse.jgit:org.eclipse.jgit:4.7.0.201704051617-r" level="project" />
-    <orderEntry type="library" name="Maven: com.jcraft:jsch:0.1.54" level="project" />
-    <orderEntry type="library" name="Maven: com.googlecode.javaewah:JavaEWAH:1.1.6" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.3.6" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.3.3" level="project" />
-    <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.3" level="project" />
     <orderEntry type="library" name="Maven: junit:junit:4.11" level="project" />
     <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
     <orderEntry type="library" name="Maven: redis.clients:jedis:2.8.1" level="project" />
     <orderEntry type="library" name="Maven: org.apache.commons:commons-pool2:2.4.2" level="project" />
     <orderEntry type="library" name="Maven: org.apache.commons:commons-text:1.3" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.7" level="project" />
     <orderEntry type="library" name="Maven: com.rabbitmq:amqp-client:4.0.0" level="project" />
   </component>
 </module>

inputData/1.txt

@@ -1,730 +0,0 @@
-https://github.com/IDPF/epubcheck.git
-https://github.com/treasure-data/td-import-java.git
-https://github.com/Atmosphere/atmosphere-extensions.git
-https://github.com/astefanutti/camel-cdi.git
-https://github.com/imagej/imagej-ui-swing.git
-https://github.com/komoot/photon.git
-https://github.com/FIWARE-Middleware/KIARA.git
-https://github.com/mbosecke/pebble.git
-https://github.com/metamx/java-util.git
-https://github.com/contextproject/discover.git
-https://github.com/btrplace/scheduler.git
-https://github.com/tuwiendsg/rSYBL.git
-https://github.com/sker65/go-dmd-clock.git
-https://github.com/liferay/liferay-maven-support.git
-https://github.com/0xCopy/RelaxFactory.git
-https://github.com/caskdata/hydrator-plugins.git
-https://github.com/joelittlejohn/jsonschema2pojo.git
-https://github.com/ArcBees/gwtquery.git
-https://github.com/redpen-cc/redpen.git
-https://github.com/sviperll/chicory.git
-https://github.com/spotify/cassandra-reaper.git
-https://github.com/sakai-mirror/calendar.git
-https://github.com/notthebees/languagegames.git
-https://github.com/imagej/ij1-patcher.git
-https://github.com/cjdev/versions-maven-plugin.git
-https://github.com/phax/as2-lib.git
-https://github.com/RolecraftDev/RolecraftCore.git
-https://github.com/dbs-leipzig/gradoop.git
-https://github.com/dbsoftcombr/dbssdk.git
-https://github.com/shabbies/clockwork.git
-https://github.com/skillcoyne/IGCSA.git
-https://github.com/GlobalTechnology/idm-user-management.git
-https://github.com/instance01/MinigamesAPI.git
-https://github.com/jaywarrick/JEX.git
-https://github.com/mwcaisse/AndroidFT.git
-https://github.com/figarocms/cucumber-jvm-fixtures.git
-https://github.com/jillesvangurp/jsonj.git
-https://github.com/SonarSource/sslr.git
-https://github.com/OpenTreeOfLife/taxomachine.git
-https://github.com/The-Dream-Team/Tardis.git
-https://github.com/digipost/digipost-api-client-java.git
-https://github.com/nuxeo/nuxeo-platform-video.git
-https://github.com/INL/BlackLab.git
-https://github.com/andrewgaul/s3proxy.git
-https://github.com/OpenRock/OpenICF-java-framework.git
-https://github.com/blurpy/kouchat-android.git
-https://github.com/hypercube1024/firefly.git
-https://github.com/Poweruser/MinetickMod.git
-https://github.com/exoplatform/wiki.git
-https://github.com/Bukkit/Bukkit.git
-https://github.com/zanata/zanata-api.git
-https://github.com/stripe/stripe-java.git
-https://github.com/allanbank/mongodb-async-driver.git
-https://github.com/AMOSTeam3/amos-ss15-proj3.git
-https://github.com/groovy/GMavenPlus.git
-https://github.com/SUSE/saltstack-netapi-client-java.git
-https://github.com/nuxeo/nuxeo-chemistry.git
-https://github.com/wattdepot/wattdepot.git
-https://github.com/nuxeo/nuxeo-platform-forms-layout-demo.git
-https://github.com/deeplearning4j/nd4j.git
-https://github.com/NFSdb/nfsdb.git
-https://github.com/cismet/cids-server.git
-https://github.com/sarahtattersall/PIPE.git
-https://github.com/apache/maven-shared.git
-https://github.com/daisy/pipeline-mod-braille.git
-https://github.com/jenkinsci/xunit-plugin.git
-https://github.com/jclouds/jclouds-karaf.git
-https://github.com/DICE-UNC/jargon.git
-https://github.com/ancoron/glassfish-main.git
-https://github.com/FallenMoonNetwork/CanaryLib.git
-https://github.com/phillipsic/SeleniumDriverFramework.git
-https://github.com/dekellum/iudex.git
-https://github.com/apache/openjpa.git
-https://github.com/Praqma/cool.git
-https://github.com/SciGraph/SciGraph.git
-https://github.com/TeamShadow/shadow.git
-https://github.com/cowtowncoder/ClusterMate.git
-https://github.com/shubhcollaborator/common-csvnew.git
-https://github.com/albfan/jmeld.git
-https://github.com/strongbox/strongbox.git
-https://github.com/dropwizard/metrics.git
-https://github.com/Studentmediene/Momus.git
-https://github.com/apache/continuum.git
-https://github.com/jenkinsci/junit-plugin.git
-https://github.com/pcpratts/rootbeer1.git
-https://github.com/nieshr/xjr.git
-https://github.com/LiveRamp/hank.git
-https://github.com/ralscha/extdirectspring.git
-https://github.com/sjanaud/jensoft-core.git
-https://github.com/marschraner/svm.git
-https://github.com/LEDS/sincap-entities.git
-https://github.com/AugGroup/hr-db.git
-https://github.com/MineSworn/UltimateArena.git
-https://github.com/benas/easy-batch.git
-https://github.com/ocpsoft/rewrite.git
-https://github.com/square/dagger.git
-https://github.com/pgjdbc/pgjdbc.git
-https://github.com/membrane/service-proxy.git
-https://github.com/getsentry/raven-java.git
-https://github.com/jboss-javassist/javassist.git
-https://github.com/mybatis/mybatis-3.git
-https://github.com/opendaylight/groupbasedpolicy.git
-https://github.com/Bammerbom/UltimateCore.git
-https://github.com/mrniko/netty-socketio.git
-https://github.com/searchbox-io/Jest.git
-https://github.com/jo-pol/DiBL.git
-https://github.com/sukirtigupta/slf4j.git
-https://github.com/immutables/immutables.git
-https://github.com/dumptruckman/PluginBase.git
-https://github.com/TridentSDK/TridentSDK.git
-https://github.com/johan-martenson/settlers.git
-https://github.com/lightblue-platform/lightblue-core.git
-https://github.com/cismet/cismet-gui-commons.git
-https://github.com/dakusui/jcunit.git
-https://github.com/Pi4J/pi4j.git
-https://github.com/lutece-secteur-public/espacepublic-plugin-dansmarue.git
-https://github.com/lexicalscope/svm.git
-https://github.com/ucam-cl-dtg/urop-2013-questions.git
-https://github.com/grzegorz2047/OpenGuild2047.git
-https://github.com/davidsoergel/ml.git
-https://github.com/apache/sirona.git
-https://github.com/Stratio/cassandra-lucene-index.git
-https://github.com/jdr0887/MaPSeq-Pipeline-NCGenes-DX.git
-https://github.com/Azure/azure-sdk-for-java.git
-https://github.com/sakai-mirror/msgcntr.git
-https://github.com/openmrs/openmrs-module-emrapi.git
-https://github.com/openmrs/openmrs-module-mdrtb.git
-https://github.com/iZettle/izettle-toolbox.git
-https://github.com/jmxtrans/jmxtrans.git
-https://github.com/effektif/effektif.git
-https://github.com/DataTorrent/Apex.git
-https://github.com/aeshell/aesh.git
-https://github.com/SophieKoonin/JavaDecaf.git
-https://github.com/jitsi/jitsi-videobridge.git
-https://github.com/renepickhardt/generalized-language-modeling-toolkit.git
-https://github.com/TeamExodus/external_gson.git
-https://github.com/minnal/minnal.git
-https://github.com/soi-toolkit/soi-toolkit-mule.git
-https://github.com/davidmoten/rtree.git
-https://github.com/zendesk/maxwell.git
-https://github.com/apache/commons-compress.git
-https://github.com/hector-client/hector.git
-https://github.com/tubav/fiteagle.git
-https://github.com/AtlasOfLivingAustralia/bie-service.git
-https://github.com/sakai-mirror/basiclti.git
-https://github.com/nuodb/migration-tools.git
-https://github.com/jahlborn/jackcess.git
-https://github.com/SebastianNiemann/ArmadilloJava.git
-https://github.com/RuedigerMoeller/kontraktor.git
-https://github.com/carewebframework/carewebframework-core.git
-https://github.com/BattleNight/BattleNight-Core.git
-https://github.com/apache/directory-studio.git
-https://github.com/apache/creadur-rat.git
-https://github.com/ARUP-NGS/Pipeline.git
-https://github.com/zenbones/SmallMind.git
-https://github.com/jayway/rest-assured.git
-https://github.com/datanucleus/datanucleus-rdbms.git
-https://github.com/TridentSDK/Trident.git
-https://github.com/wildfly-security/wildfly-elytron.git
-https://github.com/mathieu-bellange/ourses-plumes.git
-https://github.com/apache/vxquery.git
-https://github.com/openmrs/openmrs-distro-referenceapplication.git
-https://github.com/apache/httpclient.git
-https://github.com/costamojan/xbean.git
-https://github.com/masatomix/repo.git
-https://github.com/lviggiano/owner.git
-https://github.com/apache/juddi.git
-https://github.com/seulkikims/hashtable.git
-https://github.com/davidkey/supertunnel.git
-https://github.com/irstv/H2GIS.git
-https://github.com/mindwind/craft-atom.git
-https://github.com/relayrides/pushy.git
-https://github.com/jdereg/json-io.git
-https://github.com/Welchd1/resolve-lite.git
-https://github.com/jmacglashan/burlap.git
-https://github.com/fluxroot/hadaps.git
-https://github.com/matthias-mueller/movingcode.git
-https://github.com/aceleradora6-tw/RegistroLivre.git
-https://github.com/st-js/st-js.git
-https://github.com/OpenHFT/HugeCollections.git
-https://github.com/zycgit/hasor.git
-https://github.com/sesuncedu/htmlparser.git
-https://github.com/lsds/SEEP.git
-https://github.com/stephenostermiller/ostermillerutils.git
-https://github.com/FamilySearch/gedcomx-java.git
-https://github.com/apache/ddlutils.git
-https://github.com/optimizationBenchmarking/optimizationBenchmarking.git
-https://github.com/SomMeri/less4j.git
-https://github.com/xwiki/xwiki-rendering.git
-https://github.com/worm1k/OSS_Cauliflower.git
-https://github.com/sakai-mirror/portal.git
-https://github.com/aht-group/ofx.git
-https://github.com/apache/struts.git
-https://github.com/stapler/stapler.git
-https://github.com/cismet/cids-navigator.git
-https://github.com/virgo47/javasimon.git
-https://github.com/xwic/appkit.git
-https://github.com/tehbeard/BeardStat.git
-https://github.com/nuxeo/nuxeo-dam.git
-https://github.com/DavidAlphaFox/jetlang-core.git
-https://github.com/openspim/SPIMAcquisition.git
-https://github.com/dbsoftcombr/dbsfaces.git
-https://github.com/sualeh/DaylightChart.git
-https://github.com/mkovatsc/Californium.git
-https://github.com/meltmedia/cadmium.git
-https://github.com/diirt/graphene.git
-https://github.com/martiner/gooddata-java.git
-https://github.com/jdr0887/MaPSeq-Pipeline-CASAVA.git
-https://github.com/egonw/cdk.git
-https://github.com/AtlasOfLivingAustralia/biocache-service.git
-https://github.com/ChiralBehaviors/Ultrastructure.git
-https://github.com/lobid/lodmill.git
-https://github.com/paul-hammant/qdox.git
-https://github.com/SonarCommunity/sonar-javascript.git
-https://github.com/jim618/multibit.git
-https://github.com/dropwizard/dropwizard.git
-https://github.com/tranzero/SoftServe_Java-105_Project.git
-https://github.com/tinkerpop/blueprints.git
-https://github.com/webbukkit/dynmap.git
-https://github.com/bitcoinj/bitcoinj.git
-https://github.com/AxonFramework/AxonFramework.git
-https://github.com/hawkular/hawkular-metrics.git
-https://github.com/picketlink/picketlink.git
-https://github.com/opendaylight/bgpcep.git
-https://github.com/rage/tmc-cli.git
-https://github.com/openfigis/vme.git
-https://github.com/apache/commons-codec.git
-https://github.com/square/wire.git
-https://github.com/Wikidata/Wikidata-Toolkit.git
-https://github.com/itm/testbed-runtime.git
-https://github.com/tomp2p/TomP2P.git
-https://github.com/j256/ormlite-core.git
-https://github.com/nishihatapalmer/byteseek.git
-https://github.com/rapla/rapla.git
-https://github.com/Bombe/Sone.git
-https://github.com/yusuke/twitter4j.git
-https://github.com/jhpoelen/eol-globi-data.git
-https://github.com/google/error-prone.git
-https://github.com/basho/riak-java-client.git
-https://github.com/jamesagnew/hapi-fhir.git
-https://github.com/brooklyncentral/clocker.git
-https://github.com/spring-projects/spring-data-commons.git
-https://github.com/SonarCommunity/sonar-php.git
-https://github.com/imglib/imglib2.git
-https://github.com/h2oai/h2o.git
-https://github.com/lucmoreau/ProvToolbox.git
-https://github.com/threerings/tripleplay.git
-https://github.com/chapmajs/shiro.git
-https://github.com/zalando-stups/fullstop.git
-https://github.com/airlift/airlift.git
-https://github.com/dcm4che/dcm4che.git
-https://github.com/myui/hivemall.git
-https://github.com/cismet/cismap-commons.git
-https://github.com/suggitpe/java-sandbox.git
-https://github.com/zanata/zanata-client.git
-https://github.com/dalderliesten/Scrumbledore.git
-https://github.com/cojen/Tupl.git
-https://github.com/pendelhaven3/magic.git
-https://github.com/jenkinsci/acceptance-test-harness.git
-https://github.com/gbif/occurrence.git
-https://github.com/OpenHFT/Java-Lang.git
-https://github.com/doanduyhai/Achilles.git
-https://github.com/shilad/wikibrain.git
-https://github.com/xdoo/vaadin-demo.git
-https://github.com/nuxeo/nuxeo-platform-document-routing.git
-https://github.com/jitlogic/zorka.git
-https://github.com/UniTime/unitime.git
-https://github.com/anba/es6draft.git
-https://github.com/yogendra12/Rescuefy.git
-https://github.com/bcdev/ceres.git
-https://github.com/OpenTreeOfLife/treemachine.git
-https://github.com/Carboni/zebedee.git
-https://github.com/Gigaspaces/mongo-datasource.git
-https://github.com/mebigfatguy/fb-contrib.git
-https://github.com/google/guava.git
-https://github.com/mleduque/ide.git
-https://github.com/finmath/finmath-lib.git
-https://github.com/sbwhitecap/Phex-trunk.git
-https://github.com/named-data/jndn.git
-https://github.com/thinkaurelius/titan.git
-https://github.com/apache/accumulo.git
-https://github.com/Activiti/Activiti.git
-https://github.com/apache/pdfbox.git
-https://github.com/apache/servicemix4-bundles.git
-https://github.com/deeplearning4j/deeplearning4j.git
-https://github.com/checkstyle/checkstyle.git
-https://github.com/IntroPV/vainilla.git
-https://github.com/korpling/ANNIS.git
-https://github.com/undertow-io/undertow.git
-https://github.com/arjovanramshorst/bubble-bobble-sem.git
-https://github.com/bcdev/coastcolour.git
-https://github.com/nuxeo/nuxeo-platform-semantic-entities.git
-https://github.com/protegeproject/swrlapi.git
-https://github.com/jenkinsci/envinject-plugin.git
-https://github.com/jensnerche/plantuml.git
-https://github.com/teanutella/AppEmployee.git
-https://github.com/SonarSource/sonar-python.git
-https://github.com/Atmosphere/nettosphere.git
-https://github.com/apache/maven-release.git
-https://github.com/svn2github/commons-vfs2.git
-https://github.com/guibin/Knowledge.git
-https://github.com/kmbulebu/NickNack.git
-https://github.com/alecgorge/jsonapi.git
-https://github.com/aaron-santos/lanterna.git
-https://github.com/Appendium/flatpack.git
-https://github.com/google/closure-templates.git
-https://github.com/XBigTK13X/Aigilas.git
-https://github.com/greese/dasein-cloud-openstack.git
-https://github.com/Graphity/graphity-client.git
-https://github.com/mung3r/ecoCreature.git
-https://github.com/harrifeng/java-in-action.git
-https://github.com/no-hope/java-toolkit.git
-https://github.com/tinman89/tinspx-utils.git
-https://github.com/spring-cloud/spring-cloud-aws.git
-https://github.com/DigitalPebble/storm-crawler.git
-https://github.com/bitbar/testdroid-api.git
-https://github.com/takari/takari-lifecycle.git
-https://github.com/EHRI/ehri-rest.git
-https://github.com/grisu/gricli.git
-https://github.com/FasterXML/jackson-dataformat-xml.git
-https://github.com/photon-infotech/commons.git
-https://github.com/ClemsonRSRG/RESOLVE.git
-https://github.com/Ensembl/ensj-healthcheck.git
-https://github.com/haraldk/TwelveMonkeys.git
-https://github.com/lkroesen/BubbleBobble.git
-https://github.com/sugarcrm/candybean.git
-https://github.com/stackmob/stackmob-java-client-sdk.git
-https://github.com/undera/jmeter-plugins.git
-https://github.com/ldbc/ldbc_driver.git
-https://github.com/mojohaus/nbm-maven-plugin.git
-https://github.com/openpnp/openpnp.git
-https://github.com/paulhoule/infovore.git
-https://github.com/simoc/csvjdbc.git
-https://github.com/vkostyukov/la4j.git
-https://github.com/valis/vclang.git
-https://github.com/objectify/objectify.git
-https://github.com/apache/maven-surefire.git
-https://github.com/bpiwowar/experimaestro.git
-https://github.com/visiriCEP/VISIRI.git
-https://github.com/Incoding/apiTest.git
-https://github.com/revapi/revapi.git
-https://github.com/jdr0887/MaPSeq-Pipeline-RNASeq.git
-https://github.com/jdr0887/MaPSeq-Pipeline-NCGenes-DepthOfCoverage.git
-https://github.com/StopBadware/dsp-core.git
-https://github.com/DerPavlov/Cannons.git
-https://github.com/thinkofdeath/ThinkMap.git
-https://github.com/nuxeo/nuxeo-diff.git
-https://github.com/apache/mina-sshd.git
-https://github.com/buddycloud/buddycloud-server-java.git
-https://github.com/jenkinsci/remoting.git
-https://github.com/PIH/mirebalais-smoke-tests.git
-https://github.com/antoine-tran/Hedera.git
-https://github.com/carrotsearch/randomizedtesting.git
-https://github.com/keeps/db-preservation-toolkit.git
-https://github.com/jbossas/jboss-ejb-client.git
-https://github.com/hortonworks/knox.git
-https://github.com/jbossws/jbossws-spi.git
-https://github.com/VincSch/Photoplatform_Angular_Spring.git
-https://github.com/eileenzheng/playground.git
-https://github.com/selig/qea.git
-https://github.com/apache/commons-bcel.git
-https://github.com/apache/directory-shared.git
-https://github.com/triceo/splitlog.git
-https://github.com/ovgu-ccd/jchess.git
-https://github.com/jsr107/jsr107tck.git
-https://github.com/jenkinsci/matrix-project-plugin.git
-https://github.com/datasalt/pangool.git
-https://github.com/exoplatform/integration.git
-https://github.com/kovertopz/Framework-GL.git
-https://github.com/desht/ScrollingMenuSign.git
-https://github.com/FluentLenium/FluentLenium.git
-https://github.com/apache/maven-scm.git
-https://github.com/KnisterPeter/Smaller.git
-https://github.com/oboformat/oboformat.git
-https://github.com/FoxDev/FoxBot.git
-https://github.com/sonatype/nexus-maven-plugins.git
-https://github.com/bridgedb/BridgeDb.git
-https://github.com/locationtech/spatial4j.git
-https://github.com/jenkinsci/sauce-ondemand-plugin.git
-https://github.com/kohsuke/github-api.git
-https://github.com/niyue/coding.git
-https://github.com/roundrop/facebook4j.git
-https://github.com/sk89q/CommandBook.git
-https://github.com/cylong1016/NJULily.git
-https://github.com/vivantech/kc_fixes.git
-https://github.com/Weltraumschaf/JUberblog.git
-https://github.com/marytts/marytts.git
-https://github.com/richardwilly98/elasticsearch-river-mongodb.git
-https://github.com/andsel/moquette.git
-https://github.com/diorcety/maven-dependency-plugin.git
-https://github.com/gbif/checklistbank.git
-https://github.com/huangyingw/blablacode.git
-https://github.com/reinert/requestor.git
-https://github.com/tntim96/JSCover.git
-https://github.com/xenomorpheus/heisenberg.git
-https://github.com/zyong2004/mybatis-spring.git
-https://github.com/roberth/pitest.git
-https://github.com/JensBee/QueryClarity.git
-https://github.com/Weltraumschaf/commons.git
-https://github.com/greese/dasein-cloud-aws.git
-https://github.com/bguerout/jongo.git
-https://github.com/thomasjungblut/thomasjungblut-common.git
-https://github.com/goalhub/runtime.git
-https://github.com/apache/directory-server.git
-https://github.com/clojure/clojure.git
-https://github.com/wnameless/rubycollect4j.git
-https://github.com/omnifaces/omnifaces.git
-https://github.com/Razz0991/Minigames.git
-https://github.com/apache/commons-fileupload.git
-https://github.com/ChandraCXC/iris.git
-https://github.com/zyyettie/LaaS.git
-https://github.com/alibaba/druid.git
-https://github.com/thothbot/parallax.git
-https://github.com/msokolov/lux.git
-https://github.com/jenkinsci/git-client-plugin.git
-https://github.com/statsbiblioteket/newspaper-batch-event-framework.git
-https://github.com/apache/curator.git
-https://github.com/mikesname/ehri-rest.git
-https://github.com/apache/chemistry-opencmis.git
-https://github.com/Dandelion/dandelion.git
-https://github.com/yuchaosydney/kouchat.git
-https://github.com/xEssentials/xEssentials.git
-https://github.com/couchbase/couchbase-java-client.git
-https://github.com/sitewhere/sitewhere.git
-https://github.com/scriptella/scriptella-etl.git
-https://github.com/medusa-project/cantaloupe.git
-https://github.com/charite/jannovar.git
-https://github.com/code4craft/webmagic.git
-https://github.com/tavlima/fosstrak-epcis.git
-https://github.com/IMExConsortium/dip-proxy.git
-https://github.com/junit-team/junit.git
-https://github.com/twilio/twilio-java.git
-https://github.com/sannies/mp4parser.git
-https://github.com/xerial/sqlite-jdbc.git
-https://github.com/seges/sesam.git
-https://github.com/moravianlibrary/RecordManager2.git
-https://github.com/Omertron/api-themoviedb.git
-https://github.com/KittehOrg/KittehIRCClientLib.git
-https://github.com/taverna/taverna-engine-core.git
-https://github.com/dankurka/mgwt.git
-https://github.com/FITeagle/adapters.git
-https://github.com/drnoa/schemaspy.git
-https://github.com/carrotsearch/hppc.git
-https://github.com/neo4j/neo4j-ogm.git
-https://github.com/calrissian/accumulo-recipes.git
-https://github.com/apache/maven.git
-https://github.com/GluuFederation/oxTrust.git
-https://github.com/sanity/quickml.git
-https://github.com/davidmoten/rxjava-extras.git
-https://github.com/elex-bigdata/lldaMahout.git
-https://github.com/tengstrand/Laja.git
-https://github.com/spring-cloud/spring-cloud-config.git
-https://github.com/trajano/doxdb.git
-https://github.com/yegor256/s3auth.git
-https://github.com/greese/dasein-cloud-core.git
-https://github.com/jdr0887/MaPSeq-Pipeline-NCGenes.git
-https://github.com/sesuncedu/elk-reasoner.git
-https://github.com/ColoradoSchoolOfMines/interface_sdk.git
-https://github.com/rhuss/docker-maven-plugin.git
-https://github.com/k-hotta/SCAnalyzer.git
-https://github.com/tastybento/askyblock.git
-https://github.com/osiam/connector4java.git
-https://github.com/juzu/juzu.git
-https://github.com/OpenHFT/Chronicle-Queue.git
-https://github.com/junkdog/artemis-odb.git
-https://github.com/apache/archiva.git
-https://github.com/ESAPI/esapi-java-legacy.git
-https://github.com/motech/modules.git
-https://github.com/Benoker/DockingFrames.git
-https://github.com/barchart/barchart-feed.git
-https://github.com/swagger-api/swagger-core.git
-https://github.com/droolsjbpm/droolsjbpm-knowledge.git
-https://github.com/soul2zimate/resteasy2.git
-https://github.com/konsoletyper/teavm.git
-https://github.com/veraPDF/veraPDF-library.git
-https://github.com/VictorBac/LO23.git
-https://github.com/europeana/corelib.git
-https://github.com/GoogleCloudPlatform/gcloud-java.git
-https://github.com/mojohaus/jaxws-maven-plugin.git
-https://github.com/threerings/clyde.git
-https://github.com/maxymania/jxta-jxse.git
-https://github.com/xetorthio/jedis.git
-https://github.com/thervh70/SEM_Team9.git
-https://github.com/PerfCake/PerfCake.git
-https://github.com/plutext/docx4j.git
-https://github.com/slipcor/pvparena.git
-https://github.com/barchart/barchart-feed-ddf.git
-https://github.com/SpigotMC/BungeeCord.git
-https://github.com/forcedotcom/phoenix.git
-https://github.com/eFaps/eFaps-WebApp.git
-https://github.com/AtlasOfLivingAustralia/spatial-portal.git
-https://github.com/eugen-eugen/eugensjbehave.git
-https://github.com/GenomicParisCentre/aozan.git
-https://github.com/ikasanEIP/ikasan.git
-https://github.com/WorldCretornica/PlotMe-Core.git
-https://github.com/marklogic/java-client-api.git
-https://github.com/apache/jackrabbit.git
-https://github.com/tfredrich/docussandra.git
-https://github.com/codeine-cd/codeine.git
-https://github.com/Mobicents/sip-servlets.git
-https://github.com/movsim/movsim.git
-https://github.com/threerings/playn.git
-https://github.com/jcabi/jcabi-github.git
-https://github.com/apache/wss4j.git
-https://github.com/galenframework/galen.git
-https://github.com/marylinh/ESAPI_JAVA_ALL.git
-https://github.com/wso2/carbon-mediation.git
-https://github.com/SINTEF-9012/ThingML.git
-https://github.com/OhmData/hbase-public.git
-https://github.com/nodebox/nodebox.git
-https://github.com/jayway/powermock.git
-https://github.com/julianhyde/optiq.git
-https://github.com/ImmobilienScout24/deadcode4j.git
-https://github.com/rhuss/jolokia.git
-https://github.com/taverna/taverna-ui-components.git
-https://github.com/cloudera/cdk.git
-https://github.com/qcadoo/qcadoo.git
-https://github.com/ebean-orm/avaje-ebeanorm.git
-https://github.com/simon-eastwood/DependencyCheckCM.git
-https://github.com/spring-projects/spring-data-rest.git
-https://github.com/hudec/sql-processor.git
-https://github.com/aherbert/GDSC-SMLM.git
-https://github.com/rovo89/public-transport-enabler-fork.git
-https://github.com/Hidendra/LWC.git
-https://github.com/twizmwazin/CardinalPGM.git
-https://github.com/mrniko/redisson.git
-https://github.com/bigdataops/bgpcep.git
-https://github.com/GrizzlyNIO/grizzly-mirror.git
-https://github.com/adangel/pmd.git
-https://github.com/lrozenblyum/chess.git
-https://github.com/nuxeo/nuxeo-drive-server.git
-https://github.com/imagej/imagej-legacy.git
-https://github.com/tyrus-project/tyrus.git
-https://github.com/elBukkit/MagicLib.git
-https://github.com/libetl/soundtransform.git
-https://github.com/yegor256/takes.git
-https://github.com/graphaware/neo4j-framework.git
-https://github.com/sboesebeck/morphium.git
-https://github.com/OpenRock/OpenIG.git
-https://github.com/DeveloperLiberationFront/social-screencasting-core.git
-https://github.com/geenen124/Team1BubbleTrouble.git
-https://github.com/kaazing/gateway.git
-https://github.com/sakai-mirror/sam.git
-https://github.com/apache/commons-configuration.git
-https://github.com/fiji/TrackMate3.git
-https://github.com/yegor256/thindeck.git
-https://github.com/Eluinhost/ultrahardcore.git
-https://github.com/caprica/vlcj.git
-https://github.com/threerings/depot.git
-https://github.com/ysc/word.git
-https://github.com/slowenthal/classproject.git
-https://github.com/apache/directory-fortress-core.git
-https://github.com/greese/dasein-cloud-google.git
-https://github.com/insideo/randomcoder-website.git
-https://github.com/lemire/RoaringBitmap.git
-https://github.com/telefonicaid/fiware-cygnus.git
-https://github.com/hk2-project/hk2.git
-https://github.com/ninjaframework/ninja.git
-https://github.com/Xephi/AuthMeReloaded.git
-https://github.com/droolsjbpm/jbpm-form-modeler.git
-https://github.com/gwtbootstrap/gwt-bootstrap.git
-https://github.com/objectos/way.git
-https://github.com/maxapryg/UITest.git
-https://github.com/ghedlund/phon.git
-https://github.com/aadnk/ProtocolLib.git
-https://github.com/karamelchef/karamel.git
-https://github.com/Hansschouten/context_health_informatics.git
-https://github.com/apache/incubator-streams.git
-https://github.com/kuujo/vertigo.git
-https://github.com/vmi/selenese-runner-java.git
-https://github.com/spotify/docker-client.git
-https://github.com/JWebUnit/jwebunit.git
-https://github.com/johncarl81/transfuse.git
-https://github.com/sakai-mirror/kernel.git
-https://github.com/CloudSlang/cloud-slang.git
-https://github.com/datanucleus/datanucleus-core.git
-https://github.com/eXistence/TeeTime.git
-https://github.com/jitsi/libjitsi.git
-https://github.com/FasterXML/jackson-core.git
-https://github.com/mizdebsk/xmvn.git
-https://github.com/ATLauncher/ATLauncher.git
-https://github.com/maartentbm/ContextPL1.git
-https://github.com/apache/incubator-ambari.git
-https://github.com/spring-projects/spring-data-neo4j.git
-https://github.com/apache/uima-uimaj.git
-https://github.com/mongodb/morphia.git
-https://github.com/minusone13/InvoicingSystem.git
-https://github.com/jqno/equalsverifier.git
-https://github.com/sdl/Testy.git
-https://github.com/fcrepo4/fcrepo4.git
-https://github.com/GenomicParisCentre/eoulsan.git
-https://github.com/te-con/ehour.git
-https://github.com/ansell/owlapi.git
-https://github.com/opendaylight/yangtools.git
-https://github.com/OpenRock/OpenDJ.git
-https://github.com/JolantaWojcik/biojavaOwn.git
-https://github.com/DirtyUnicorns/android_external_spongycastle.git
-https://github.com/owlcs/owlapi.git
-https://github.com/stormpath/stormpath-sdk-java.git
-https://github.com/apache/clerezza.git
-https://github.com/aht-group/utils.git
-https://github.com/webanno/webanno.git
-https://github.com/apache/mahout.git
-https://github.com/hal/core.git
-https://github.com/playernodie/weupnp.git
-https://github.com/apache/servicemix-bundles.git
-https://github.com/robovm/robovm.git
-https://github.com/graphhopper/graphhopper.git
-https://github.com/perfectsense/dari.git
-https://github.com/svn2github/SAT4J.git
-https://github.com/jeremylong/DependencyCheck.git
-https://github.com/apache/qpid-proton.git
-https://github.com/svn2github/forge.git
-https://github.com/droolsjbpm/optaplanner.git
-https://github.com/soluvas/soluvas-framework.git
-https://github.com/droolsjbpm/droolsjbpm-integration.git
-https://github.com/swagger-api/swagger-codegen.git
-https://github.com/druid-io/druid.git
-https://github.com/FasterXML/jackson-databind.git
-https://github.com/biojava/biojava.git
-https://github.com/telefonicaid/fiware-cosmos-ambari.git
-https://github.com/kyoken74/gwt-angular.git
-https://github.com/apache/commons-lang.git
-https://github.com/scifio/scifio.git
-https://github.com/alibaba/RocketMQ.git
-https://github.com/kuujo/copycat.git
-https://github.com/jankotek/MapDB.git
-https://github.com/droolsjbpm/kie-wb-distributions.git
-https://github.com/buschmais/jqassistant.git
-https://github.com/PLOS/ambra.git
-https://github.com/spring-cloud/spring-cloud-netflix.git
-https://github.com/apache/commons-math.git
-https://github.com/OpenHFT/Chronicle-Network.git
-https://github.com/chocoteam/choco3.git
-https://github.com/apache/flume.git
-https://github.com/rinde/RinSim.git
-https://github.com/kotcrab/VisEditor.git
-https://github.com/void256/nifty-gui.git
-https://github.com/apache/uima-ducc.git
-https://github.com/windup/windup.git
-https://github.com/heuermh/dishevelled.git
-https://github.com/salyh/javamailspec.git
-https://github.com/SpoutDev/Spout.git
-https://github.com/antlr/antlr4.git
-https://github.com/Flipkart/quartz.git
-https://github.com/rasto/lcmc.git
-https://github.com/mafagafogigante/dungeon.git
-https://github.com/PerfGeeks/pinpoint.git
-https://github.com/opendaylight/openflowplugin.git
-https://github.com/EngineHub/CommandHelper.git
-https://github.com/tananaev/traccar.git
-https://github.com/BroadleafCommerce/BroadleafCommerce.git
-https://github.com/apache/hadoop-common.git
-https://github.com/spring-projects/spring-boot.git
-https://github.com/bcdev/beam.git
-https://github.com/weld/core.git
-https://github.com/elki-project/elki.git
-https://github.com/belaban/JGroups.git
-https://github.com/molgenis/molgenis.git
-https://github.com/lennartj/jaxb2-maven-plugin.git
-https://github.com/bugcy013/opennms-tmp-tools.git
-https://github.com/Talend/tcommon-studio-se.git
-https://github.com/netty/netty.git
-https://github.com/openmicroscopy/bioformats.git
-https://github.com/droolsjbpm/guvnor.git
-https://github.com/jetty-project/codehaus-jetty6.git
-https://github.com/apache/jackrabbit-oak.git
-https://github.com/deegree/deegree3.git
-https://github.com/apache/sling.git
-https://github.com/EriclLee/ActiveMQ-On-Azure.git
-https://github.com/amplab/tachyon.git
-https://github.com/neo4j/neo4j.git
-https://github.com/darranl/directory-server.git
-https://github.com/hazelcast/hazelcast.git
-https://github.com/infinispan/infinispan.git
-https://github.com/DSpace/DSpace.git
-https://github.com/mulesoft/mule.git
-https://github.com/imCodePartnerAB/imcms.git
-https://github.com/backslash47/webstart-maven-plugin.git
-https://github.com/apache/hbase.git
-https://github.com/languagetool-org/languagetool.git
-https://github.com/droolsjbpm/drools.git
-https://github.com/SpigotMC/Spigot-API.git
-https://github.com/irstv/orbisgis.git
-https://github.com/jgheerardyn/yields.git
-https://github.com/ning/killbill.git
-https://github.com/jline/jline2.git
-https://github.com/altran/Whydah-UserIdentityBackend.git
-https://github.com/encog/encog-java-core.git
-https://github.com/highsource/jaxb2-basics.git
-https://github.com/msoute/vertx-deploy-tools.git
-https://github.com/apache/portals-pluto.git
-https://github.com/antlr/stringtemplate4.git
-https://github.com/kongchen/swagger-maven-plugin.git
-https://github.com/gertvv/addis.git
-https://github.com/ProjectCCNx/ccnx.git
-https://github.com/mulesoft/mule-common.git
-https://github.com/cismet/cismap-plugin.git
-https://github.com/greese/dasein-cloud-azure.git
-https://github.com/Requinard/TeamTab.git
-https://github.com/SonarSource/jenkins-sonar-plugin.git
-https://github.com/fbacchella/jrds.git
-https://github.com/cdi-spec/cdi-tck.git
-https://github.com/gwtbootstrap3/gwtbootstrap3.git
-https://github.com/apache/commons-dbcp.git
-https://github.com/timmolter/XChart.git
-https://github.com/aranega/testgen.git
-https://github.com/mysticfall/pivot4j.git
-https://github.com/datasift/datasift-java.git
-https://github.com/viktor-z/fb2pdf.git
-https://github.com/Cas-B/Group17-BubbleBobble.git
-https://github.com/TheCoder4eu/BootsFaces-OSP.git
-https://github.com/UnifiedViews/Plugin-DevEnv.git
-https://github.com/jidesoft/jide-oss.git
-https://github.com/codescape/bitvunit.git
-https://github.com/grandwazir/BanHammer.git
-https://github.com/wildfly/wildfly-arquillian.git
-https://github.com/Eluinhost/pluginframework.git
-https://github.com/mtedone/podam.git
-https://github.com/Mobicents/jss7.git
-https://github.com/basis-technology-corp/rosette-common-java-api.git
-https://github.com/webbit/webbit.git
-https://github.com/GWASpi/GWASpi.git
-https://github.com/jenkinsci/warnings-plugin.git
-https://github.com/google/auto.git
-https://github.com/TechnicPack/LauncherV3.git
-https://github.com/ArtificerRepo/artificer.git
-https://github.com/Jahia/external-provider.git
-https://github.com/ICGC-TCGA-PanCancer/SeqWare-CGP-SomaticCore.git
-https://github.com/PEXPlugins/PermissionsEx.git

logs/Null.txt

@@ -1,124 +0,0 @@
-1
-    BC_VACUOUS_INSTANCEOF   Ignore it.  no source code, no source code change
-    CN_IDIOM_NO_SUPER_CALL  Ignore it. no source code, no source code change
-    CN_IMPLEMENTS_CLONE_BUT_NOT_CLONEABLE  Ignore it. no source code, no source code change
-    DLS_DEAD_LOCAL_STORE Ignore it. no source code, no source code change
-    DM_DEFAULT_ENCODING
-    DM_NUMBER_CTOR
-    DM_STRING_CTOR
-    DM_STRING_VOID_CTOR
-    DP_DO_INSIDE_DO_PRIVILEGED
-    EI_EXPOSE_REP
-    EQ_COMPARETO_USE_OBJECT_EQUALS
-    EQ_DOESNT_OVERRIDE_EQUALS
-    EQ_SELF_USE_OBJECT
-    HE_EQUALS_USE_HASHCODE
-    HE_HASHCODE_USE_OBJECT_EQUALS
-    HE_INHERITS_EQUALS_USE_HASHCODE
-    IS2_INCONSISTENT_SYNC
-    MS_CANNOT_BE_FINAL
-    MS_MUTABLE_ARRAY
-    MS_PKGPROTECT
-    MS_SHOULD_BE_FINAL
-    NM_CLASS_NAMING_CONVENTION
-    NM_CLASS_NOT_EXCEPTION
-    NM_SAME_SIMPLE_NAME_AS_SUPERCLASS
-    OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE
-    OS_OPEN_STREAM
-    OS_OPEN_STREAM_EXCEPTION_PATH
-    RI_REDUNDANT_INTERFACES
-    SA_FIELD_DOUBLE_ASSIGNMENT
-    SE_COMPARATOR_SHOULD_BE_SERIALIZABLE
-    SE_NO_SERIALVERSIONID
-    SIO_SUPERFLUOUS_INSTANCEOF
-    UCF_USELESS_CONTROL_FLOW
-    UG_SYNC_SET_UNSYNC_GET
-    UPM_UNCALLED_PRIVATE_METHOD
-    URF_UNREAD_FIELD
-    URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD
-    UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR
-    UWF_UNWRITTEN_FIELD
-    UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD
-    WMI_WRONG_MAP_ITERATOR
--1
-    CI_CONFUSED_INHERITANCE
-    CO_ABSTRACT_SELF
-    DMI_COLLECTION_OF_URLS
-    EQ_ABSTRACT_SELF
-    HE_SIGNATURE_DECLARES_HASHING_OF_UNHASHABLE_CLASS
-    JCIP_FIELD_ISNT_FINAL_IN_IMMUTABLE_CLASS
-    ME_MUTABLE_ENUM_FIELD
-    MF_CLASS_MASKS_FIELD
-    MS_CANNOT_BE_FINAL
-    MS_PKGPROTECT
-    MS_SHOULD_BE_FINAL
-    NM_FIELD_NAMING_CONVENTION
-    NM_SAME_SIMPLE_NAME_AS_INTERFACE
-    SE_BAD_FIELD
-    SE_TRANSIENT_FIELD_NOT_RESTORED
-    STCAL_STATIC_SIMPLE_DATE_FORMAT_INSTANCE
-    UPM_UNCALLED_PRIVATE_METHOD
-    UUF_UNUSED_FIELD
-    UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD
-    UWF_NULL_FIELD
-    UWF_UNWRITTEN_FIELD
-    UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD
-    VO_VOLATILE_REFERENCE_TO_ARRAY
-
-    
-    
-    CI_CONFUSED_INHERITANCE  change modifier of fields from protected to private or public, or remove final of class.
-	CO_ABSTRACT_SELF    Interface, remove compareTo() method.
-    
-    SE_NO_SERIALVERSIONID  add a field: serialVersionUID
-    EQ_ABSTRACT_SELF    Interface, remove compareTo() method.
-    EQ_COMPARETO_USE_OBJECT_EQUALS:    Update or Delete compareTo(), Add equals()
-	EQ_DOESNT_OVERRIDE_EQUALS override equals()
-	HE_SIGNATURE_DECLARES_HASHING_OF_UNHASHABLE_CLASS  remove equals()  only one instance
-	ME_MUTABLE_ENUM_FIELD  enum, field add final.
-    MF_CLASS_MASKS_FIELD, change super class or delete the field with a same name in super class.
-    MS_SHOULD_BE_FINAL  Add final key word
-	STCAL_STATIC_SIMPLE_DATE_FORMAT_INSTANCE  remove public static final DateFormat DATE_FORMAT....  or SimpleDateFormat
-    UUF_UNUSED_FIELD  remove unused fields.  not sure
-	UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD  field
-	UWF_NULL_FIELD  update field, remove field
-	UWF_UNWRITTEN_FIELD  field
-	UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD remove field
-	VO_VOLATILE_REFERENCE_TO_ARRAY  field
-	
-	all GumTree results. class, field, method, //statements.
-	     
-NM_SAME_SIMPLE_NAME_AS_INTERFACE  rename class name or remove super class
-NM_SAME_SIMPLE_NAME_AS_SUPERCLASS,   class name
-NM_METHOD_NAMING_CONVENTION
-NM_CLASS_NAMING_CONVENTION  class name
-NM_CLASS_NOT_EXCEPTION  class name
-RI_REDUNDANT_INTERFACES  class implemented interface
-SE_NO_SUITABLE_CONSTRUCTOR  Serializable  Class level  remove Serializable interface and serialVersionUID
-
-SIC_INNER_SHOULD_BE_STATIC  add static to inner class, not sure, delete it,   如果是匿名内部类，该如何处理？ ，其他的直接内部类的范围。
-SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS  同上
-===
-CO_ABSTRACT_SELF  inner class
-SE_INNER_CLASS  inner class
-SE_COMPARATOR_SHOULD_BE_SERIALIZABLE, inner class, 读definition
-SE_BAD_FIELD_INNER_CLASS inner class
-SIC_INNER_SHOULD_BE_STATIC_ANON  inner class
-
-HE_INHERITS_EQUALS_USE_HASHCODE inner class or class
-CN_IDIOM  add clone method. or update clone method
-
-DM_NUMBER_CTOR  multi v multi patches
-EQ_COMPARETO_USE_OBJECT_EQUALS,    the same as before
-IC_INIT_CIRCULARITY, multi V, multi patches>
-
-
-
-SE_NO_SUITABLE_CONSTRUCTOR_FOR_EXTERNALIZATION, add a constructor or add public to old constructor, 
-
-
-
-NP_NONNULL_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR
-
-SE_NO_SERIALVERSIONID   change superclass or interface, add field or remove @SuppressWarnings("serial"),   some are inner class
-    

logs/fixedTypes.txt

@@ -1,339 +0,0 @@
-SIC_INNER_SHOULD_BE_STATIC_ANON
-DLS_DEAD_LOCAL_STORE
-DM_CONVERT_CASE
-DM_DEFAULT_ENCODING
-UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR
-RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE
-NM_METHOD_NAMING_CONVENTION
-URF_UNREAD_FIELD
-BC_UNCONFIRMED_CAST
-REC_CATCH_EXCEPTION
-BC_UNCONFIRMED_CAST_OF_RETURN_VALUE
-SE_NO_SERIALVERSIONID
-UPM_UNCALLED_PRIVATE_METHOD
-VA_FORMAT_STRING_USES_NEWLINE
-MS_SHOULD_BE_FINAL
-RV_RETURN_VALUE_IGNORED_BAD_PRACTICE
-ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD
-EI_EXPOSE_REP2
-URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD
-WMI_WRONG_MAP_ITERATOR
-OBL_UNSATISFIED_OBLIGATION
-EI_EXPOSE_REP
-NP_LOAD_OF_KNOWN_NULL_VALUE
-DM_NUMBER_CTOR
-SIC_INNER_SHOULD_BE_STATIC
-SBSC_USE_STRINGBUFFER_CONCATENATION
-OS_OPEN_STREAM_EXCEPTION_PATH
-NP_NONNULL_RETURN_VIOLATION
-SF_SWITCH_NO_DEFAULT
-UWF_UNWRITTEN_FIELD
-DE_MIGHT_IGNORE
-IS2_INCONSISTENT_SYNC
-DM_BOXED_PRIMITIVE_FOR_PARSING
-RV_RETURN_VALUE_IGNORED_NO_SIDE_EFFECT
-ODR_OPEN_DATABASE_RESOURCE
-PZLA_PREFER_ZERO_LENGTH_ARRAYS
-RI_REDUNDANT_INTERFACES
-NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE
-UCF_USELESS_CONTROL_FLOW
-UC_USELESS_CONDITION
-NP_NULL_ON_SOME_PATH
-UC_USELESS_OBJECT
-DM_FP_NUMBER_CTOR
-MS_PKGPROTECT
-SQL_PREPARED_STATEMENT_GENERATED_FROM_NONCONSTANT_STRING
-OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE
-ES_COMPARING_STRINGS_WITH_EQ
-OS_OPEN_STREAM
-RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE
-NP_PARAMETER_MUST_BE_NONNULL_BUT_MARKED_AS_NULLABLE
-SS_SHOULD_BE_STATIC
-FE_FLOATING_POINT_EQUALITY
-HE_EQUALS_USE_HASHCODE
-DM_EXIT
-NM_CONFUSING
-LI_LAZY_INIT_STATIC
-BX_UNBOXING_IMMEDIATELY_REBOXED
-EQ_COMPARETO_USE_OBJECT_EQUALS
-SQL_NONCONSTANT_STRING_PASSED_TO_EXECUTE
-NP_NULL_ON_SOME_PATH_EXCEPTION
-NP_UNWRITTEN_FIELD
-MS_MUTABLE_COLLECTION_PKGPROTECT
-UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD
-CN_IMPLEMENTS_CLONE_BUT_NOT_CLONEABLE
-DMI_HARDCODED_ABSOLUTE_FILENAME
-SE_BAD_FIELD
-DM_STRING_TOSTRING
-UUF_UNUSED_FIELD
-ICAST_INTEGER_MULTIPLY_CAST_TO_LONG
-EC_UNRELATED_TYPES
-BC_VACUOUS_INSTANCEOF
-ICAST_IDIV_CAST_TO_DOUBLE
-RCN_REDUNDANT_NULLCHECK_OF_NULL_VALUE
-ES_COMPARING_PARAMETER_STRING_WITH_EQ
-RV_RETURN_VALUE_IGNORED
-CI_CONFUSED_INHERITANCE
-DB_DUPLICATE_SWITCH_CLAUSES
-ODR_OPEN_DATABASE_RESOURCE_EXCEPTION_PATH
-NP_ALWAYS_NULL
-RpC_REPEATED_CONDITIONAL_TEST
-SE_BAD_FIELD_STORE
-NP_NULL_PARAM_DEREF
-GC_UNRELATED_TYPES
-DLS_DEAD_LOCAL_STORE_OF_NULL
-RC_REF_COMPARISON_BAD_PRACTICE
-MS_MUTABLE_ARRAY
-SE_INNER_CLASS
-UL_UNRELEASED_LOCK_EXCEPTION_PATH
-SE_COMPARATOR_SHOULD_BE_SERIALIZABLE
-CN_IDIOM_NO_SUPER_CALL
-NP_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD
-UC_USELESS_VOID_METHOD
-NP_NONNULL_PARAM_VIOLATION
-DMI_INVOKING_TOSTRING_ON_ARRAY
-DP_DO_INSIDE_DO_PRIVILEGED
-SF_SWITCH_FALLTHROUGH
-NP_BOOLEAN_RETURN_NULL
-NM_CLASS_NOT_EXCEPTION
-SIO_SUPERFLUOUS_INSTANCEOF
-NP_GUARANTEED_DEREF
-
-UL_UNRELEASED_LOCK
-IP_PARAMETER_IS_DEAD_BUT_OVERWRITTEN
-HE_INHERITS_EQUALS_USE_HASHCODE
-MS_CANNOT_BE_FINAL
-DB_DUPLICATE_BRANCHES
-STCAL_INVOKE_ON_STATIC_DATE_FORMAT_INSTANCE
-MS_MUTABLE_COLLECTION
-IL_INFINITE_RECURSIVE_LOOP
-VO_VOLATILE_INCREMENT
-JLM_JSR166_UTILCONCURRENT_MONITORENTER
-NP_NULL_PARAM_DEREF_NONVIRTUAL
-DM_STRING_CTOR
-UR_UNINIT_READ
-XFB_XML_FACTORY_BYPASS
-RV_EXCEPTION_NOT_THROWN
-UI_INHERITANCE_UNSAFE_GETRESOURCE
-VA_FORMAT_STRING_EXTRA_ARGUMENTS_PASSED
-IT_NO_SUCH_ELEMENT
-NM_CLASS_NAMING_CONVENTION
-RC_REF_COMPARISON
-RC_REF_COMPARISON_BAD_PRACTICE_BOOLEAN
-DLS_DEAD_LOCAL_STORE_SHADOWS_FIELD
-HE_EQUALS_NO_HASHCODE
-NS_NON_SHORT_CIRCUIT
-NP_DEREFERENCE_OF_READLINE_VALUE
-NP_GUARANTEED_DEREF_ON_EXCEPTION_PATH
-EQ_DOESNT_OVERRIDE_EQUALS
-DM_STRING_VOID_CTOR
-DP_CREATE_CLASSLOADER_INSIDE_DO_PRIVILEGED
-BIT_SIGNED_CHECK
-ME_ENUM_FIELD_SETTER
-BC_EQUALS_METHOD_SHOULD_WORK_FOR_ALL_OBJECTS
-NS_DANGEROUS_NON_SHORT_CIRCUIT
-NP_EQUALS_SHOULD_HANDLE_NULL_ARGUMENT
-SR_NOT_CHECKED
-RR_NOT_CHECKED
-UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD
-VA_FORMAT_STRING_MISSING_ARGUMENT
-EC_BAD_ARRAY_COMPARE
-NP_NONNULL_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR
-DM_BOXED_PRIMITIVE_FOR_COMPARE
-NP_NULL_ON_SOME_PATH_MIGHT_BE_INFEASIBLE
-UMAC_UNCALLABLE_METHOD_OF_ANONYMOUS_CLASS
-UWF_NULL_FIELD
-CO_COMPARETO_INCORRECT_FLOATING
-NP_NULL_PARAM_DEREF_ALL_TARGETS_DANGEROUS
-NO_NOTIFY_NOT_NOTIFYALL
-SC_START_IN_CTOR
-RV_RETURN_VALUE_IGNORED_INFERRED
-UM_UNNECESSARY_MATH
-SA_FIELD_SELF_ASSIGNMENT
-BC_IMPOSSIBLE_CAST
-LI_LAZY_INIT_UPDATE_STATIC
-NP_TOSTRING_COULD_RETURN_NULL
-SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS
-AT_OPERATION_SEQUENCE_ON_CONCURRENT_ABSTRACTION
-EQ_UNUSUAL
-SE_NO_SUITABLE_CONSTRUCTOR
-UW_UNCOND_WAIT
-MF_CLASS_MASKS_FIELD
-FE_TEST_IF_EQUAL_TO_NOT_A_NUMBER
-IA_AMBIGUOUS_INVOCATION_OF_INHERITED_OR_OUTER_METHOD
-SE_BAD_FIELD_INNER_CLASS
-RV_NEGATING_RESULT_OF_COMPARETO
-ISC_INSTANTIATE_STATIC_CLASS
-HE_HASHCODE_USE_OBJECT_EQUALS
-DM_BOOLEAN_CTOR
-DMI_RANDOM_USED_ONLY_ONCE
-EQ_CHECK_FOR_OPERAND_NOT_COMPATIBLE_WITH_THIS
-DM_GC
-NM_SAME_SIMPLE_NAME_AS_SUPERCLASS
-EC_NULL_ARG
-EQ_SELF_USE_OBJECT
-RV_ABSOLUTE_VALUE_OF_RANDOM_INT
-SE_NO_SUITABLE_CONSTRUCTOR_FOR_EXTERNALIZATION
-MS_EXPOSE_REP
-SE_TRANSIENT_FIELD_NOT_RESTORED
-IM_AVERAGE_COMPUTATION_COULD_OVERFLOW
-NP_METHOD_PARAMETER_TIGHTENS_ANNOTATION
-NP_METHOD_RETURN_RELAXING_ANNOTATION
-UG_SYNC_SET_UNSYNC_GET
-NM_FIELD_NAMING_CONVENTION
-MS_OOI_PKGPROTECT
-UCF_USELESS_CONTROL_FLOW_NEXT_LINE
-VA_FORMAT_STRING_BAD_CONVERSION
-BX_BOXING_IMMEDIATELY_UNBOXED_TO_PERFORM_COERCION
-SA_FIELD_DOUBLE_ASSIGNMENT
-BC_BAD_CAST_TO_CONCRETE_COLLECTION
-SF_DEAD_STORE_DUE_TO_SWITCH_FALLTHROUGH
-MS_FINAL_PKGPROTECT
-DMI_COLLECTION_OF_URLS
-INT_BAD_COMPARISON_WITH_SIGNED_BYTE
-RV_CHECK_FOR_POSITIVE_INDEXOF
-RE_CANT_USE_FILE_SEPARATOR_AS_REGULAR_EXPRESSION
-RU_INVOKE_RUN
-BC_IMPOSSIBLE_DOWNCAST_OF_TOARRAY
-ICAST_BAD_SHIFT_AMOUNT
-ICAST_INT_CAST_TO_FLOAT_PASSED_TO_ROUND
-DM_BOXED_PRIMITIVE_TOSTRING
-UR_UNINIT_READ_CALLED_FROM_SUPER_CONSTRUCTOR
-WA_NOT_IN_LOOP
-CN_IDIOM
-DMI_BLOCKING_METHODS_ON_URL
-EC_UNRELATED_CLASS_AND_INTERFACE
-SWL_SLEEP_WITH_LOCK_HELD
-IM_BAD_CHECK_FOR_ODD
-RE_POSSIBLE_UNINTENDED_PATTERN
-INT_BAD_COMPARISON_WITH_NONNEGATIVE_VALUE
-ICAST_INT_CAST_TO_DOUBLE_PASSED_TO_CEIL
-EQ_OVERRIDING_EQUALS_NOT_SYMMETRIC
-LG_LOST_LOGGER_DUE_TO_WEAK_REFERENCE
-DLS_DEAD_LOCAL_STORE_IN_RETURN
-J2EE_STORE_OF_NON_SERIALIZABLE_OBJECT_INTO_SESSION
-NP_STORE_INTO_NONNULL_FIELD
-RANGE_ARRAY_INDEX
-IL_INFINITE_LOOP
-DC_DOUBLECHECK
-NN_NAKED_NOTIFY
-EC_UNRELATED_TYPES_USING_POINTER_EQUALITY
-SE_PRIVATE_READ_RESOLVE_NOT_INHERITED
-INT_VACUOUS_BIT_OPERATION
-DM_NEXTINT_VIA_NEXTDOUBLE
-VA_FORMAT_STRING_ILLEGAL
-DMI_INVOKING_HASHCODE_ON_ARRAY
-RV_DONT_JUST_NULL_CHECK_READLINE
-RE_BAD_SYNTAX_FOR_REGULAR_EXPRESSION
-SA_LOCAL_SELF_ASSIGNMENT_INSTEAD_OF_FIELD
-NM_VERY_CONFUSING
-MSF_MUTABLE_SERVLET_FIELD
-BC_IMPOSSIBLE_INSTANCEOF
-SA_LOCAL_SELF_COMPARISON
-SA_LOCAL_SELF_ASSIGNMENT
-IC_SUPERCLASS_USES_SUBCLASS_DURING_INITIALIZATION
-CNT_ROUGH_CONSTANT_VALUE
-SI_INSTANCE_BEFORE_FINALS_ASSIGNED
-DLS_DEAD_STORE_OF_CLASS_LITERAL
-RV_ABSOLUTE_VALUE_OF_HASHCODE
-NM_SAME_SIMPLE_NAME_AS_INTERFACE
-HE_HASHCODE_NO_EQUALS
-DM_NEW_FOR_GETCLASS
-SA_FIELD_SELF_COMPARISON
-NM_METHOD_CONSTRUCTOR_CONFUSION
-EQ_COMPARING_CLASS_NAMES
-UC_USELESS_CONDITION_TYPE
-RV_01_TO_INT
-SA_LOCAL_DOUBLE_ASSIGNMENT
-SQL_BAD_RESULTSET_ACCESS
-EQ_GETCLASS_AND_CLASS_CONSTANT
-BSHIFT_WRONG_ADD_PRIORITY
-HRS_REQUEST_PARAMETER_TO_HTTP_HEADER
-DMI_USING_REMOVEALL_TO_CLEAR_COLLECTION
-STCAL_STATIC_SIMPLE_DATE_FORMAT_INSTANCE
-FI_FINALIZER_NULLS_FIELDS
-ML_SYNC_ON_FIELD_TO_GUARD_CHANGING_THAT_FIELD
-JCIP_FIELD_ISNT_FINAL_IN_IMMUTABLE_CLASS
-CO_COMPARETO_RESULTS_MIN_VALUE
-IMSE_DONT_CATCH_IMSE
-QF_QUESTIONABLE_FOR_LOOP
-MWN_MISMATCHED_NOTIFY
-RV_RETURN_VALUE_OF_PUTIFABSENT_IGNORED
-DMI_NONSERIALIZABLE_OBJECT_WRITTEN
-BC_BAD_CAST_TO_ABSTRACT_COLLECTION
-SW_SWING_METHODS_INVOKED_IN_SWING_THREAD
-EC_ARRAY_AND_NONARRAY
-NP_NULL_INSTANCEOF
-MTIA_SUSPECT_SERVLET_INSTANCE_FIELD
-EQ_ALWAYS_FALSE
-INT_BAD_COMPARISON_WITH_INT_VALUE
-NP_OPTIONAL_RETURN_NULL
-BX_BOXING_IMMEDIATELY_UNBOXED
-VA_FORMAT_STRING_EXPECTED_MESSAGE_FORMAT_SUPPLIED
-BIT_IOR
-FI_MISSING_SUPER_CALL
-VO_VOLATILE_REFERENCE_TO_ARRAY
-SF_DEAD_STORE_DUE_TO_SWITCH_FALLTHROUGH_TO_THROW
-DMI_CONSTANT_DB_PASSWORD
-NP_IMMEDIATE_DEREFERENCE_OF_READLINE
-ML_SYNC_ON_UPDATED_FIELD
-HE_USE_OF_UNHASHABLE_CLASS
-FI_PUBLIC_SHOULD_BE_PROTECTED
-DMI_BIGDECIMAL_CONSTRUCTED_FROM_DOUBLE
-TQ_NEVER_VALUE_USED_WHERE_ALWAYS_REQUIRED
-XSS_REQUEST_PARAMETER_TO_SERVLET_WRITER
-NP_ALWAYS_NULL_EXCEPTION
-DM_INVALID_MIN_MAX
-NM_WRONG_PACKAGE
-MS_SHOULD_BE_REFACTORED_TO_BE_FINAL
-DC_PARTIALLY_CONSTRUCTED
-WA_AWAIT_NOT_IN_LOOP
-INT_VACUOUS_COMPARISON
-RV_CHECK_COMPARETO_FOR_SPECIFIC_RETURN_VALUE
-RCN_REDUNDANT_COMPARISON_OF_NULL_AND_NONNULL_VALUE
-DL_SYNCHRONIZATION_ON_SHARED_CONSTANT
-EQ_ALWAYS_TRUE
-DMI_EMPTY_DB_PASSWORD
-DMI_ENTRY_SETS_MAY_REUSE_ENTRY_OBJECTS
-WL_USING_GETCLASS_RATHER_THAN_CLASS_LITERAL
-FI_USELESS
-VA_FORMAT_STRING_BAD_CONVERSION_FROM_ARRAY
-SP_SPIN_ON_FIELD
-BOA_BADLY_OVERRIDDEN_ADAPTER
-MWN_MISMATCHED_WAIT
-NP_CLONE_COULD_RETURN_NULL
-CO_ABSTRACT_SELF
-DMI_COLLECTIONS_SHOULD_NOT_CONTAIN_THEMSELVES
-QBA_QUESTIONABLE_BOOLEAN_ASSIGNMENT
-IC_INIT_CIRCULARITY
-ICAST_INT_2_LONG_AS_INSTANT
-FI_EXPLICIT_INVOCATION
-ME_MUTABLE_ENUM_FIELD
-RCN_REDUNDANT_COMPARISON_TWO_NULL_VALUES
-HE_SIGNATURE_DECLARES_HASHING_OF_UNHASHABLE_CLASS
-RS_READOBJECT_SYNC
-SQL_BAD_PREPARED_STATEMENT_ACCESS
-VA_FORMAT_STRING_BAD_CONVERSION_TO_BOOLEAN
-EQ_ABSTRACT_SELF
-NP_CLOSING_NULL
-RV_REM_OF_HASHCODE
-PT_RELATIVE_PATH_TRAVERSAL
-TLW_TWO_LOCK_WAIT
-INT_BAD_REM_BY_1
-ICAST_QUESTIONABLE_UNSIGNED_RIGHT_SHIFT
-VA_PRIMITIVE_ARRAY_PASSED_TO_OBJECT_VARARG
-DM_USELESS_THREAD
-DMI_DOH
-IJU_ASSERT_METHOD_INVOKED_FROM_RUN_METHOD
-BIT_IOR_OF_SIGNED_BYTE
-DMI_THREAD_PASSED_WHERE_RUNNABLE_EXPECTED
-SA_LOCAL_SELF_COMPUTATION
-	This method performs a nonsensical computation of a local variable with another reference to the same variable (e.g., x&x or x-x). 
-	Because of the nature of the computation, this operation doesn't seem to make sense, and may indicate a typo or a logic error. Double check the computation.
-IM_MULTIPLYING_RESULT_OF_IREM
-	The code multiplies the result of an integer remaining by an integer constant. 
-	Be sure you don't have your operator precedence confused. For example i % 60 * 1000 is (i % 60) * 1000, not i % (60 * 1000).
-MS_MUTABLE_HASHTABLE
-	Field is a mutable Hashtable (MS_MUTABLE_HASHTABLE)
-	A final static field references a Hashtable and can be accessed by malicious code or by accident from another package. 
-	This code can freely modify the contents of the Hashtable.

pom.xml

@@ -25,11 +25,11 @@
 		    <version>1.2</version>
 		</dependency>
 				
-		<dependency>
+		<!--<dependency>-->
-			<groupId>edu.lu.uni</groupId>
+			<!--<groupId>edu.lu.uni</groupId>-->
-			<artifactId>simple-utils</artifactId>
+			<!--<artifactId>simple-utils</artifactId>-->
-			<version>0.0.1-SNAPSHOT</version>
+			<!--<version>0.0.1-SNAPSHOT</version>-->
-		</dependency>
+		<!--</dependency>-->
 		
 		<!-- akka -->
 		<dependency>
@@ -69,18 +69,13 @@
 			<version>${logback.version}</version>
 		</dependency>
 		
+
 		<!--<dependency>-->
 			<!--<groupId>edu.lu.uni.serval</groupId>-->
-			<!--<artifactId>SourceCodeParser</artifactId>-->
+			<!--<artifactId>GitTraveller</artifactId>-->
 			<!--<version>0.0.1-SNAPSHOT</version>-->
 		<!--</dependency>-->
 
-		<dependency>
-			<groupId>edu.lu.uni.serval</groupId>
-			<artifactId>GitTraveller</artifactId>
-			<version>0.0.1-SNAPSHOT</version>
-		</dependency>
-
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>

src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java

@@ -1,101 +0,0 @@
-package edu.lu.uni.serval.FixPattern.utils;
-
-import java.util.HashMap;
-import java.util.Map;
-
-public class CNodeMap {
-	
-	public static Map<Integer, String> map;
-	
-	static {
-		map  = new HashMap<Integer, String>();
-		map.put(20100,"Left");
-		map.put(30100,"ActMisc");
-		map.put(40000,"FullType");
-		map.put(50000,"TypeQualifier");
-		map.put(60100,"BaseType");
-		map.put(60200,"Pointer");
-		map.put(60800,"EnumName");
-		map.put(60900,"StructUnionName");
-		map.put(61000,"TypeName");
-		map.put(70002,"SizeType");
-		map.put(70100,"IntType");
-		map.put(80001,"CChar");
-		map.put(80100,"Si");
-		map.put(90002,"UnSigned");
-		map.put(100003,"CInt");
-		map.put(200000,"ParamList");
-		map.put(210000,"DotsParameter");
-		map.put(220100,"ParameterType");
-		map.put(240100,"Ident");
-		map.put(240200,"Constant");
-		map.put(240400,"FunCall");
-		map.put(240500,"CondExpr");
-		map.put(240600,"Sequence");
-		map.put(240700,"Assignment");
-		map.put(240800,"Postfix");
-		map.put(240900,"Infix");
-		map.put(241000,"Unary");
-		map.put(241100,"Binary");
-		map.put(241200,"ArrayAccess");
-		map.put(241300,"RecordAccess");
-		map.put(241400,"RecordPtAccess");
-		map.put(241500,"SizeOfExpr");
-		map.put(241600,"SizeOfType");
-		map.put(241700,"Cast");
-		map.put(241900,"Constructor");
-		map.put(242000,"ParenExpr");
-		map.put(260300,"ExprStatement");
-		map.put(260800,"Asm");
-		map.put(270100,"Label");
-		map.put(270200,"Case");
-		map.put(270300,"CaseRange");
-		map.put(270400,"Default");
-		map.put(280001,"Continue");
-		map.put(280002,"Break");
-		map.put(280003,"Return");
-		map.put(280100,"Goto");
-		map.put(280200,"ReturnExpr");
-		map.put(290001,"None");
-		map.put(290100,"Some");
-		map.put(300100,"If");
-		map.put(300200,"Switch");
-		map.put(310100,"While");
-		map.put(310200,"DoWhile");
-		map.put(310300,"For");
-		map.put(310400,"MacroIteration");
-		map.put(330000,"Compound");
-		map.put(340000,"Storage");
-		map.put(350100,"DeclList");
-		map.put(350200,"MacroDecl");
-		map.put(360100,"InitExpr");
-		map.put(360200,"InitList");
-		map.put(360300,"InitDesignators");
-		map.put(370100,"DesignatorField");
-		map.put(370200,"DesignatorIndex");
-		map.put(370300,"DesignatorRange");
-		map.put(380000,"Definition");
-		map.put(400100,"Define");
-		map.put(400200,"Include");
-		map.put(400400,"OtherDirective");
-		map.put(410001,"DefineVar");
-		map.put(410002,"Undef");
-		map.put(410100,"DefineFunc");
-		map.put(420001,"DefineEmpty");
-		map.put(420100,"DefineExpr");
-		map.put(420200,"DefineStmt");
-		map.put(420400,"DefineDoWhileZero");
-		map.put(420600,"DefineInit");
-		map.put(440100,"IfdefDirective");
-		map.put(450100,"Declaration");
-		map.put(450200,"Definition");
-		map.put(450300,"CppTop");
-		map.put(450400,"IfdefTop");
-		map.put(450700,"NotParsedCorrectly");
-		map.put(450800,"FinalDef");
-		map.put(460000,"Program");
-		map.put(470000,"GenericList");
-		map.put(480000,"GenericString");
-		map.put(490100,"IfToken");
-	}
-}

src/main/java/edu/lu/uni/serval/FixPattern/utils/EDiff.java

@@ -0,0 +1,98 @@
+package edu.lu.uni.serval.FixPattern.utils;
+
+import com.github.gumtreediff.actions.model.*;
+import com.github.gumtreediff.tree.ITree;
+import com.github.gumtreediff.tree.TreeContext;
+import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import redis.clients.jedis.Jedis;
+import redis.clients.jedis.JedisPool;
+
+import java.io.IOException;
+import java.util.List;
+
+/**
+ * Created by anilkoyuncu on 17/09/2018.
+ */
+public class EDiff {
+    private static Logger log = LoggerFactory.getLogger(EDiff.class);
+    public static ITree getSimpliedTree(String fn, JedisPool outerPool) {
+
+        ITree tree = null;
+        Jedis inner = null;
+        try {
+            inner = outerPool.getResource();
+            while (!inner.ping().equals("PONG")){
+                log.info("wait");
+            }
+            inner.select(1);
+            String dist2load = inner.get(fn);
+            inner.select(0);
+            String s = inner.get(dist2load);
+            HierarchicalActionSet actionSet = (HierarchicalActionSet) EDiffHelper.fromString(s);
+
+            ITree parent = null;
+            ITree children =null;
+            TreeContext tc = new TreeContext();
+            tree = EDiffHelper.getASTTree(actionSet, parent, children,tc);
+            tree.setParent(null);
+            tc.validate();
+
+        } catch (IOException e) {
+            e.printStackTrace();
+        } catch (ClassNotFoundException e) {
+            e.printStackTrace();
+        }finally {
+            if (inner != null) {
+                inner.close();
+            }
+        }
+        return tree;
+
+    }
+    public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){
+
+        int newType = 0;
+
+        Action action = actionSet.getAction();
+        if (action instanceof Update){
+            newType = 101;
+        }else if(action instanceof Insert){
+            newType =100;
+        }else if(action instanceof Move){
+            newType = 102;
+        }else if(action instanceof Delete){
+            newType=103;
+        }else{
+            new Exception("unknow action");
+        }
+        if(actionSet.getParent() == null){
+            //root
+
+            parent = tc.createTree(newType, "", null);
+            tc.setRoot(parent);
+
+//            parent = new Tree(newType,"");
+        }else{
+            children = tc.createTree(newType, "", null);
+            children.setParentAndUpdateChildren(parent);
+//            children = new Tree(newType,"");
+//            parent.addChild(children);
+        }
+        List<HierarchicalActionSet> subActions = actionSet.getSubActions();
+        if (subActions.size() != 0){
+            for (HierarchicalActionSet subAction : subActions) {
+
+                if(actionSet.getParent() == null){
+                    children = parent;
+                }
+                getActionTree(subAction,children,null,tc);
+
+            }
+
+
+        }
+        return parent;
+    }
+}

src/main/java/edu/lu/uni/serval/FixPattern/utils/EDiffHelper.java

@@ -0,0 +1,88 @@
+package edu.lu.uni.serval.FixPattern.utils;
+
+import com.github.gumtreediff.tree.ITree;
+import com.github.gumtreediff.tree.TreeContext;
+import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.*;
+import java.util.Base64;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.stream.Collectors;
+
+/**
+ * Created by anilkoyuncu on 17/09/2018.
+ */
+public class EDiffHelper {
+    private static Logger log = LoggerFactory.getLogger(EDiffHelper.class);
+    /** Read the object from Base64 string. */
+    public static Object fromString( String s ) throws IOException,
+            ClassNotFoundException {
+        byte [] data = Base64.getDecoder().decode( s );
+        ObjectInputStream ois = new ObjectInputStream(
+                new ByteArrayInputStream(  data ) );
+        Object o  = ois.readObject();
+        ois.close();
+        return o;
+    }
+
+    /** Write the object to a Base64 string. */
+    public static String toString( Serializable o ) throws IOException {
+        ByteArrayOutputStream baos = new ByteArrayOutputStream();
+        ObjectOutputStream oos = new ObjectOutputStream( baos );
+        oos.writeObject( o );
+        oos.close();
+        return Base64.getEncoder().encodeToString(baos.toByteArray());
+    }
+
+    public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children, TreeContext tc){
+
+        int newType = 0;
+
+        String astNodeType = actionSet.getAstNodeType();
+        List<Integer> keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType);
+
+        if(keysByValue.size() != 1){
+            log.error("More than 1");
+        }
+        newType = keysByValue.get(0);
+        if(actionSet.getParent() == null){
+            //root
+
+//            parent = new Tree(newType,"");
+            parent = tc.createTree(newType, "", null);
+            tc.setRoot(parent);
+        }else{
+//            children = new Tree(newType,"");
+//            parent.addChild(children);
+            children = tc.createTree(newType, "", null);
+            children.setParentAndUpdateChildren(parent);
+        }
+        List<HierarchicalActionSet> subActions = actionSet.getSubActions();
+        if (subActions.size() != 0){
+            for (HierarchicalActionSet subAction : subActions) {
+
+                if(actionSet.getParent() == null){
+                    children = parent;
+                }
+                getASTTree(subAction,children,null,tc);
+
+            }
+
+
+        }
+        return parent;
+    }
+
+
+    public static <T, E> List<T> getKeysByValue(Map<T, E> map, E value) {
+        return map.entrySet()
+                .stream()
+                .filter(entry -> Objects.equals(entry.getValue(), value))
+                .map(Map.Entry::getKey)
+                .collect(Collectors.toList());
+    }
+}

src/main/java/edu/lu/uni/serval/FixPattern/utils/PoolBuilder.java

@@ -0,0 +1,33 @@
+package edu.lu.uni.serval.FixPattern.utils;
+
+import redis.clients.jedis.JedisPoolConfig;
+
+import java.time.Duration;
+
+/**
+ * Created by anilkoyuncu on 17/09/2018.
+ */
+public class PoolBuilder {
+    public static JedisPoolConfig getPoolConfig() {
+        return poolConfig;
+    }
+
+    static final JedisPoolConfig poolConfig = buildPoolConfig();
+
+
+    private static JedisPoolConfig buildPoolConfig() {
+        final JedisPoolConfig poolConfig = new JedisPoolConfig();
+        poolConfig.setMaxTotal(128);
+        poolConfig.setMaxIdle(128);
+        poolConfig.setMinIdle(16);
+        poolConfig.setTestOnBorrow(true);
+        poolConfig.setTestOnReturn(true);
+        poolConfig.setTestWhileIdle(true);
+        poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis());
+        poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis());
+        poolConfig.setNumTestsPerEvictionRun(3);
+        poolConfig.setBlockWhenExhausted(true);
+
+        return poolConfig;
+    }
+}

src/main/java/edu/lu/uni/serval/FixPatternParser/CUCreator.java

@@ -1,15 +1,11 @@
 package edu.lu.uni.serval.FixPatternParser;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-
 import org.eclipse.jdt.core.dom.AST;
 import org.eclipse.jdt.core.dom.ASTParser;
 import org.eclipse.jdt.core.dom.CompilationUnit;
 
+import java.io.*;
+
 /**
  * Creator of a CompilationUnit.
  * 

src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java

@@ -1,19 +1,6 @@
 package edu.lu.uni.serval.FixPatternParser;
 
 import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Locale;
-
-import com.github.gumtreediff.actions.model.Action;
-import com.github.gumtreediff.actions.model.Move;
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.gumtree.GumTreeComparer;
-import edu.lu.uni.serval.gumtree.regroup.ActionFilter;
-import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
-import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper;
-import edu.lu.uni.serval.gumtree.regroup.SimplifyTree;
 
 /**
  * Parse fix patterns with GumTree.
@@ -33,434 +20,6 @@ public abstract class Parser implements ParserInterface {
 
 	public abstract void parseFixPatterns(File prevFile, File revFile, File diffEntryFile,String project);
 	
-	protected List<HierarchicalActionSet> parseChangedSourceCodeWithGumTree(File prevFile, File revFile) {
-		List<HierarchicalActionSet> actionSets = new ArrayList<>();
-		// GumTree results
-		List<Action> gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTree(prevFile, revFile);
-//		List<Action> gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTreeForCCode(prevFile, revFile);
-		if (gumTreeResults != null && gumTreeResults.size() > 0) {
-			// Regroup GumTre results.
-			List<HierarchicalActionSet> allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults);
-			
-			// Filter out modified actions of changing method names, method parameters, variable names and field names in declaration part.
-			// TODO: variable effects range, sub-actions are these kinds of modification?
-			actionSets.addAll(new ActionFilter().filterOutUselessActions(allActionSets));
-		}
-		
-		return actionSets;
-	}
-	
-	protected List<Move> getFirstAndLastMoveAction(HierarchicalActionSet gumTreeResult) {
-		List<Move> firstAndLastMoveActions = new ArrayList<>();
-		List<HierarchicalActionSet> actions = gumTreeResult.getSubActions();
-		if (actions.size() == 0) {
-			return null;
-		}
-		Move firstMoveAction = null;
-		Move lastMoveAction = null;
-		while (actions.size() > 0) {
-			List<HierarchicalActionSet> subActions = new ArrayList<>();
-			for (HierarchicalActionSet action : actions) {
-				subActions.addAll(action.getSubActions());
-				if (action.toString().startsWith("MOV")) {
-					if (firstMoveAction == null) {
-						firstMoveAction = (Move) action.getAction();
-						lastMoveAction = (Move) action.getAction();
-					} else {
-						int startPosition = action.getStartPosition();
-						int length = action.getLength();
-						int startPositionFirst = firstMoveAction.getPosition();
-						int startPositionLast = lastMoveAction.getPosition();
-						int lengthLast = lastMoveAction.getNode().getLength();
-						if (startPosition < startPositionFirst || (startPosition == startPositionFirst && length > firstMoveAction.getLength())) {
-							firstMoveAction = (Move) action.getAction();
-						}
-						if ((startPosition + length) > (startPositionLast + lengthLast)) {
-							lastMoveAction = (Move) action.getAction();
-						} 
-					}
-				}
-			}
-			
-			actions.clear();
-			actions.addAll(subActions);
-		}
-		if (firstMoveAction == null) {
-			return null;
-		}
-		firstAndLastMoveActions.add(firstMoveAction);
-		firstAndLastMoveActions.add(lastMoveAction);
-		return firstAndLastMoveActions;
-	}
-	
-	protected String getSemiSourceCodeEditScripts(HierarchicalActionSet actionSet) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	protected String getAbstractIdentifiersEditScripts(HierarchicalActionSet actionSet) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	protected String getRawTokenEditScripts(HierarchicalActionSet actionSet) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	protected int getEndPosition(List<ITree> children) {
-		int endPosition = 0;
-		for (ITree child : children) {
-			if (child.getLabel().endsWith("Body")) {
-				endPosition = child.getPos() - 1;
-				break;
-			}
-		}
-		return endPosition;
-	}
-
-	/**
-	 * Get the AST node based edit script of patches in terms of breadth first.
-	 * 
-	 * @param actionSet
-	 * @return
-	 */
-	protected String getASTEditScriptsBreadthFirst(HierarchicalActionSet actionSet) {
-		String editScript = "";
-		
-		List<HierarchicalActionSet> actionSets = new ArrayList<>();
-		actionSets.add(actionSet);
-		while (actionSets.size() != 0) {
-			List<HierarchicalActionSet> subSets = new ArrayList<>();
-			for (HierarchicalActionSet set : actionSets) {
-				subSets.addAll(set.getSubActions());
-				String actionStr = set.getActionString();
-				int index = actionStr.indexOf("@@");
-				String singleEdit = actionStr.substring(0, index).replace(" ", "");
-				
-				singleEdit = handleSimpleNameNode(singleEdit, actionStr, index);
-				
-				editScript += singleEdit + " ";
-			}
-			actionSets.clear();
-			actionSets.addAll(subSets);
-		}
-		return editScript;
-	}
-	
-	private String handleSimpleNameNode(String singleEdit, String actionStr, int index) {
-		// TODO
-		if (singleEdit.endsWith("SimpleName")) {
-			actionStr = actionStr.substring(index + 2);
-			if (actionStr.startsWith("MethodName")) {
-				singleEdit = singleEdit.replace("SimpleName", "MethodName");
-			} else if (actionStr.startsWith("ClassName")) {
-				singleEdit = singleEdit.replace("SimpleName", "ClassName");
-			} else {
-				if (actionStr.startsWith("Name")) {
-					char c = actionStr.charAt(5);
-					if (Character.isUpperCase(c)) {
-						singleEdit = singleEdit.replace("SimpleName", "Name");
-					} else {
-						singleEdit = singleEdit.replace("SimpleName", "Variable");
-					}
-				} else {
-					singleEdit = singleEdit.replace("SimpleName", "Variable");
-				}
-			}
-		}
-		return singleEdit;
-	}
-
-	/**
-	 * Get the AST node based edit script of patches in terms of deep first.
-	 * 
-	 * @param actionSet
-	 * @return
-	 */
-	protected String getASTEditScriptsDeepFirst(HierarchicalActionSet actionSet) {
-		String editScript = "";
-		String actionStr = actionSet.getActionString();
-		int index = actionStr.indexOf("@@");
-		String singleEdit = actionStr.substring(0, index).replace(" ", "");
-		
-		singleEdit = handleSimpleNameNode(singleEdit, actionStr, index);
-		
-		editScript = singleEdit + " ";
-		
-		List<HierarchicalActionSet> subActionSets = actionSet.getSubActions();;
-		for (HierarchicalActionSet subActionSet : subActionSets) {
-			editScript += getASTEditScriptsDeepFirst(subActionSet);
-		}
-		return editScript;
-	}
-
-	/**
-	 * 
-	 * @param hunkActionSets
-	 * @param bugStartLine
-	 * @param bugEndLine
-	 * @param fixStartLine
-	 * @param fixEndLine
-	 * @return
-	 */
-	protected String getASTEditScriptsBreadthFirst(List<HierarchicalActionSet> hunkActionSets, int bugEndPosition, int fixEndPosition) {
-		String editScript = "";
-		
-		for (HierarchicalActionSet hunkActionSet : hunkActionSets) {
-			editScript += getASTEditScriptsBreadthFirst(hunkActionSet, bugEndPosition, fixEndPosition);
-		}
-		return editScript;
-	}
-	
-	private String getASTEditScriptsBreadthFirst(HierarchicalActionSet hunkActionSet, int bugEndPosition, int fixEndPosition) {
-		String editScript = "";
-		List<HierarchicalActionSet> actionSets = new ArrayList<>();
-		actionSets.add(hunkActionSet);
-		while (actionSets.size() != 0) {
-			List<HierarchicalActionSet> subSets = new ArrayList<>();
-			for (HierarchicalActionSet set : actionSets) {
-				int position = set.getAction().getPosition();
-				String actionStr = set.getActionString();
-				if (isOutofPosition(actionStr, position, bugEndPosition, fixEndPosition)) {
-					continue;
-				}
-				
-				subSets.addAll(set.getSubActions());
-				int index = actionStr.indexOf("@@");
-				String singleEdit = actionStr.substring(0, index).replace(" ", "");
-				
-				singleEdit = handleSimpleNameNode(singleEdit, actionStr, index);
-				
-				editScript += singleEdit + " ";
-			}
-			actionSets.clear();
-			actionSets.addAll(subSets);
-		}
-		return editScript;
-	}
-	
-	private boolean isOutofPosition(String actionStr, int actionPosition, int bugEndPosition, int fixEndPosition) {
-		if (actionStr.startsWith("INS")) {
-			if (actionPosition > fixEndPosition) {
-				return true;
-			}
-		} else if (!actionStr.startsWith("MOV") && actionPosition > bugEndPosition) {
-			return true;
-		}
-		return false;
-	}
-
-	protected String getASTEditScriptsDeepFirst(List<HierarchicalActionSet> hunkActionSets, int bugEndPosition, int fixEndPosition) {
-		StringBuilder editScript = new StringBuilder();
-		
-		for (HierarchicalActionSet hunkActionSet : hunkActionSets) {
-			editScript.append(getASTEditScriptsDeepFirst2(hunkActionSet, bugEndPosition, fixEndPosition));
-		}
-		return editScript.toString();
-	}
-	
-	private String getASTEditScriptsDeepFirst(HierarchicalActionSet actionSet, int bugEndPosition, int fixEndPosition) {
-		String editScripts = "";
-		String actionStr = actionSet.getActionString();
-		int index = actionStr.indexOf("@@");
-		String singleEdit = actionStr.substring(0, index).replace(" ", "");
-		
-		singleEdit = handleSimpleNameNode(singleEdit, actionStr, index);
-		
-		editScripts += singleEdit + " ";
-		
-		for (HierarchicalActionSet subActionSet : actionSet.getSubActions()) {
-			int position = subActionSet.getAction().getPosition();
-			actionStr = subActionSet.getActionString();
-			if (isOutofPosition(actionStr, position, bugEndPosition, fixEndPosition)) {
-				continue;
-			}
-			editScripts += getASTEditScriptsDeepFirst(subActionSet, bugEndPosition, fixEndPosition);
-		}
-		
-		return editScripts;
-	}
-	
-	private String getASTEditScriptsDeepFirst2(HierarchicalActionSet actionSet, int bugEndPosition, int fixEndPosition) {
-		StringBuilder editScripts = new StringBuilder();
-		String actionStr = actionSet.getActionString();
-		int index = actionStr.indexOf("@@");
-		String singleEdit = actionStr.substring(0, index);
-		
-		if (singleEdit.endsWith("Statement")) {
-			singleEdit = singleEdit + " " + singleEdit.substring(4, singleEdit.indexOf("Statement")).toLowerCase(Locale.ENGLISH);
-		} else {
-			singleEdit = handleSimpleNameNode2(singleEdit, actionStr, index, actionSet);
-		}
-		editScripts.append(singleEdit).append(" ");
-		
-		for (HierarchicalActionSet subActionSet : actionSet.getSubActions()) {
-			int position = subActionSet.getAction().getPosition();
-			actionStr = subActionSet.getActionString();
-			if (isOutofPosition(actionStr, position, bugEndPosition, fixEndPosition)) {
-				continue;
-			}
-			editScripts.append(getASTEditScriptsDeepFirst2(subActionSet, bugEndPosition, fixEndPosition));
-		}
-		
-		return editScripts.toString();
-	}
-	
-	private String handleSimpleNameNode2(String singleEdit, String actionStr, int index, HierarchicalActionSet actionSet) {
-		if (singleEdit.endsWith("SimpleName")) {
-			actionStr = actionStr.substring(index + 2);
-			if (actionStr.startsWith("MethodName")) {
-				singleEdit = singleEdit.replace("SimpleName", "MethodName");
-				String methodName = actionStr.substring(actionStr.indexOf("MethodName:") + 11);
-				int index1 = methodName.indexOf(":");
-				int index2 = methodName.indexOf(" ");
-				index = (index1 < 0 || index1 > index2) ? index2 : index1;
-				methodName = methodName.substring(0, index);
-				singleEdit += " " + methodName;
-			} else if (actionStr.startsWith("ClassName")) {
-				singleEdit = singleEdit.replace("SimpleName", "ClassName");
-				String className = actionStr.substring(actionStr.indexOf("ClassName:") + 10);
-				int index1 = className.indexOf(" ");
-				index = index1 < 0 ? className.length() : index1;
-				className = className.substring(0, index);
-				singleEdit += " " + className;
-			} else {
-				if (actionStr.startsWith("Name")) {
-					char c = actionStr.charAt(5);
-					if (Character.isUpperCase(c)) {
-						singleEdit = singleEdit.replace("SimpleName", "Name");
-						String name = actionStr.substring(actionStr.indexOf("Name:") + 5);
-						int index1 = name.indexOf(" ");
-						index = index1 < 0 ? name.length() : index1;
-						name = name.substring(0, index);
-						singleEdit += " " + name;
-					} else {
-						singleEdit = singleEdit.replace("SimpleName", "Variable");
-						int index1 = actionStr.indexOf(" ");
-						index = index1 < 0 ? actionStr.length() : index1;
-						String var = actionStr.substring(0, index);
-						var = new SimplifyTree().canonicalVariableName(var, actionSet.getAction().getNode());
-						singleEdit += " " + var.replaceAll(" ", "");
-					}
-				} else {
-					singleEdit = singleEdit.replace("SimpleName", "Variable");
-					String var = actionStr.substring(0, (actionStr.indexOf(" ") < 0 ? actionStr.length() : actionStr.indexOf(" ")));
-					var = new SimplifyTree().canonicalVariableName(var, actionSet.getAction().getNode());
-					singleEdit += " " + var.replaceAll(" ", "");
-				}
-			}
-		} else {
-			if (actionSet.getSubActions() != null && actionSet.getSubActions().size() > 0) {
-				singleEdit += " " + actionSet.getAstNodeType()+ "exp";
-			} else {
-				if (singleEdit.endsWith("CharacterLiteral")) {
-					singleEdit += " charLiteral";
-				} else if (singleEdit.endsWith("NumberLiteral")) {
-					singleEdit += " numLiteral";
-				} else if (singleEdit.endsWith("StringLiteral")) {
-					singleEdit += " strLiteral";
-				} else if (singleEdit.endsWith("BooleanLiteral") || singleEdit.endsWith("NullLiteral") || singleEdit.endsWith("Operator") ||
-						singleEdit.endsWith("ThisExpression") || singleEdit.endsWith("TypeLiteral") || singleEdit.endsWith("Instanceof") ||
-						singleEdit.endsWith("New") || singleEdit.endsWith("WildcardType") || singleEdit.endsWith("SimpleType") ||
-						singleEdit.endsWith("QualifiedType") || singleEdit.endsWith("PrimitiveType") || singleEdit.endsWith("NameQualifiedType")) {
-					singleEdit += " " + actionSet.getNode().getLabel();
-				} else if (singleEdit.endsWith("SuperConstructorInvocation")) {
-					singleEdit += " super";
-				} else if (singleEdit.endsWith("ConstructorInvocation")) {
-					singleEdit += " this";
-				} else if (singleEdit.endsWith("SimpleName")) {
-					actionStr = actionStr.substring(index + 2);
-					if (actionStr.startsWith("MethodName")) {
-						singleEdit = singleEdit.replace("SimpleName", "MethodName");
-						String methodName = actionStr.substring(actionStr.indexOf("MethodName:") + 11);
-						int index1 = methodName.indexOf(":");
-						int index2 = methodName.indexOf(" ");
-						index = (index1 < 0 || index1 > index2) ? index2 : index1;
-						methodName = methodName.substring(0, index);
-						singleEdit += " " + methodName;
-					} else if (actionStr.startsWith("ClassName")) {
-						singleEdit = singleEdit.replace("SimpleName", "ClassName");
-						String className = actionStr.substring(actionStr.indexOf("ClassName:") + 10);
-						int index1 = className.indexOf(" ");
-						index = index1 < 0 ? className.length() : index1;
-						className = className.substring(0, index);
-						singleEdit += " " + className;
-					} else {
-						if (actionStr.startsWith("Name")) {
-							char c = actionStr.charAt(5);
-							if (Character.isUpperCase(c)) {
-								singleEdit = singleEdit.replace("SimpleName", "Name");
-								String name = actionStr.substring(actionStr.indexOf("Name:") + 5);
-								int index1 = name.indexOf(" ");
-								index = index1 < 0 ? name.length() : index1;
-								name = name.substring(0, index);
-								singleEdit += " " + name;
-							} else {
-								singleEdit = singleEdit.replace("SimpleName", "Variable");
-								int index1 = actionStr.indexOf(" ");
-								index = index1 < 0 ? actionStr.length() : index1;
-								String var = actionStr.substring(0, index);
-								var = new SimplifyTree().canonicalVariableName(var, actionSet.getAction().getNode());
-								singleEdit += " " + var.replaceAll(" ", "");
-							}
-						} else {
-							singleEdit = singleEdit.replace("SimpleName", "Variable");
-							String var = actionStr.substring(0, (actionStr.indexOf(" ") < 0 ? actionStr.length() : actionStr.indexOf(" ")));
-							var = new SimplifyTree().canonicalVariableName(var, actionSet.getAction().getNode());
-							singleEdit += " " + var.replaceAll(" ", "");
-						}
-					}
-				} else {
-					ITree nodeTree = actionSet.getNode();
-					if (nodeTree.getChildren().size() > 0) {
-						singleEdit += " " + actionSet.getAstNodeType()+ "exp";
-					} else {
-						singleEdit += " " +  nodeTree.getLabel().replaceAll(" ", "");
-					}
-				}
-			}
-		}
-		return singleEdit;
-	}
-	
-	protected String getAstEditScripts(List<HierarchicalActionSet> actionSets, int bugEndLine, int fixEndLine) {
-		String editScripts = "";
-		for (HierarchicalActionSet actionSet : actionSets) {
-			editScripts += getActionString(actionSet, bugEndLine, fixEndLine, "");
-		}
-		return editScripts;
-	}
-
-	private String getActionString(HierarchicalActionSet actionSet, int bugEndPosition, int fixEndPosition, String hierarchicalLabel) {
-		String editScripts = "";
-
-		String actionStr = actionSet.getActionString();
-		int index = actionStr.indexOf("@@");
-		String singleEdit = actionStr.substring(0, index);
-		
-		singleEdit = handleSimpleNameNode(singleEdit, actionStr, index);
-		
-		editScripts += hierarchicalLabel + singleEdit + "\n";
-		
-		for (HierarchicalActionSet subActionSet : actionSet.getSubActions()) {
-			int position = subActionSet.getAction().getPosition();
-			actionStr = subActionSet.getActionString();
-			if (isOutofPosition(actionStr, position, bugEndPosition, fixEndPosition)) {
-				continue;
-			}
-			editScripts += getActionString(subActionSet, bugEndPosition, fixEndPosition, hierarchicalLabel + "---");
-		}
-
-		return editScripts;
-	}
-	
-	protected void clearITree(HierarchicalActionSet actionSet) {
-		actionSet.getAction().setNode(null);
-		for (HierarchicalActionSet subActionSet : actionSet.getSubActions()) {
-			clearITree(subActionSet);
-		}
-	}
 
 	@Override
 	public String getAstEditScripts() {
@@ -472,10 +31,10 @@ public abstract class Parser implements ParserInterface {
 		return patchesSourceCode;
 	}
 
-	@Override
+//	@Override
-	public String getBuggyTrees() {
+//	public String getBuggyTrees() {
-		return buggyTrees;
+//		return buggyTrees;
-	}
+//	}
 
 	@Override
 	public String getSizes() {
@@ -487,13 +46,13 @@ public abstract class Parser implements ParserInterface {
 		return tokensOfSourceCode;
 	}
 
-	@Override
+//	@Override
-	public String getOriginalTree() {
+//	public String getOriginalTree() {
-		return originalTree;
+//		return originalTree;
-	}
+//	}
-
+//
-	@Override
+//	@Override
-	public String getActionSets() {
+//	public String getActionSets() {
-		return actionSets;
+//		return actionSets;
-	}
+//	}
 }

src/main/java/edu/lu/uni/serval/FixPatternParser/ParserInterface.java

@@ -1,23 +1,21 @@
 package edu.lu.uni.serval.FixPatternParser;
 
-import java.io.File;
-
 public interface ParserInterface {
 	
 
-	public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile);
+//	public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile);
 	
 	public String getAstEditScripts();
 
 	public String getPatchesSourceCode();
 
-	public String getBuggyTrees();
+//	public String getBuggyTrees();
 
 	public String getSizes();
 
 	public String getTokensOfSourceCode();
 
-	public String getOriginalTree();
+//	public String getOriginalTree();
 
-	public String getActionSets();
+//	public String getActionSets();
 }

src/main/java/edu/lu/uni/serval/FixPatternParser/Tokenizer.java

@@ -1,75 +0,0 @@
-package edu.lu.uni.serval.FixPatternParser;
-
-import java.util.List;
-
-import edu.lu.uni.serval.gumtree.regroup.SimpleTree;
-
-public class Tokenizer {
-
-	public static String getTokensDeepFirst(SimpleTree simpleTree) {
-		String tokens = "";
-		List<SimpleTree> children = simpleTree.getChildren();
-		String astNodeType = simpleTree.getNodeType();
-		
-		if (children.isEmpty()) { // BreakStatement, ContinueStatement, ReturnStatement, TryStatement
-			if (astNodeType.endsWith("Statement")) {
-				String label = astNodeType;
-				label = label.substring(0, label.lastIndexOf("S")).toLowerCase();
-				tokens += astNodeType + " " + label + " ";
-			} else if ("SuperConstructorInvocation".equals(astNodeType)) {
-				tokens += astNodeType + " super ";
-			} else if ("ConstructorInvocation".equals(astNodeType)) {
-				tokens += astNodeType + " this ";
-			} else if ("StringLiteral".equals(astNodeType)) {
-				tokens += astNodeType + " stringLiteral ";
-			} else if ("CharacterLiteral".equals(astNodeType)) {
-				tokens += astNodeType + " charLiteral ";
-			} else if ("ArrayInitializer".equals(astNodeType)) {
-				tokens += astNodeType + " arrayInitializer ";
-			} else if ("LambdaExpression".equals(astNodeType)) {
-				tokens += astNodeType + " lambda ";
-			} else if ("NumberLiteral".equals(astNodeType)) {
-				tokens += astNodeType + " numberLiteral ";
-			} else {
-				tokens += astNodeType + " " + simpleTree.getLabel() + " ";
-			}
-		} else {
-			if ("AssertStatement".equals(astNodeType) || "DoStatement".equals(astNodeType)
-					|| "ForStatement".equals(astNodeType) || "IfStatement".equals(astNodeType)
-					|| "ReturnStatement".equals(astNodeType) || "SwitchStatement".equals(astNodeType) 
-					|| "SynchronizedStatement".equals(astNodeType) || "ThrowStatement".equals(astNodeType)
-					|| "TryStatement".equals(astNodeType) || "WhileStatement".equals(astNodeType)) {
-				String label = astNodeType;
-				label = label.substring(0, label.lastIndexOf("S")).toLowerCase();
-				tokens += astNodeType + " " + label + " ";
-			} else if ("EnhancedForStatement".equals(astNodeType)) {
-				tokens += astNodeType + " " + "for ";
-			} else if ("CatchClause".equals(astNodeType)) {
-				tokens += astNodeType + " " + "catch ";
-			} else if ("SwitchCase".equals(astNodeType)) {
-				tokens += astNodeType + " case ";
-			} else if ("SuperConstructorInvocation".equals(astNodeType)) {
-				tokens += astNodeType + " super ";
-			} else if ("ConstructorInvocation".equals(astNodeType)) {
-				tokens += astNodeType + " this ";
-			} else if ("FinallyBody".equals(astNodeType)) {
-				tokens += astNodeType + " finally ";
-			} else if ("LabeledStatement".equals(astNodeType)) {
-				tokens += "LabeledStatement " + simpleTree.getLabel();
-			} else if ("SuperMethodInvocation".equals(astNodeType)) {
-				tokens += astNodeType + " super ";
-			} else if ("MethodName".equals(astNodeType)) {
-				tokens += "MethodName " + simpleTree.getLabel() + " ";
-			}
-			
-			if ("ArrayInitializer".equals(astNodeType)) {
-				tokens += astNodeType + " arrayInitializer ";
-			} else {
-				for (SimpleTree child : children) {
-					tokens += getTokensDeepFirst(child);
-				}
-			}
-		}
-		return tokens;
-	}
-}

src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchHunkParser.java

@@ -1,113 +0,0 @@
-package edu.lu.uni.serval.FixPatternParser.patch;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import edu.lu.uni.serval.FixPatternParser.Tokenizer;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.diffentry.DiffEntryHunk;
-import edu.lu.uni.serval.diffentry.DiffEntryReader;
-import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
-import edu.lu.uni.serval.gumtree.regroup.HunkActionFilter;
-import edu.lu.uni.serval.gumtree.regroup.HunkFixPattern;
-import edu.lu.uni.serval.gumtree.regroup.SimpleTree;
-import edu.lu.uni.serval.gumtree.regroup.SimplifyTree;
-
-/**
- * Parse fix patterns with GumTree.
- * 
- * Multiple statements bugs.
- * 
- * @author kui.liu
- *
- */
-public class CommitPatchHunkParser extends CommitPatchParser {
-	
-
-	@Override
-	public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) {
-		
-		// GumTree results
-		List<HierarchicalActionSet> actionSets = parseChangedSourceCodeWithGumTree(prevFile, revFile);
-		
-		if (actionSets.size() > 0) {
-			// DiffEntry size: filter out big hunks.
-			List<DiffEntryHunk> diffentryHunks = new DiffEntryReader().readHunks(diffEntryFile);
-			//Filter out the modify actions, which are not in the DiffEntry hunks.
-			HunkActionFilter hunkFilter = new HunkActionFilter();
-			List<HunkFixPattern> allHunkFixPatterns = hunkFilter.filterActionsByDiffEntryHunk2(diffentryHunks, actionSets, revFile, prevFile);
-			
-			for (HunkFixPattern hunkFixPattern : allHunkFixPatterns) {
-				// Range of buggy source code
-				int startLine = 0;
-				int endLine = 0;
-				// Range of fixing source code
-				int startLine2 = 0;
-				int endLine2 = 0;
-				/*
-				 * Convert the ITree of buggy code to a simple tree.
-				 * It will be used to compute the similarity. 
-				 */
-				List<HierarchicalActionSet> hunkActionSets = hunkFixPattern.getHunkActionSets();
-				SimpleTree simpleTree = new SimpleTree();
-				simpleTree.setLabel("Block");
-				simpleTree.setNodeType("Block");
-				List<SimpleTree> children = new ArrayList<>();
-				String astEditScripts = "";
-				for (HierarchicalActionSet hunkActionSet : hunkActionSets) {
-					SimplifyTree abstractIdentifier = new SimplifyTree();
-					abstractIdentifier.abstractTree(hunkActionSet);
-					SimpleTree simpleT = hunkActionSet.getSimpleTree();
-					if (simpleT == null) { // Failed to get the simple tree for INS actions.
-						continue;
-					} 
-					children.add(simpleT);
-					
-					/**
-					 * Select edit scripts for deep learning. 
-					 * Edit scripts will be used to mine common fix patterns.
-					 */
-					// 1. First level: AST node type.
-					astEditScripts += getASTEditScriptsBreadthFirst(hunkActionSet);
-					// 2. source code: raw tokens
-					// 3. abstract identifiers: 
-					// 4. semi-source code: 
-					
-					if (startLine == 0) {
-						startLine = hunkActionSet.getBugStartLineNum();
-						endLine = hunkActionSet.getBugEndLineNum();
-						startLine2 = hunkActionSet.getFixStartLineNum();
-						endLine2 = hunkActionSet.getFixEndLineNum();
-					} else {
-						if (startLine > hunkActionSet.getBugStartLineNum()) startLine = hunkActionSet.getBugStartLineNum();
-						if (startLine2 > hunkActionSet.getFixStartLineNum()) startLine2 = hunkActionSet.getFixStartLineNum();
-						if (endLine < hunkActionSet.getBugEndLineNum()) endLine = hunkActionSet.getBugEndLineNum();
-						if (endLine2 < hunkActionSet.getFixEndLineNum()) endLine2 = hunkActionSet.getFixEndLineNum();
-					}
-				}
-				if (children.size() == 0) continue;
-				if (endLine - startLine >= Configuration.HUNK_SIZE - 2 || endLine2 - startLine2 >= Configuration.HUNK_SIZE - 2 ) continue;
-
-				simpleTree.setChildren(children);
-				simpleTree.setParent(null);
-				
-				// Source Code of patches.
-				String patchSourceCode = getPatchSourceCode(hunkFixPattern.getHunk(), startLine, endLine, startLine2, endLine2);
-				if ("".equals(patchSourceCode)) continue;
-				
-				this.patchesSourceCode += "PATCH###\n" + patchSourceCode + "\n";
-				int size = astEditScripts.split(" ").length;
-				this.sizes += size + "\n";
-				this.astEditScripts += astEditScripts + "\n";
-				
-//				this.buggyTrees += Configuration.BUGGY_TREE_TOKEN + "\n" + simpleTree.toString() + "\n";
-				this.tokensOfSourceCode += Tokenizer.getTokensDeepFirst(simpleTree).trim() + "\n";
-//				this.actionSets += Configuration.BUGGY_TREE_TOKEN + "\n" + readActionSet(actionSet, "") + "\n";
-//				this.originalTree += Configuration.BUGGY_TREE_TOKEN + "\n" + actionSet.getOriginalTree().toString() + "\n";
-				
-			}
-		}
-	}
-	
-}

src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java

@@ -1,105 +0,0 @@
-package edu.lu.uni.serval.FixPatternParser.patch;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.List;
-
-import edu.lu.uni.serval.FixPatternParser.Parser;
-import edu.lu.uni.serval.diffentry.DiffEntryHunk;
-
-/**
- * Parse fix patterns with GumTree.
- * 
- * @author kui.liu
- *
- */
-public class CommitPatchParser extends Parser{
-	
-	@Override
-	public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) {
-	}
-
-	protected DiffEntryHunk matchHunk(int startLine, int endLine, int startLine2, int endLine2, String actionStr, List<DiffEntryHunk> hunks) {
-		for (DiffEntryHunk hunk : hunks) {
-			int bugStartLine = hunk.getBugLineStartNum();
-			int bugRange = hunk.getBugRange();
-			int fixStartLine = hunk.getFixLineStartNum();
-			int fixRange = hunk.getFixRange();
-			
-			if (actionStr.startsWith("INS")) {
-				if (fixStartLine + fixRange < startLine2)  {
-					continue;
-				} 
-				if (endLine2 < fixStartLine ) {
-					return null;
-				} 
-				return hunk;
-			} else {
-				if (bugStartLine + bugRange < startLine)  {
-					continue;
-				} 
-				if (endLine < bugStartLine ) {
-					return null;
-				} 
-				return hunk;
-			}
-		}
-		return null;
-	}
-
-	protected String getPatchSourceCode(DiffEntryHunk hunk, int startLineNum, int endLineNum, int startLineNum2, int endLineNum2) {
-		String sourceCode = hunk.getHunk();
-		int bugStartLine = hunk.getBugLineStartNum();
-		int fixStartLine = hunk.getFixLineStartNum();
-		String buggyStatements = "";
-		String fixedStatements = "";
-		BufferedReader reader = null;
-		try {
-			reader = new BufferedReader(new StringReader(sourceCode));
-			String line = null;
-			int bugLines = 0;
-			int fixLines = 0;
-			int contextLines = 0; // counter of non-buggy code line.
-			while ((line = reader.readLine()) != null) {
-				int bugLineIndex = bugLines + contextLines;
-				int fixLineIndex = fixLines + contextLines;
-				if (line.startsWith("-")) {
-					if (bugStartLine + bugLineIndex >= startLineNum && bugStartLine + bugLineIndex <= endLineNum) {
-						buggyStatements += line + "\n";
-					}
-					bugLines ++;
-				} else if (line.startsWith("+")) {
-					if (fixStartLine + fixLineIndex >= startLineNum2 && fixStartLine + fixLineIndex <= endLineNum2) {
-						fixedStatements += line + "\n";
-					}
-					fixLines ++;
-				} else {
-					contextLines ++;
-				}
-				
-				if (bugStartLine + bugLineIndex > endLineNum && fixStartLine + fixLineIndex > endLineNum2) {
-					break;
-				}
-			}
-		} catch (IOException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				if (reader != null) {
-					reader.close();
-					reader = null;
-				}
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		return buggyStatements + fixedStatements;
-	}
-
-	@Override
-	public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile, String project) {
-
-	}
-}

src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchSingleStatementParser.java

@@ -1,158 +0,0 @@
-package edu.lu.uni.serval.FixPatternParser.patch;
-
-import java.io.File;
-import java.util.List;
-
-import org.eclipse.jdt.core.dom.CompilationUnit;
-
-import com.github.gumtreediff.actions.model.Move;
-import com.github.gumtreediff.actions.model.Update;
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.FixPattern.utils.Checker;
-import edu.lu.uni.serval.FixPatternParser.CUCreator;
-import edu.lu.uni.serval.FixPatternParser.Tokenizer;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.diffentry.DiffEntryHunk;
-import edu.lu.uni.serval.diffentry.DiffEntryReader;
-import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
-import edu.lu.uni.serval.gumtree.regroup.SimpleTree;
-import edu.lu.uni.serval.gumtree.regroup.SimplifyTree;
-
-/**
- * Parse fix patterns with GumTree.
- * 
- * Single Statement bugs.
- * 
- * @author kui.liu
- *
- */
-public class CommitPatchSingleStatementParser extends CommitPatchParser {
-
-	@Override
-	public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) {
-		// GumTree results
-		List<HierarchicalActionSet> actionSets = parseChangedSourceCodeWithGumTree(prevFile, revFile);
-
-		if (actionSets.size() > 0) {
-			// DiffEntry Hunks: filter out big hunks.
-			List<DiffEntryHunk> diffentryHunks = new DiffEntryReader().readHunks(diffEntryFile);
-			CUCreator cuCreator = new CUCreator();
-			CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile);
-			CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile);
-			if (prevUnit == null || revUnit == null) {
-				return;
-			}
-			for (HierarchicalActionSet actionSet : actionSets) {
-				// position of buggy statements
-				int startPosition = 0;
-				int endPosition = 0;
-				// position of fixed statements
-				int startPosition2 = 0;
-				int endPosition2 = 0;
-
-				String actionStr = actionSet.getActionString();
-				String astNodeType = actionSet.getAstNodeType();
-				if (actionStr.startsWith("INS")) {
-					startPosition2 = actionSet.getStartPosition();
-					endPosition2 = startPosition2 + actionSet.getLength();
-					List<Move> firstAndLastMov = getFirstAndLastMoveAction(actionSet);
-					if (firstAndLastMov != null) {
-						startPosition = firstAndLastMov.get(0).getNode().getPos();
-						ITree lastTree = firstAndLastMov.get(1).getNode();
-						endPosition = lastTree.getPos() + lastTree.getLength();
-					} else { // Ignore the pure insert actions without any move actions.
-						continue;
-					}
-				} else if (actionStr.startsWith("UPD")) {
-					startPosition = actionSet.getStartPosition();
-					endPosition = startPosition + actionSet.getLength();
-					Update update = (Update) actionSet.getAction();
-					ITree newNode = update.getNewNode();
-					startPosition2 = newNode.getPos();
-					endPosition2 = startPosition2 + newNode.getLength();
-
-					if (Checker.containsBodyBlock(astNodeType)) {
-						List<ITree> children = update.getNode().getChildren();
-						endPosition = getEndPosition(children);
-						List<ITree> newChildren = newNode.getChildren();
-						endPosition2 = getEndPosition(newChildren);
-
-						if (endPosition == 0) {
-							endPosition = startPosition + actionSet.getLength();
-						}
-						if (endPosition2 == 0) {
-							endPosition2 = startPosition2 + newNode.getLength();
-						}
-					}
-				} else {// DEL actions and MOV actions: we don't need these actions, as for now.
-					continue;
-				}
-				if (startPosition == 0 || startPosition2 == 0) {
-					continue;
-				}
-
-				// Get line numbers.
-				int startLine = prevUnit.getLineNumber(startPosition);
-				int endLine = prevUnit.getLineNumber(endPosition);
-				int startLine2 = revUnit.getLineNumber(startPosition2);
-				int endLine2 = revUnit.getLineNumber(endPosition2);
-				if (endLine - startLine >= Configuration.HUNK_SIZE - 2 || endLine2 - startLine2 >= Configuration.HUNK_SIZE - 2)
-					continue;
-				// Filter out the modify actions, which are not in the DiffEntry hunks.
-				DiffEntryHunk hunk = matchHunk(startLine, endLine, startLine2, endLine2, actionStr, diffentryHunks);
-				if (hunk == null) {
-					continue;
-				}
-
-				/*
-				 * Convert the ITree of buggy code to a simple tree. It will be
-				 * used to compute the similarity.
-				 */
-				SimplifyTree abstractIdentifier = new SimplifyTree();
-				abstractIdentifier.abstractTree(actionSet);
-				SimpleTree simpleTree = actionSet.getSimpleTree();
-				if (simpleTree == null) { // Failed to get the simple tree for INS actions.
-					continue;
-				}
-
-				/**
-				 * Select edit scripts for deep learning. Edit scripts will be
-				 * used to mine common fix patterns.
-				 */
-				// 1. First level: AST node type.
-				String astEditScripts = getASTEditScriptsBreadthFirst(actionSet);
-				int size = astEditScripts.split(" ").length;
-				if (size < 2) {
-					// System.out.println(actionSet);
-					continue;
-				}
-
-				// Source Code of patches.
-				String patchSourceCode = getPatchSourceCode(hunk, startLine, endLine, startLine2, endLine2);
-				if ("".equals(patchSourceCode))
-					continue;
-
-				this.patchesSourceCode += Configuration.PATCH_SIGNAL + "\n" + patchSourceCode + "\n";
-				this.sizes += size + "\n";
-				this.astEditScripts += astEditScripts + "\n";
-//				// 2. source code: raw tokens
-//				String rawTokenEditScripts = getRawTokenEditScripts(actionSet);
-//				// 3. abstract identifiers:
-//				String abstractIdentifiersEditScripts = getAbstractIdentifiersEditScripts(actionSet);
-//				// 4. semi-source code:
-//				String semiSourceCodeEditScripts = getSemiSourceCodeEditScripts(actionSet);
-
-				// this.buggyTrees += Configuration.BUGGY_TREE_TOKEN + "\n" +
-				// simpleTree.toString() + "\n";
-				this.tokensOfSourceCode += Tokenizer.getTokensDeepFirst(simpleTree).trim() + "\n";
-				// this.actionSets += Configuration.BUGGY_TREE_TOKEN + "\n" +
-				// readActionSet(actionSet, "") + "\n";
-				// this.originalTree += Configuration.BUGGY_TREE_TOKEN + "\n" +
-				// actionSet.getOriginalTree().toString() + "\n";
-			}
-			actionSets.clear();
-		}
-	}
-
-}

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CSVUtils.java

@@ -1,62 +0,0 @@
-package edu.lu.uni.serval.FixPatternParser.violations;
-
-import java.io.IOException;
-import java.io.Writer;
-import java.util.List;
-
-/**
- * Created by anilkoyuncu on 19/03/2018.
- */
-public class CSVUtils {
-
-    private static final char DEFAULT_SEPARATOR = ',';
-
-    public static void writeLine(Writer w, List<String> values) throws IOException {
-        writeLine(w, values, DEFAULT_SEPARATOR, ' ');
-    }
-
-    public static void writeLine(Writer w, List<String> values, char separators) throws IOException {
-        writeLine(w, values, separators, ' ');
-    }
-
-    //https://tools.ietf.org/html/rfc4180
-    private static String followCVSformat(String value) {
-
-        String result = value;
-        if (result.contains("\"")) {
-            result = result.replace("\"", "\"\"");
-        }
-        return result;
-
-    }
-
-    public static void writeLine(Writer w, List<String> values, char separators, char customQuote) throws IOException {
-
-        boolean first = true;
-
-        //default customQuote is empty
-
-        if (separators == ' ') {
-            separators = DEFAULT_SEPARATOR;
-        }
-
-        StringBuilder sb = new StringBuilder();
-        for (String value : values) {
-            if (!first) {
-                sb.append(separators);
-            }
-            if (customQuote == ' ') {
-                sb.append(followCVSformat(value));
-            } else {
-                sb.append(customQuote).append(followCVSformat(value)).append(customQuote);
-            }
-
-            first = false;
-        }
-        sb.append("\n");
-        w.append(sb.toString());
-
-
-    }
-
-}

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Consumer.java

@@ -1,226 +0,0 @@
-package edu.lu.uni.serval.FixPatternParser.violations;
-
-import com.github.gumtreediff.actions.ActionGenerator;
-import com.github.gumtreediff.actions.model.Action;
-import com.github.gumtreediff.matchers.Matcher;
-import com.github.gumtreediff.matchers.Matchers;
-import com.github.gumtreediff.tree.ITree;
-import com.github.gumtreediff.tree.Tree;
-import com.rabbitmq.client.*;
-import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap;
-import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import redis.clients.jedis.Jedis;
-import redis.clients.jedis.JedisPool;
-import redis.clients.jedis.JedisPoolConfig;
-
-import java.io.*;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.concurrent.TimeoutException;
-import java.util.stream.Collectors;
-
-/**
- * Created by anilkoyuncu on 03/04/2018.
- */
-public class Consumer {
-
-    private static Logger log = LoggerFactory.getLogger(Consumer.class);
-    private static String inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2";
-
-    public static void main(String[] args) {
-
-        ConnectionFactory factory = new ConnectionFactory();
-        factory.setHost("10.240.5.10");
-//        factory.setVirtualHost("treeCompare");
-        factory.setPort(5672);
-        factory.setUsername("anil");
-        factory.setPassword("changeme2018");
-        factory.setConnectionTimeout(1000);
-        Connection connection = null;
-        Channel channel = null;
-        try {
-            connection = factory.newConnection();
-
-            channel = connection.createChannel();
-            channel.queueDeclare("tree_queue", false, false, false, null);
-
-
-            boolean autoAck = false;
-            Channel finalChannel = channel;
-            channel.basicConsume("tree_queue", autoAck,"myConsumerTag",
-                new DefaultConsumer(finalChannel) {
-                    @Override
-                    public void handleDelivery(
-                            String consumerTag,
-                            Envelope envelope,
-                            AMQP.BasicProperties properties,
-                            byte[] body) throws IOException {
-
-                        String message = new String(body, "UTF-8");
-                        String[] split = message.split(",");
-                        String key = split[0];
-                        String firstV = split[1];
-                        String secondV = split[2];
-                        try{
-                            calculateSimi(firstV,secondV,key);
-                        }catch (Exception e){
-                            finalChannel.basicNack(envelope.getDeliveryTag(),false,false);
-                        }
-                        finalChannel.basicAck(envelope.getDeliveryTag(),false);
-
-                        // process the message
-                    }
-                });
-
-//            channel.basicConsume("tree_queue", true, consumer);
-
-        } catch (IOException e) {
-            e.printStackTrace();
-        } catch (TimeoutException e) {
-            e.printStackTrace();
-        }
-    }
-
-    public static void calculateSimi(String firstVal,String secondVal, String key){
-
-        String[] split = key.split("_");
-
-
-        String i = split[1];
-        String j = split[2];
-
-        String[] firstValueSplit = firstVal.split("GumTreeOutput2");
-        String[] secondValueSplit = secondVal.split("GumTreeOutput2");
-
-        String firstValue;
-        if (firstValueSplit.length == 1) {
-            firstValue = inputPath + firstValueSplit[0];
-        } else {
-            firstValue = inputPath + firstValueSplit[1];
-        }
-
-        String secondValue;
-        if (secondValueSplit.length == 1) {
-            secondValue = inputPath + secondValueSplit[0];
-        } else {
-            secondValue = inputPath + secondValueSplit[1];
-        }
-
-        ITree oldTree = getSimpliedTree(firstValue);
-
-        ITree newTree = getSimpliedTree(secondValue);
-
-        Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree);
-        m.match();
-
-
-        ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings());
-        ag.generate();
-        List<Action> actions = ag.getActions();
-
-        double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree);
-        String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1);
-        double diceSimilarity1 = m.diceSimilarity(oldTree, newTree);
-        String diceSimilarity = String.format("%1.2f", diceSimilarity1);
-        double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree);
-        String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1);
-
-        String editDistance = String.valueOf(actions.size());
-
-        String result = firstVal + "," + secondVal + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance;
-
-
-        if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0)
-                || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) {
-            String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j);
-            log.info(matchKey);
-//            JedisPool jedisPool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(port), 20000000);
-//            try (Jedis outer = jedisPool.getResource()) {
-//                outer.select(1);
-//                outer.set(matchKey, result);
-//            }
-        }
-
-
-//        try (Jedis jedis = pool.getResource()) {
-//            jedis.del("pair_"+ (String.valueOf(i)) + "_" + String.valueOf(j));
-//        }
-
-    }
-
-    public static ITree getSimpliedTree(String fn) {
-        HierarchicalActionSet actionSet = null;
-        try {
-            FileInputStream fi = new FileInputStream(new File(fn));
-            ObjectInputStream oi = new ObjectInputStream(fi);
-            actionSet = (HierarchicalActionSet) oi.readObject();
-            oi.close();
-            fi.close();
-
-
-        } catch (FileNotFoundException e) {
-            log.error("File not found");
-            e.printStackTrace();
-        } catch (IOException e) {
-            log.error("Error initializing stream");
-            e.printStackTrace();
-        } catch (ClassNotFoundException e) {
-            // TODO Auto-generated catch block
-            e.printStackTrace();
-        }
-
-        ITree parent = null;
-        ITree children =null;
-        ITree tree = getASTTree(actionSet, parent, children);
-        tree.setParent(null);
-
-        return tree;
-
-    }
-
-    public static <T, E> List<T> getKeysByValue(Map<T, E> map, E value) {
-        return map.entrySet()
-                .stream()
-                .filter(entry -> Objects.equals(entry.getValue(), value))
-                .map(Map.Entry::getKey)
-                .collect(Collectors.toList());
-    }
-
-    public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children){
-
-        int newType = 0;
-
-        String astNodeType = actionSet.getAstNodeType();
-        List<Integer> keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType);
-
-        if(keysByValue.size() != 1){
-            log.error("Birden cok astnodemapmapping");
-        }
-        newType = keysByValue.get(0);
-        if(actionSet.getParent() == null){
-            //root
-
-            parent = new Tree(newType,"");
-        }else{
-            children = new Tree(newType,"");
-            parent.addChild(children);
-        }
-        List<HierarchicalActionSet> subActions = actionSet.getSubActions();
-        if (subActions.size() != 0){
-            for (HierarchicalActionSet subAction : subActions) {
-
-                if(actionSet.getParent() == null){
-                    children = parent;
-                }
-                getASTTree(subAction,children,null);
-
-            }
-
-
-        }
-        return parent;
-    }
-}

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FieldViolation.java

@@ -1,121 +0,0 @@
-package edu.lu.uni.serval.FixPatternParser.violations;
-
-public enum FieldViolation {
-	       UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR,
-	       ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD,
-	       LI_LAZY_INIT_STATIC,
-	URF_UNREAD_FIELD,
-	MS_SHOULD_BE_FINAL,
-	URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD,
-	UWF_UNWRITTEN_FIELD,
-	MS_PKGPROTECT,
-	SS_SHOULD_BE_STATIC,
-	NP_UNWRITTEN_FIELD,
-	UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD,
-	SE_BAD_FIELD,
-	UUF_UNUSED_FIELD,
-	SE_BAD_FIELD_STORE,
-	MS_MUTABLE_ARRAY,
-	NP_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD,
-}
-
-enum ClassViolation{
-	SIC_INNER_SHOULD_BE_STATIC_ANON, //inner class.  ClassInstanceCreation by overriding some methods.
-	SIC_INNER_SHOULD_BE_STATIC,
-	RI_REDUNDANT_INTERFACES,
-	SE_COMPARATOR_SHOULD_BE_SERIALIZABLE,
-	
-	SE_NO_SERIALVERSIONID,
-		CI_CONFUSED_INHERITANCE,
-		SE_INNER_CLASS,
-
-		NM_CLASS_NOT_EXCEPTION,
-}
-
-enum MethodViolation {
-	NM_METHOD_NAMING_CONVENTION,
-	UPM_UNCALLED_PRIVATE_METHOD,
-		DE_MIGHT_IGNORE,
-	
-		NM_CONFUSING,
-		CN_IMPLEMENTS_CLONE_BUT_NOT_CLONEABLE,
-		UC_USELESS_VOID_METHOD,
-}
-
-enum StmtViolation {
-	DLS_DEAD_LOCAL_STORE, //Assignment statement. false positives may be high.
-	//This instruction assigns a value to a local variable, but the value is not read or used in any subsequent instruction.
-	
-	DM_BOXED_PRIMITIVE_FOR_PARSING,
-	
-	DM_CONVERT_CASE,
-	DM_DEFAULT_ENCODING,
-	IS2_INCONSISTENT_SYNC,
-	
-	NP_GUARANTEED_DEREF,
-	SIO_SUPERFLUOUS_INSTANCEOF,
-	NP_BOOLEAN_RETURN_NULL,
-	SF_SWITCH_FALLTHROUGH,
-	DP_DO_INSIDE_DO_PRIVILEGED,
-	DMI_INVOKING_TOSTRING_ON_ARRAY,
-	NP_NONNULL_PARAM_VIOLATION,
-	CN_IDIOM_NO_SUPER_CALL,
-	UL_UNRELEASED_LOCK_EXCEPTION_PATH,
-	RC_REF_COMPARISON_BAD_PRACTICE,
-	NP_ALWAYS_NULL,
-	NP_NULL_PARAM_DEREF,
-	GC_UNRELATED_TYPES,
-	DLS_DEAD_LOCAL_STORE_OF_NULL,
-	RpC_REPEATED_CONDITIONAL_TEST,
-	ODR_OPEN_DATABASE_RESOURCE_EXCEPTION_PATH,
-	DB_DUPLICATE_SWITCH_CLAUSES,
-	RV_RETURN_VALUE_IGNORED,
-	ES_COMPARING_PARAMETER_STRING_WITH_EQ,
-	RCN_REDUNDANT_NULLCHECK_OF_NULL_VALUE,
-	ICAST_IDIV_CAST_TO_DOUBLE,
-	BC_VACUOUS_INSTANCEOF,
-	EC_UNRELATED_TYPES,
-	ICAST_INTEGER_MULTIPLY_CAST_TO_LONG,
-	DM_STRING_TOSTRING,
-	DMI_HARDCODED_ABSOLUTE_FILENAME,
-	MS_MUTABLE_COLLECTION_PKGPROTECT,
-	NP_NULL_ON_SOME_PATH_EXCEPTION,
-	SQL_NONCONSTANT_STRING_PASSED_TO_EXECUTE,
-	EQ_COMPARETO_USE_OBJECT_EQUALS,
-	BX_UNBOXING_IMMEDIATELY_REBOXED,
-	HE_EQUALS_USE_HASHCODE,
-	DM_EXIT,
-	FE_FLOATING_POINT_EQUALITY,
-	RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE,
-	BC_UNCONFIRMED_CAST,
-	REC_CATCH_EXCEPTION,
-	BC_UNCONFIRMED_CAST_OF_RETURN_VALUE,
-	VA_FORMAT_STRING_USES_NEWLINE,
-	RV_RETURN_VALUE_IGNORED_BAD_PRACTICE,
-	EI_EXPOSE_REP2,
-	WMI_WRONG_MAP_ITERATOR,
-	EI_EXPOSE_REP,
-	NP_LOAD_OF_KNOWN_NULL_VALUE,
-	DM_NUMBER_CTOR,
-	SBSC_USE_STRINGBUFFER_CONCATENATION,
-	OS_OPEN_STREAM_EXCEPTION_PATH,
-	NP_NONNULL_RETURN_VIOLATION, 
-	SF_SWITCH_NO_DEFAULT,
-	RV_RETURN_VALUE_IGNORED_NO_SIDE_EFFECT,
-	ODR_OPEN_DATABASE_RESOURCE,
-	PZLA_PREFER_ZERO_LENGTH_ARRAYS,
-	NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE,
-	UCF_USELESS_CONTROL_FLOW,
-	UC_USELESS_CONDITION,
-	NP_NULL_ON_SOME_PATH,
-	DM_FP_NUMBER_CTOR,
-	SQL_PREPARED_STATEMENT_GENERATED_FROM_NONCONSTANT_STRING,
-	OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE,
-	ES_COMPARING_STRINGS_WITH_EQ,
-	OS_OPEN_STREAM,
-	RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE,
-	NP_PARAMETER_MUST_BE_NONNULL_BUT_MARKED_AS_NULLABLE,
-	
-	UC_USELESS_OBJECT,
-	OBL_UNSATISFIED_OBLIGATION,
-}

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java

@@ -1,25 +1,11 @@
 package edu.lu.uni.serval.FixPatternParser.violations;
 
-import java.io.*;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import com.github.gumtreediff.actions.model.Delete;
-import com.github.gumtreediff.actions.model.Insert;
-import com.github.gumtreediff.actions.model.Move;
-import com.github.gumtreediff.actions.model.Update;
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.FixPatternParser.Tokenizer;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.diffentry.DiffEntryHunk;
-import edu.lu.uni.serval.diffentry.DiffEntryReader;
 import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
-import edu.lu.uni.serval.gumtree.regroup.HunkActionFilter;
+
-import edu.lu.uni.serval.gumtree.regroup.SimplifyTree;
+import java.io.*;
-import edu.lu.uni.serval.violation.code.parser.ViolationSourceCodeTree;
+import java.util.List;
+
+
 
 /**
  * Parse fix violations with GumTree in terms of multiple statements.
@@ -97,232 +83,5 @@ public class FixedViolationHunkParser extends FixedViolationParser {
 	}
 
 
-//	public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) {
-//		// GumTree results
-//		List<HierarchicalActionSet> actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile);
-//
-//
-//		if (this.resultType != 0) {
-////			String type = "";
-////			if (this.resultType == 1) {
-////				type = "#NullGumTreeResult:";
-////			} else if (this.resultType == 2) {
-////				type = "#NoSourceCodeChange:";
-////			} else if (this.resultType == 3) {
-////				type = "#NoStatementChange:";
-////			}
-//		} else {
-//			List<DiffEntryHunk> diffentryHunks = new DiffEntryReader().readHunks3(diffentryFile);
-//
-//			//Filter out the modify actions, which are not in the DiffEntry hunks.
-//			HunkActionFilter hunkFilter = new HunkActionFilter();
-//			List<DiffEntryHunk> selectedPatchHunks = hunkFilter.filterActionsByModifiedRange2(diffentryHunks, actionSets, revFile, prevFile);
-//
-//			for (DiffEntryHunk patchHunk : selectedPatchHunks) {
-//				List<HierarchicalActionSet> hunkActionSets = patchHunk.getActionSets();
-//				// multiple UPD, and some UPD contain other UPD.
-//				removeOverlapperdUPD(hunkActionSets);
-//
-//				// Range of buggy source code
-//				int bugStartLine = 0;
-//				int bugEndLine = 0;
-//				// Range of fixing source code
-//				int fixStartLine = 0;
-//				int fixEndLine = 0;
-//				int bugEndPosition = 0;
-//				int fixEndPosition = 0;
-//				int hunkSet = 0;
-//				for (HierarchicalActionSet hunkActionSet : hunkActionSets) {
-//
-//
-//					FileOutputStream f = null;
-//					try {
-//						String pj = diffentryFile.getParent().split("GumTreeInputBug4")[1];
-//						String root = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2";
-//						String hunkTreeFileName = root+pj.replace("DiffEntries","ASTDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet);
-//						f = new FileOutputStream(new File(hunkTreeFileName));
-//						ObjectOutputStream o = new ObjectOutputStream(f);
-//						o.writeObject(hunkActionSet.getNode());
-//
-//						o.close();
-//						f.close();
-//					} catch (FileNotFoundException e) {
-//						e.printStackTrace();
-//					} catch (IOException e) {
-//						e.printStackTrace();
-//					}
-//					hunkSet++;
-//
-//
-//
-//					int actionBugStart = hunkActionSet.getBugStartLineNum();
-//					int actionBugEnd = hunkActionSet.getBugEndLineNum();
-//					int actionFixStart = hunkActionSet.getFixStartLineNum();
-//					int actionFixEnd = hunkActionSet.getFixEndLineNum();
-//					if (bugStartLine == 0) {
-//						bugStartLine = actionBugStart;
-//					} else if (actionBugStart != 0 && actionBugStart < bugStartLine) {
-//						bugStartLine = actionBugStart;
-//					}
-//					if (fixStartLine == 0) {
-//						fixStartLine = actionFixStart;
-//					} else if (actionFixStart != 0 && actionFixStart < fixStartLine) {
-//						fixStartLine = actionFixStart;
-//					}
-//					if (bugEndLine < actionBugEnd) {
-//						bugEndLine = actionBugEnd;
-//						bugEndPosition = hunkActionSet.getBugEndPosition();
-//					}
-//					if (fixEndLine < actionFixEnd) {
-//						fixEndLine = actionFixEnd;
-//						fixEndPosition = hunkActionSet.getFixEndPosition();
-//					}
-//				}
-//
-//				if (fixStartLine == 0 && bugStartLine == 0) {
-//					this.unfixedViolations += "#WRONG: " + revFile.getName() + ":" + patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize() + "\n";
-//					this.nullMappingGumTreeResult ++;
-//					continue;
-//				}
-//
-//				if (fixStartLine == 0 && bugStartLine != 0) {// pure delete actions.
-//					// get the exact buggy code by violation's position. TODO later
-//				}
-//
-////				if (children.size() == 0) continue;
-//				boolean isPureInsert = false;
-//				if (bugStartLine == 0 && patchHunk.getBugLineStartNum() > 0) {
-//					bugStartLine = patchHunk.getBugLineStartNum();
-//					bugEndLine = bugStartLine + patchHunk.getBuggyHunkSize() - 1;
-//					isPureInsert = true;
-////					continue;
-//				}
-////				if ((bugEndLine - bugStartLine > Configuration.HUNK_SIZE ) || fixEndLine - fixStartLine > Configuration.HUNK_SIZE) {
-////					continue; //TODO hunk size
-////				}
-//				if(patchHunk.getBuggyHunkSize() > Configuration.HUNK_SIZE || patchHunk.getFixedHunkSize() > Configuration.HUNK_SIZE){
-//					continue;
-//				}
-//
-//				/**
-//				 * Select edit scripts for deep learning.
-//				 * Edit scripts will be used to mine common fix patterns.
-//				 */
-//				// 1. First level: AST node type.
-//				String astEditScripts = getASTEditScriptsDeepFirst(hunkActionSets, bugEndPosition, fixEndPosition);
-//				if (astEditScripts.contains("\n") || astEditScripts.split(" ").length % 3 != 0) {
-//					System.err.println("===+++===: "  + revFile.getName() + ":" +patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize());
-//				}
-//				// 2. source code: raw tokens
-//				// 3. abstract identifiers:
-//				// 4. semi-source code:
-//				String[] editScriptTokens = astEditScripts.split(" ");
-//				int size = editScriptTokens.length;
-//				if (size == 1) {
-//					this.nullMappingGumTreeResult ++;
-//					this.unfixedViolations += "#NullMatchedGumTreeResult1:"  + revFile.getName() + ":" + patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize() + "\n";
-//					continue;
-//				}
-//
-//				String patchPosition = "\n" + revFile.getName() + "\n@@ -" + bugStartLine + ", " + bugEndLine + " +" + fixStartLine + ", " + fixEndLine + "@@\n";
-////				String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets, bugEndPosition, fixEndPosition) + "\n";
-////TODO uncomment the line below for more detailed gumtree input.
-//				String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets) + "\n";
-////				if (noUpdate(editScriptTokens)) {
-////				}
-//
-//				String canonicalVariableNames = getBuggyCodeTree(patchHunk, prevFile, revFile);
-//				this.patchesSourceCode += info;
-//				this.patchesSourceCode += "\nRenamed_Variables###:\n" + canonicalVariableNames;
-//				this.sizes += size + "\n";
-//				this.astEditScripts += astEditScripts + "\n";
-////				String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim();
-////				this.tokensOfSourceCode += tokens + "\n";
-//			}
-//		}
-//	}
-
-	private String getAstEditScripts(List<HierarchicalActionSet> hunkActionSets) {
-		String scripts = "";
-		for (HierarchicalActionSet hunkActionSet : hunkActionSets) {
-			scripts += hunkActionSet.toString() + "\n";
-		}
-		return scripts;
-	}
-
-	private String getBuggyCodeTree(DiffEntryHunk patchHunk, File prevFile, File revFile) {
-		int bugStartLine = patchHunk.getBugLineStartNum();
-		int bugEndLine = bugStartLine + patchHunk.getBugRange() - 1;
-		
-		ViolationSourceCodeTree parser = new ViolationSourceCodeTree(prevFile, bugStartLine, bugEndLine);
-		parser.extract();
-		List<ITree> matchedTrees = parser.getViolationSourceCodeTrees();
-		Map<String, String> renamedVariablesMap = new HashMap<>();
-		Map<String, Integer> canonicalVariables = new HashMap<>();
-		if (matchedTrees.size() > 0) {
-			SimplifyTree st = new SimplifyTree();
-			for (ITree matchedTree : matchedTrees) {
-				st.canonicalizeSourceCodeTree(matchedTree);
-			}
-			renamedVariablesMap = st.canonicalVariableMap;
-			canonicalVariables = st.canonicalVariables;
-		}
-		
-		int fixStartLine = patchHunk.getFixLineStartNum();
-		int fixEndLine = fixStartLine + patchHunk.getFixRange() - 1;
-		ViolationSourceCodeTree fixedParser = new ViolationSourceCodeTree(revFile, fixStartLine, fixEndLine);
-		fixedParser.extract();
-		matchedTrees = fixedParser.getViolationSourceCodeTrees();
-		if (matchedTrees.size() > 0) {
-			SimplifyTree st = new SimplifyTree();
-			st.canonicalVariableMap = renamedVariablesMap;
-			st.canonicalVariables = canonicalVariables;
-			for (ITree matchedTree : matchedTrees) {
-				st.canonicalizeSourceCodeTree(matchedTree);
-			}
-			renamedVariablesMap = st.canonicalVariableMap;
-		}
-		
-		StringBuilder builder = new StringBuilder();
-		for (Map.Entry<String, String> entry : renamedVariablesMap.entrySet()) {
-			builder.append(entry.getKey()).append(" = ").append(entry.getValue()).append("\n");
-		}
-		return builder.toString();
-	}
-
-	private void removeOverlapperdUPD(List<HierarchicalActionSet> actionSets) {
-		if (actionSets.size() == 1) {
-			return;
-		}
-		List<HierarchicalActionSet> updates = new ArrayList<>();
-		for (HierarchicalActionSet actionSet : actionSets) {
-			if (actionSet.getActionString().startsWith("UPD")) {
-				updates.add(actionSet);
-			}
-		}
-		
-		List<HierarchicalActionSet> overlappedUpdates = new ArrayList<>();
-		if (updates.size() > 1) {
-			for (HierarchicalActionSet update : updates) {
-				int startLine = update.getBugStartLineNum();
-				int endLine = update.getBugEndLineNum();
-				int endPosition = update.getBugEndPosition();
-				for (HierarchicalActionSet update2 : updates) {
-					if (update.equals(update2)) continue;
-					int startLine2 = update2.getBugStartLineNum();
-					int endLine2 = update2.getBugEndLineNum();
-					int endPosition2 = update2.getBugEndPosition();
-					if (startLine <= startLine2
-						&& endLine2 <= endLine && endPosition2 < endPosition) {
-						if (!overlappedUpdates.contains(update)) {
-							overlappedUpdates.add(update);
-						}
-						break;
-					}
-				}
-			}
-		}
-		actionSets.removeAll(overlappedUpdates);
-	}
 
 }

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java

@@ -1,21 +1,16 @@
 package edu.lu.uni.serval.FixPatternParser.violations;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.List;
-
 import com.github.gumtreediff.actions.model.Action;
-
 import edu.lu.uni.serval.FixPatternParser.Parser;
 import edu.lu.uni.serval.gumtree.GumTreeComparer;
 import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
 import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper;
-import edu.lu.uni.serval.utils.FileHelper;
 import edu.lu.uni.serval.utils.ListSorter;
 
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Parse fix patterns with GumTree.
  *
@@ -60,16 +55,7 @@ public class FixedViolationParser extends Parser {
 		} else {
 			// Regroup GumTre results.
 			List<HierarchicalActionSet> allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults);
-//			for (HierarchicalActionSet actionSet : allActionSets) {
-//				String astNodeType = actionSet.getAstNodeType();
-//				if (astNodeType.endsWith("Statement") || "FieldDeclaration".equals(astNodeType)) {
-//					actionSets.add(actionSet);
-//				}
-//			}
 
-			// Filter out modified actions of changing method names, method parameters, variable names and field names in declaration part.
-			// variable effects range, sub-actions are these kinds of modification?
-//			actionSets.addAll(new ActionFilter().filterOutUselessActions(allActionSets));
 			
 			ListSorter<HierarchicalActionSet> sorter = new ListSorter<>(allActionSets);
 			actionSets = sorter.sortAscending();
@@ -82,63 +68,14 @@ public class FixedViolationParser extends Parser {
 		}
 	}
 
-	/**
-	 * Read patch source code from buggy and fixed files.
-	 * @param prevFile
-	 * @param revFile
-	 * @param bugStartLineNum
-	 * @param bugEndLineNum
-	 * @param fixStartLineNum
-	 * @param fixEndLineNum
-	 * @param isInsert
-	 * @return
-	 */
-	protected String getPatchSourceCode(File prevFile, File revFile, int bugStartLineNum, int bugEndLineNum, int fixStartLineNum, int fixEndLineNum, boolean isInsert) {
-		String buggyStatements = "";
-		if (isInsert) {
-			buggyStatements = readSourceCode(prevFile, bugStartLineNum, bugEndLineNum, "");
-		} else {
-			buggyStatements = readSourceCode(prevFile, bugStartLineNum, bugEndLineNum, "-");
-		}
-		String fixedStatements = readSourceCode(revFile, fixStartLineNum, fixEndLineNum, "+");
-		return buggyStatements + fixedStatements;
-	}
 
-	private String readSourceCode(File file, int startLineNum, int endLineNum, String type) {
-		String sourceCode = "";
-		String fileContent = FileHelper.readFile(file);
-		BufferedReader reader = null;
-		try {
-			reader = new BufferedReader(new StringReader(fileContent));
-			String line = null;
-			int lineIndex = 0;
-			while ((line = reader.readLine()) != null) {
-				lineIndex ++;
-				if (lineIndex >= startLineNum && lineIndex <= endLineNum) {
-					sourceCode += type + line + "\n";
-				}
-				if (lineIndex == endLineNum) break;
-			}
-		} catch (IOException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				reader.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		return sourceCode;
-	}
 
-	public String getAlarmTypes() {
-		return violationTypes;
-	}
 
-	@Override
-	public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) {
 
-	}
+//	@Override
+//	public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) {
+//
+//	}
 
 //	public void setUselessViolations(List<Violation> uselessViolations) {
 //		this.uselessViolations = uselessViolations;

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationSingleStatementParser.java

@@ -1,156 +0,0 @@
-package edu.lu.uni.serval.FixPatternParser.violations;
-
-import java.io.File;
-import java.util.List;
-
-import org.eclipse.jdt.core.dom.CompilationUnit;
-
-import com.github.gumtreediff.actions.model.Move;
-import com.github.gumtreediff.actions.model.Update;
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.FixPattern.utils.Checker;
-import edu.lu.uni.serval.FixPatternParser.CUCreator;
-import edu.lu.uni.serval.FixPatternParser.Tokenizer;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
-import edu.lu.uni.serval.gumtree.regroup.SimpleTree;
-import edu.lu.uni.serval.gumtree.regroup.SimplifyTree;
-
-/**
- * Parse fixed violations with GumTree in terms of single statement.
- * 
- * @author kui.liu
- *
- */
-public class FixedViolationSingleStatementParser extends FixedViolationParser {
-	
-	@Override
-	public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) {
-		// GumTree results
-		List<HierarchicalActionSet> actionSets = parseChangedSourceCodeWithGumTree(prevFile, revFile);
-		
-		if (actionSets.size() > 0) {
-			CUCreator cuCreator = new CUCreator();
-			CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile);
-			CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile);
-			if (prevUnit == null || revUnit == null) {
-				return;
-			}
-			
-			// Read the positions of checked violations
-			for (HierarchicalActionSet actionSet : actionSets) {
-				// position of buggy statements
-				int startPosition = 0;
-				int endPosition = 0;
-				// position of fixed statements
-				int startPosition2 = 0;
-				int endPosition2 = 0;
-
-				String actionStr = actionSet.getActionString();
-				String astNodeType = actionSet.getAstNodeType();
-				if (actionStr.startsWith("INS")) {
-					startPosition2 = actionSet.getStartPosition();
-					endPosition2 = startPosition2 + actionSet.getLength();
-					List<Move> firstAndLastMov = getFirstAndLastMoveAction(actionSet);
-					if (firstAndLastMov != null) {
-						startPosition = firstAndLastMov.get(0).getNode().getPos();
-						ITree lastTree = firstAndLastMov.get(1).getNode();
-						endPosition = lastTree.getPos() + lastTree.getLength();
-					} else { // Ignore the pure insert actions without any move actions.
-						continue;
-					}
-				} else if (actionStr.startsWith("UPD")) {
-					startPosition = actionSet.getStartPosition();
-					endPosition = startPosition + actionSet.getLength();
-					Update update = (Update) actionSet.getAction();
-					ITree newNode = update.getNewNode();
-					startPosition2 = newNode.getPos();
-					endPosition2 = startPosition2 + newNode.getLength();
-
-					if (Checker.containsBodyBlock(astNodeType)) {
-						List<ITree> children = update.getNode().getChildren();
-						endPosition = getEndPosition(children);
-						List<ITree> newChildren = newNode.getChildren();
-						endPosition2 = getEndPosition(newChildren);
-						
-						if (endPosition == 0) {
-							endPosition = startPosition + actionSet.getLength();
-						}
-						if (endPosition2 == 0) {
-							endPosition2 = startPosition2 + newNode.getLength();
-						}
-					}
-				}  else {// DEL actions and MOV actions: we don't need these actions, as for now.
-					continue;
-				}
-				if (startPosition == 0 || startPosition2 == 0) {
-					continue;
-				}
-				
-				// Get line numbers.
-				int startLine = prevUnit.getLineNumber(startPosition);
-				int endLine = prevUnit.getLineNumber(endPosition);
-				int startLine2 = revUnit.getLineNumber(startPosition2);
-				int endLine2 = revUnit.getLineNumber(endPosition2);
-				
-				Violation violation = null;//findViolation(startLine, endLine, violations);
-				if (violation == null) continue;
-				
-				if (endLine - startLine >= Configuration.HUNK_SIZE - 2 || endLine2 - startLine2 >= Configuration.HUNK_SIZE - 2 ) continue;
-				
-				/*
-				 * Convert the ITree of buggy code to a simple tree.
-				 * It will be used to compute the similarity. 
-				 */
-				SimplifyTree abstractIdentifier = new SimplifyTree();
-				abstractIdentifier.abstractTree(actionSet);
-				SimpleTree simpleTree = actionSet.getSimpleTree();
-				if (simpleTree == null) { // Failed to get the simple tree for INS actions.
-					continue;
-				}
-				
-				/**
-				 * Select edit scripts for deep learning. 
-				 * Edit scripts will be used to mine common fix patterns.
-				 */
-				// 1. First level: AST node type.
-				String astEditScripts = getASTEditScriptsBreadthFirst(actionSet);
-				int size = astEditScripts.split(" ").length;
-				if (size == 1) {
-					continue;
-				}
-				
-				// Source Code of patches.
-				String patchSourceCode = getPatchSourceCode(prevFile, revFile, startLine, endLine, startLine2, endLine2, false);
-				this.patchesSourceCode += Configuration.PATCH_SIGNAL + "\n" + revFile.getName() + "\n" + patchSourceCode + "\n";
-				this.sizes += size + "\n";
-				this.astEditScripts += astEditScripts + "\n";
-				this.violationTypes += violation.getViolationType() + "\n";
-				// 2. source code: raw tokens
-//				String rawTokenEditScripts = getRawTokenEditScripts(actionSet);
-//				// 3. abstract identifiers: 
-//				String abstractIdentifiersEditScripts = getAbstractIdentifiersEditScripts(actionSet);
-//				// 4. semi-source code: 
-//				String semiSourceCodeEditScripts = getSemiSourceCodeEditScripts(actionSet);
-				
-//				this.buggyTrees += Configuration.BUGGY_TREE_TOKEN + "\n" + simpleTree.toString() + "\n";
-				this.tokensOfSourceCode += Tokenizer.getTokensDeepFirst(simpleTree).trim() + "\n";
-//				this.actionSets += Configuration.BUGGY_TREE_TOKEN + "\n" + readActionSet(actionSet, "") + "\n";
-//				this.originalTree += Configuration.BUGGY_TREE_TOKEN + "\n" + actionSet.getOriginalTree().toString() + "\n";
-			}
-			actionSets.clear();
-		} else {
-			System.out.println(1);
-		}
-	}
-	
-	protected Violation findViolation(int startLine, int endLine, List<Violation> violations) {
-		for (Violation violation : violations) {
-			int vStartLine = violation.getStartLineNum();
-			int vEndLine = violation.getEndLineNum();
-			if (!(startLine > vEndLine && endLine< vStartLine)) return violation;
-		}
-		return null;
-	}
-}

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java

@@ -1,20 +0,0 @@
-package edu.lu.uni.serval.FixPatternParser.violations;
-
-import java.io.File;
-
-public class Message {
-
-	private String name;
-	private String inputPath;
-	private String innerPort;
-
-	public Message(String name , String inputPath, String innerPort) {
-		super();
-		this.name = name;
-		this.inputPath = inputPath;
-		this.innerPort = innerPort;
-	}
-
-
-	
-}

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java

@@ -1,150 +0,0 @@
-package edu.lu.uni.serval.FixPatternParser.violations;
-
-import com.rabbitmq.client.Channel;
-import com.rabbitmq.client.Connection;
-import com.rabbitmq.client.ConnectionFactory;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.io.FilenameFilter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.concurrent.TimeoutException;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
-/**
- * Created by anilkoyuncu on 03/04/2018.
- */
-public class Producer {
-    private static Logger log = LoggerFactory.getLogger(Producer.class);
-    public static void main(String[] args) {
-
-
-        String inputPath;
-        String outputPath;
-        String port;
-        String portInner;
-        String pairsCSVPath;
-        String importScript;
-        String pairsCompletedPath;
-        String serverWait;
-        if (args.length > 0) {
-            inputPath = args[0];
-            port = args[1];
-            portInner = args[2];
-            serverWait = args[3];
-//            pairsCSVPath = args[3];
-//            importScript = args[4];
-//            pairsCompletedPath = args[3];
-        } else {
-            inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2";
-            outputPath = "/Users/anilkoyuncu/bugStudy/dataset/";
-            port = "6379";
-            portInner = "6380";
-            serverWait = "10000";
-            pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test";
-            importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh";
-            pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed";
-        }
-
-
-        calculatePairs(inputPath, port);
-        log.info("Calculate pairs done");
-
-
-
-    }
-    public static void calculatePairs(String inputPath,String port) {
-        File folder = new File(inputPath);
-        File[] listOfFiles = folder.listFiles();
-        Stream<File> stream = Arrays.stream(listOfFiles);
-        List<File> pjs = stream
-                .filter(x -> !x.getName().startsWith("."))
-                .collect(Collectors.toList());
-
-        List<File> fileToCompare = new ArrayList<>();
-        for (File pj : pjs) {
-            File[] files = pj.listFiles(new FilenameFilter() {
-                public boolean accept(File dir, String name) {
-                    return name.startsWith("ActionSetDumps");
-                }
-            });
-            Collections.addAll(fileToCompare, files[0].listFiles());
-
-        }
-        System.out.println("a");
-//        compareAll(fileToCompare);
-        readMessageFiles(fileToCompare, port);
-    }
-
-    private static void readMessageFiles(List<File> folders, String port) {
-
-        List<String> treesFileNames = new ArrayList<>();
-
-
-        for (File target : folders) {
-
-            treesFileNames.add(target.toString());
-        }
-
-
-        log.info("Calculating pairs");
-
-        int fileCounter = 0;
-
-        ConnectionFactory factory = new ConnectionFactory();
-        factory.setHost("10.240.5.10");
-//        factory.setVirtualHost("treeCompare");
-        factory.setPort(5672);
-        factory.setUsername("anil");
-        factory.setPassword("changeme2018");
-        factory.setConnectionTimeout(1000);
-        Connection connection = null;
-        Channel channel = null;
-        try {
-            connection = factory.newConnection();
-
-            channel = connection.createChannel();
-            channel.queueDeclare("tree_queue", false, false, false, null);
-
-        } catch (IOException e) {
-            e.printStackTrace();
-        } catch (TimeoutException e) {
-            e.printStackTrace();
-        }
-
-
-        for (int i = 0; i < treesFileNames.size(); i++) {
-            for (int j = i + 1; j < treesFileNames.size(); j++) {
-
-
-                // do operations with jedis resource
-
-                String key = "pair_" + String.valueOf(i) + "_" + String.valueOf(j);
-//                        String value = treesFileNames.get(i).split("GumTreeOutput2")[1] +","+treesFileNames.get(j).split("GumTreeOutput2")[1];
-//                        jedis.set(key,value);
-
-                String message = key +","+treesFileNames.get(i).split("GumTreeOutput2")[1] + "," + treesFileNames.get(j).split("GumTreeOutput2")[1];
-                try {
-                    channel.basicPublish("", "tree_queue", null, message.getBytes());
-                } catch (IOException e) {
-                    e.printStackTrace();
-                }
-
-
-
-
-            }
-        }
-
-
-
-
-    log.info("Done pairs");
-    }
-}

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Violation.java

@@ -1,133 +0,0 @@
-package edu.lu.uni.serval.FixPatternParser.violations;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import edu.lu.uni.serval.diffentry.DiffEntryHunk;
-import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
-
-public class Violation implements Comparable<Violation> {
-	
-	private String fileName = "";
-	private Integer startLineNum;
-	private int endLineNum;
-	private int bugStartLineNum;
-	private int bugEndLineNum;
-	private int fixStartLineNum = 0;
-	private int fixEndLineNum;
-	private String violationType;
-	private List<DiffEntryHunk> hunks = new ArrayList<>();
-	private List<HierarchicalActionSet> actionSets;
-	private int bugFixStartLineNum = 0; // the heuristic matched fix start line of a violation
-	private int bugFixEndLineNum = 0; // the heuristic matched fix end line of a violation
-
-	public Violation(Integer startLineNum, int endLineNum, String violationType) {
-		super();
-		this.startLineNum = startLineNum;
-		this.endLineNum = endLineNum;
-		this.violationType = violationType;
-		this.actionSets = new ArrayList<>();
-	}
-
-	public String getFileName() {
-		return fileName;
-	}
-
-	public void setFileName(String fileName) {
-		this.fileName = fileName;
-	}
-
-	public Integer getStartLineNum() {
-		return startLineNum;
-	}
-
-	public int getEndLineNum() {
-		return endLineNum;
-	}
-
-	public int getBugStartLineNum() {
-		return bugStartLineNum;
-	}
-
-	public void setBugStartLineNum(int bugStartLineNum) {
-		this.bugStartLineNum = bugStartLineNum;
-	}
-
-	public int getBugEndLineNum() {
-		return bugEndLineNum;
-	}
-
-	public void setBugEndLineNum(int bugEndLineNum) {
-		this.bugEndLineNum = bugEndLineNum;
-	}
-
-	public int getFixStartLineNum() {
-		return fixStartLineNum;
-	}
-
-	public void setFixStartLineNum(int fixStartLineNum) {
-		this.fixStartLineNum = fixStartLineNum;
-	}
-
-	public int getFixEndLineNum() {
-		return fixEndLineNum;
-	}
-
-	public void setFixEndLineNum(int fixEndLineNum) {
-		this.fixEndLineNum = fixEndLineNum;
-	}
-
-	public List<DiffEntryHunk> getHunks() {
-		return hunks;
-	}
-
-	public void setHunks(List<DiffEntryHunk> hunks) {
-		this.hunks = hunks;
-	}
-
-	public String getViolationType() {
-		return violationType;
-	}
-
-	public List<HierarchicalActionSet> getActionSets() {
-		return actionSets;
-	}
-
-	public int getBugFixStartLineNum() {
-		return bugFixStartLineNum;
-	}
-
-	public void setBugFixStartLineNum(int bugFixStartLineNum) {
-		this.bugFixStartLineNum = bugFixStartLineNum;
-	}
-
-	public int getBugFixEndLineNum() {
-		return bugFixEndLineNum;
-	}
-
-	public void setBugFixEndLineNum(int bugFixEndLineNum) {
-		this.bugFixEndLineNum = bugFixEndLineNum;
-	}
-
-	@Override
-	public int compareTo(Violation v) {
-		return this.startLineNum.compareTo(v.startLineNum);
-	}
-	
-	@Override
-	public String toString() {
-		return this.startLineNum + " : " + this.endLineNum + " : " + this.violationType;
-	}
-
-	@Override
-	public boolean equals(Object obj) {
-		if (obj instanceof Violation) {
-			Violation v = (Violation) obj;
-			if (this.fileName.equals(v.fileName) && this.violationType.equals(v.violationType) && this.startLineNum == v.startLineNum && this.endLineNum == v.endLineNum) {
-				return true;
-			}
-		}
-		return false;
-	}
-	
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java

@@ -1,121 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import akka.actor.ActorRef;
-import akka.actor.ActorSystem;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-
-/**
- * Multi-thread parser of parsing the difference between buggy code file and fixed code file.
- * 
- * @author kui.liu
- *
- */
-public class AkkaParser {
-	
-	private static Logger log = LoggerFactory.getLogger(AkkaParser.class);
-
-	/**
-	 * Two parameters: 
-	 * 		First one: the root path of input data.
-	 * 		Second one: the number of threads.
-	 * 		Third one: the threshold of selecting patch hunks.
-	 * @param args
-	 */
-	@SuppressWarnings("deprecation")
-	public static void main(String[] args) {
-//		String inputRootPath = args[0];
-		int numberOfWorkers = 5; //Integer.parseInt(args[1]);
-		int hunkThreshold = 10;
-//		try {
-//			hunkThreshold = Integer.parseInt(args[2]);
-//		} catch (NumberFormatException e1) {
-//			hunkThreshold = 10;
-//		}
-		
-//		Configuration.ROOT_PATH = inputRootPath;
-		Configuration.HUNK_SIZE = hunkThreshold;
-
-		List<String> pjList = Arrays.asList("APACHE-CAMEL","APACHE-HBASE","APACHE-HIVE","COMMONS-CODEC","COMMONS-COLLECTIONS",
-				"COMMONS-COMPRESS","COMMONS-CONFIGURATION","COMMONS-CRYPTO","COMMONS-CSV","COMMONS-IO","COMMONS-LANG",
-				"COMMONS-MATH","COMMONS-WEAVER","JBOSS-ENTESB","JBOSS-JBMETA","SPRING-AMQP","SPRING-ANDROID","SPRING-BATCH",
-				"SPRING-BATCHADM","SPRING-DATACMNS","SPRING-DATAGRAPH","SPRING-DATAJPA","SPRING-DATAMONGO","SPRING-DATAREDIS",
-				"SPRING-DATAREST","SPRING-LDAP","SPRING-MOBILE","SPRING-ROO","SPRING-SEC","SPRING-SECOAUTH","SPRING-SGF","SPRING-SHDP",
-				"SPRING-SOCIAL","SPRING-SOCIALFB","SPRING-SOCIALLI","SPRING-SOCIALTW","SPRING-SPR","SPRING-SWF","SPRING-SWS","WILDFLY-ELY",
-				"WILDFLY-SWARM","WILDFLY-WFARQ","WILDFLY-WFCORE","WILDFLY-WFLY","WILDFLY-WFMP");
-		for (String pj : pjList) {
-			String[] split = pj.split("-");
-			String pjPath = split[0];
-			String pjName = split[1];
-//			String rootPath = "/Volumes/data/bugStudy/";
-//			String DATASET_FILE_PATH = rootPath + "/dataset/GumTreeInput/" + pjName;
-//			String GIT_REPOSITORY_PATH = "/Users/anilkoyuncu/bugLocalizationStudy/irblsensitivity/data/" + pjPath + "/" + pjName + "/gitrepo/.git";
-			log.info(pjName);
-			// input data
-			log.info("Get the input data...");
-			final List<MessageFile> msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT +pjName +"gitrepo/");
-			log.info("MessageFiles: " + msgFiles.size());
-
-			// output path
-			final String editScriptsFilePath =  Configuration.EDITSCRIPTS_FILE_PATH + pjName + "/";
-			final String patchesSourceCodeFilePath = Configuration.PATCH_SOURCECODE_FILE_PATH+ pjName + "/";
-			final String buggyTokensFilePath = Configuration.BUGGY_CODE_TOKEN_FILE_PATH+ pjName + "/";
-			final String editScriptSizesFilePath = Configuration.EDITSCRIPT_SIZES_FILE_PATH+ pjName + "/";
-			FileHelper.deleteDirectory(editScriptsFilePath);
-			FileHelper.deleteDirectory(patchesSourceCodeFilePath);
-			FileHelper.deleteDirectory(buggyTokensFilePath);
-			FileHelper.deleteDirectory(editScriptSizesFilePath);
-
-			ActorSystem system = null;
-			ActorRef parsingActor = null;
-			final WorkMessage msg = new WorkMessage(0, msgFiles);
-			try {
-				log.info("Akka begins...");
-				system = ActorSystem.create("Mining-FixPattern-System");
-//				parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath,
-//						patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor");
-				parsingActor.tell(msg, ActorRef.noSender());
-			} catch (Exception e) {
-				system.shutdown();
-				e.printStackTrace();
-			}
-		}
-		
-	}
-	
-	/**
-	 * Get violation-related files.
-	 * 
-	 * @param gumTreeInput
-	 * @return
-	 */
-	public static List<MessageFile> getMessageFiles(String gumTreeInput) {
-		String inputPath = gumTreeInput; // prevFiles  revFiles diffentryFile positionsFile
-		File revFilesPath = new File(inputPath + "revFiles/");
-		File[] revFiles = revFilesPath.listFiles();   // project folders
-		List<MessageFile> msgFiles = new ArrayList<>();
-		
-		for (File revFile : revFiles) {
-			if (revFile.getName().endsWith(".java")) {
-				String fileName = revFile.getName();
-				File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file
-				fileName = fileName.replace(".java", ".txt");
-				File diffentryFile = new File(gumTreeInput + "diffentries/" + fileName); // DiffEntry file
-				File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file
-				MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile);
-				msgFile.setPositionFile(positionFile);
-				msgFiles.add(msgFile);
-			}
-		}
-		
-		return msgFiles;
-	}
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java

@@ -1,146 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser;
-
-import akka.actor.ActorRef;
-import akka.actor.ActorSystem;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
-/**
- * Multi-thread parser of parsing the difference between buggy code file and fixed code file.
- * 
- * @author kui.liu
- *
- */
-public class AkkaParser2 {
-	
-	private static Logger log = LoggerFactory.getLogger(AkkaParser2.class);
-
-	/**
-	 * Two parameters: 
-	 * 		First one: the root path of input data.
-	 * 		Second one: the number of threads.
-	 * 		Third one: the threshold of selecting patch hunks.
-	 * @param args
-	 */
-	@SuppressWarnings("deprecation")
-	public static void main(String[] args) {
-		String inputRootPath;
-		String outputRootPath;
-		int numberOfWorkers;
-		if(args.length > 0){
-		inputRootPath = args[0];
-		outputRootPath = args[1];
-		numberOfWorkers = Integer.parseInt(args[2]);
-		}else{
-			inputRootPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug";
-			outputRootPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutputBug/";
-			numberOfWorkers = 1;
-		}
-
-//		try {
-//			hunkThreshold = Integer.parseInt(args[2]);
-//		} catch (NumberFormatException e1) {
-//			hunkThreshold = 10;
-//		}
-		
-//		Configuration.ROOT_PATH = inputRootPath;
-//		log.info(Configuration.ROOT_PATH);
-//		Configuration.HUNK_SIZE = hunkThreshold;
-
-
-
-		// input data
-//		String GUM_TREE_INPUT = inputRootPath + "GumTreeInput/";
-		log.info("Get the input data..." + inputRootPath );
-
-		log.info("Set the output data..." + outputRootPath );
-
-
-		File folder = new File(inputRootPath);
-		File[] listOfFiles = folder.listFiles();
-		Stream<File> stream = Arrays.stream(listOfFiles);
-		List<File> folders = stream
-				.filter(x -> !x.getName().startsWith("."))
-				.collect(Collectors.toList());
-
-		for (File target : folders) {
-			log.info("MessageFiles: " + target.toString());
-			final List<MessageFile> msgFiles = getMessageFiles(target.toString() + "/");
-			log.info("MessageFiles: " + msgFiles.size());
-			// output path
-
-
-			String pjName = target.getName();
-			// output path
-			String GUM_TREE_OUTPUT = outputRootPath +  pjName + "/";
-			final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts/";
-			final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode/";
-			final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens/";
-			final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes/";
-			final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes/";
-
-			FileHelper.deleteDirectory(editScriptsFilePath);
-			FileHelper.deleteDirectory(patchesSourceCodeFilePath);
-			FileHelper.deleteDirectory(buggyTokensFilePath);
-			FileHelper.deleteDirectory(editScriptSizesFilePath);
-
-			ActorSystem system = null;
-			ActorRef parsingActor = null;
-			final WorkMessage msg = new WorkMessage(0, msgFiles);
-			try {
-				log.info("Akka begins...");
-				system = ActorSystem.create("Mining-FixPattern-System");
-//				parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath,
-//						patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor");
-				parsingActor.tell(msg, ActorRef.noSender());
-			} catch (Exception e) {
-				system.shutdown();
-				e.printStackTrace();
-			}
-
-
-		}
-
-		
-	}
-	
-	/**
-	 * Get violation-related files.
-	 * 
-	 * @param gumTreeInput
-	 * @return
-	 */
-	public static List<MessageFile> getMessageFiles(String gumTreeInput) {
-		String inputPath = gumTreeInput; // prevFiles  revFiles diffentryFile positionsFile
-		File revFilesPath = new File(inputPath + "revFiles/");
-		File[] revFiles = revFilesPath.listFiles();   // project folders
-		List<MessageFile> msgFiles = new ArrayList<>();
-		
-		for (File revFile : revFiles) {
-//			if (revFile.getName().endsWith(".c") || revFile.getName().endsWith(".h")) {
-			if (revFile.getName().endsWith(".java")) {
-				String fileName = revFile.getName();
-				File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file
-				fileName = fileName.replace(".java", ".txt");
-				File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file
-				File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file
-				MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile);
-				msgFile.setPositionFile(positionFile);
-				msgFiles.add(msgFile);
-
-			}
-//			}
-		}
-		
-		return msgFiles; //.subList(10,20);
-	}
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java

@@ -1,15 +1,14 @@
 package edu.lu.uni.serval.MultipleThreadsParser;
 
-import java.util.List;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 import akka.actor.ActorRef;
 import akka.actor.Props;
 import akka.actor.UntypedActor;
 import akka.japi.Creator;
 import akka.routing.RoundRobinPool;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.List;
 
 public class ParseFixPatternActor extends UntypedActor {
 	

src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java

@@ -1,28 +1,17 @@
 package edu.lu.uni.serval.MultipleThreadsParser;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.List;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 import akka.actor.Props;
 import akka.actor.UntypedActor;
 import akka.japi.Creator;
 import edu.lu.uni.serval.FixPatternParser.RunnableParser;
 import edu.lu.uni.serval.FixPatternParser.violations.FixedViolationHunkParser;
-import edu.lu.uni.serval.FixPatternParser.violations.Violation;
 import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.util.List;
+import java.util.concurrent.*;
 
 public class ParseFixPatternWorker extends UntypedActor {
 	private static Logger log = LoggerFactory.getLogger(ParseFixPatternActor.class);
@@ -79,10 +68,6 @@ public class ParseFixPatternWorker extends UntypedActor {
 				File diffentryFile = msgFile.getDiffEntryFile();
 
 
-//				File positionFile = msgFile.getPositionFile();
-				/*if (revFile.getName().toLowerCase().contains("test")) {
-					continue;
-				}*/
 				FixedViolationHunkParser parser =  new FixedViolationHunkParser();
 				
 				final ExecutorService executor = Executors.newSingleThreadExecutor();
@@ -103,13 +88,7 @@ public class ParseFixPatternWorker extends UntypedActor {
 					
 					String editScript = parser.getAstEditScripts();
 					if ("".equals(editScript)) {
-//						if (parser.resultType == 1) {
+
-//							nullGumTreeResults += countAlarms(positionFile, "");
-//						} else if (parser.resultType == 2) {
-//							noSourceCodeChanges += countAlarms(positionFile, "");
-//						} else if (parser.resultType == 3) {
-//							noStatementChanges += countAlarms(positionFile, "");
-//						}
 					} else {
 						editScripts.append(editScript);
 						patchesSourceCode.append(parser.getPatchesSourceCode());
@@ -118,29 +97,21 @@ public class ParseFixPatternWorker extends UntypedActor {
 						
 						counter ++;
 						if (counter % 100 == 0) {
-//							FileHelper.outputToFile(editScriptsFilePath + "edistScripts_" + id + ".list", editScripts, true);
-//							FileHelper.outputToFile(patchesSourceCodeFilePath + "patches_" + id + ".list", patchesSourceCode, true);
-//							FileHelper.outputToFile(editScriptSizesFilePath + "sizes_" + id + ".list", sizes, true);
-//							FileHelper.outputToFile(buggyTokensFilePath + "tokens_" + id + ".list", tokens, true);
 							editScripts.setLength(0);
 							patchesSourceCode.setLength(0);
 							sizes.setLength(0);
 							tokens.setLength(0);
 							log.info("Worker #" + id +" finialized parsing " + counter + " files...");
-//							FileHelper.outputToFile("OUTPUT/testingInfo_" + id + ".list", testingInfo, true);
 							testingInfo.setLength(0);
 						}
 					}
 				} catch (TimeoutException e) {
 					future.cancel(true);
-//					timeouts += countAlarms(positionFile, "#Timeout:");
 					System.err.println("#Timeout: " + revFile.getName());
 				} catch (InterruptedException e) {
-//					timeouts += countAlarms(positionFile, "#TimeInterrupted:");
 					System.err.println("#TimeInterrupted: " + revFile.getName());
 					e.printStackTrace();
 				} catch (ExecutionException e) {
-//					timeouts += countAlarms(positionFile, "#TimeAborted:");
 					System.err.println("#TimeAborted: " + revFile.getName());
 					e.printStackTrace();
 				} finally {
@@ -149,24 +120,13 @@ public class ParseFixPatternWorker extends UntypedActor {
 			}
 			
 			if (sizes.length() > 0) {
-//				FileHelper.outputToFile(editScriptsFilePath + "editScripts_" + id + ".list", editScripts, true);
-//				FileHelper.outputToFile(patchesSourceCodeFilePath + "patches_" + id + ".list", patchesSourceCode, true);
-//				FileHelper.outputToFile(editScriptSizesFilePath + "sizes_" + id + ".list", sizes, true);
-//				FileHelper.outputToFile(buggyTokensFilePath + "tokens_" + id + ".list", tokens, true);
 				editScripts.setLength(0);
 				patchesSourceCode.setLength(0);
 				sizes.setLength(0);
 				tokens.setLength(0);
 				
-//				FileHelper.outputToFile("OUTPUT/testingInfo_" + id + ".list", testingInfo, true);
 				testingInfo.setLength(0);
 			}
-//			String statistic = "\nNullGumTreeResults: " + nullGumTreeResults + "\nNoSourceCodeChanges: " + noSourceCodeChanges +
-//					"\nNoStatementChanges: " + noStatementChanges + "\nNullDiffEntry: " + nullDiffEntry + "\nNullMatchedGumTreeResults: " + nullMappingGumTreeResults +
-//					"\nPureDeletion: " + pureDeletion + "\nLargeHunk: " + largeHunk + "\nNullSourceCode: " + nullSourceCode +
-//					"\nTestingInfo: " + testInfos + "\nTimeout: " + timeouts;
-//			FileHelper.outputToFile("OUTPUT/statistic_" + id + ".list", statistic, false);
-//			FileHelper.outputToFile("OUTPUT/UnfixedV_" + id + ".list", builder, false);
 
 			log.info("Worker #" + id +"finialized parsing " + counter + " files...");
 			log.info("Worker #" + id + " finialized the work...");

src/main/java/edu/lu/uni/serval/MultipleThreadsParser/SingleThreadParser.java

@@ -1,190 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.List;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-
-import edu.lu.uni.serval.FixPatternParser.RunnableParser;
-import edu.lu.uni.serval.FixPatternParser.violations.FixedViolationHunkParser;
-import edu.lu.uni.serval.FixPatternParser.violations.Violation;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-
-public class SingleThreadParser {
-
-	public static void main(String[] args) {
-		// output path
-		final String editScriptsFilePath = Configuration.EDITSCRIPTS_FILE_PATH;
-		final String patchesSourceCodeFilePath = Configuration.PATCH_SOURCECODE_FILE_PATH;
-		final String buggyTokensFilePath = Configuration.BUGGY_CODE_TOKEN_FILE_PATH;
-		final String editScriptSizesFilePath = Configuration.EDITSCRIPT_SIZES_FILE_PATH;
-		final String alarmTypesFilePath = Configuration.ALARM_TYPES_FILE_PATH;
-		FileHelper.deleteDirectory(editScriptsFilePath);
-		FileHelper.deleteDirectory(patchesSourceCodeFilePath);
-		FileHelper.deleteDirectory(buggyTokensFilePath);
-		FileHelper.deleteDirectory(editScriptSizesFilePath);
-		FileHelper.deleteDirectory(alarmTypesFilePath);
-		
-		final List<MessageFile> files = AkkaParser.getMessageFiles(Configuration.GUM_TREE_INPUT);
-		
-		StringBuilder editScripts = new StringBuilder();
-		StringBuilder patchesSourceCode = new StringBuilder();
-		StringBuilder sizes = new StringBuilder();
-		StringBuilder tokens = new StringBuilder();
-		StringBuilder alarmTypes = new StringBuilder();
-		StringBuilder testingInfo = new StringBuilder();
-
-		int counter = 0;
-		
-		int testViolations = 0;
-		int nullGumTreeResults = 0;
-		int noSourceCodeChanges = 0;
-		int noStatementChanges = 0;
-		int nullDiffEntry = 0;
-		int nullMappingGumTreeResults = 0;
-		int pureDeletion = 0;
-		int largeHunk = 0;
-		int nullSourceCode = 0;
-		int testInfos = 0;
-		int timeouts = 0;
-		StringBuilder builder = new StringBuilder();
-
-		for (MessageFile msgFile : files) {
-			File revFile = msgFile.getRevFile();
-			File prevFile = msgFile.getPrevFile();
-			File diffentryFile = msgFile.getDiffEntryFile();
-			File positionFile = msgFile.getPositionFile();
-			if (revFile.getName().toLowerCase().contains("test#") || revFile.getName().toLowerCase().contains("tests#")) {
-				testViolations += countAlarms(positionFile, "#TestViolation:");
-				continue;
-			}
-			FixedViolationHunkParser parser =  new FixedViolationHunkParser();
-//			parser.setUselessViolations(uselessViolations);
-			
-			final ExecutorService executor = Executors.newSingleThreadExecutor();
-			// schedule the work
-			final Future<?> future = executor.submit(new RunnableParser(prevFile, revFile, diffentryFile, parser));
-			try {
-				// wait for task to complete
-				future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS);
-
-				nullDiffEntry += parser.nullMatchedDiffEntry;
-				nullMappingGumTreeResults += parser.nullMappingGumTreeResult;
-				pureDeletion += parser.pureDeletions;
-				largeHunk += parser.largeHunk;
-				nullSourceCode += parser.nullSourceCode;
-				testInfos += parser.testInfos;
-				testingInfo.append(parser.testingInfo);
-				builder.append(parser.unfixedViolations);
-				
-				String editScript = parser.getAstEditScripts();
-				if ("".equals(editScript)) {
-					if (parser.resultType == 1) {
-						nullGumTreeResults += countAlarms(positionFile, "");
-					} else if (parser.resultType == 2) {
-						noSourceCodeChanges += countAlarms(positionFile, "");
-					} else if (parser.resultType == 3) {
-						noStatementChanges += countAlarms(positionFile, "");
-//					} else if (parser.resultType == 4) {
-					}
-				} else {
-					editScripts.append(editScript);
-					patchesSourceCode.append(parser.getPatchesSourceCode());
-					sizes.append(parser.getSizes());
-					alarmTypes.append(parser.getAlarmTypes());
-					tokens.append(parser.getTokensOfSourceCode());
-					
-					counter ++;
-					if (counter % 5000 == 0) {
-						FileHelper.outputToFile(editScriptsFilePath + "edistScripts.list", editScripts, true);
-						FileHelper.outputToFile(patchesSourceCodeFilePath + "patches.list", patchesSourceCode, true);
-						FileHelper.outputToFile(editScriptSizesFilePath + "sizes.list", sizes, true);
-						FileHelper.outputToFile(buggyTokensFilePath + "tokens.list", tokens, true);
-						editScripts.setLength(0);
-						patchesSourceCode.setLength(0);
-						sizes.setLength(0);
-						tokens.setLength(0);
-						FileHelper.outputToFile(alarmTypesFilePath + "alarmTypes.list", alarmTypes, true);
-						alarmTypes.setLength(0);
-						FileHelper.outputToFile("OUTPUT/testingInfo.list", testingInfo, true);
-						testingInfo.setLength(0);
-					}
-				}
-			} catch (TimeoutException e) {
-//				err.println("task timed out");
-				future.cancel(true);
-				timeouts += countAlarms(positionFile, "#Timeout:");
-//				System.err.println("#Timeout: " + revFile.getName());
-			} catch (InterruptedException e) {
-				timeouts += countAlarms(positionFile, "#TimeInterrupted:");
-//				err.println("task interrupted");
-//				System.err.println("#TimeInterrupted: " + revFile.getName());
-			} catch (ExecutionException e) {
-				timeouts += countAlarms(positionFile, "#TimeAborted:");
-//				err.println("task aborted");
-//				System.err.println("#TimeAborted: " + revFile.getName());
-			} finally {
-				executor.shutdownNow();
-			}
-		}
-		
-		if (sizes.length() > 0) {
-			FileHelper.outputToFile(editScriptsFilePath + "edistScripts.list", editScripts, true);
-			FileHelper.outputToFile(patchesSourceCodeFilePath + "patches.list", patchesSourceCode, true);
-			FileHelper.outputToFile(editScriptSizesFilePath + "sizes.list", sizes, true);
-			FileHelper.outputToFile(buggyTokensFilePath + "tokens.list", tokens, true);
-			editScripts.setLength(0);
-			patchesSourceCode.setLength(0);
-			sizes.setLength(0);
-			tokens.setLength(0);
-			
-			FileHelper.outputToFile(alarmTypesFilePath + "alarmTypes.list", alarmTypes, true);
-			alarmTypes.setLength(0);
-			FileHelper.outputToFile("OUTPUT/testingInfo.list", testingInfo, true);
-			testingInfo.setLength(0);
-		}
-		String statistic = "TestViolations: " + testViolations + "\nNullGumTreeResults: " + nullGumTreeResults + "\nNoSourceCodeChanges: " + noSourceCodeChanges + 
-				"\nNoStatementChanges: " + noStatementChanges + "\nNullDiffEntry: " + nullDiffEntry + "\nNullMatchedGumTreeResults: " + nullMappingGumTreeResults +
-				"\nPureDeletion: " + pureDeletion + "\nLargeHunk: " + largeHunk + "\nNullSourceCode: " + nullSourceCode + 
-				"\nTestingInfo: " + testInfos + "\nTimeout: " + timeouts;
-		FileHelper.outputToFile("OUTPUT/statistic.list", statistic, false);
-		FileHelper.outputToFile("OUTPUT/UnfixedV.list", builder, false);
-	}
-
-	private static int countAlarms(File positionFile, String type) {//, List<Violation> uselessViolations) {
-		int counter = 0;
-		String content = FileHelper.readFile(positionFile);
-		BufferedReader reader = new BufferedReader(new StringReader(content));
-		String line = null;
-		try {
-			while ((line = reader.readLine()) != null) {
-				String[] elements = line.split(":");
-				Violation v = new Violation(Integer.parseInt(elements[1]), Integer.parseInt(elements[2]), elements[0]);
-				String fileName = positionFile.getName().replace(".txt", ".java");
-				v.setFileName(fileName);
-				counter ++;
-				if (!"".equals(type)) {
-					System.err.println(type + fileName + ":" + elements[1] + ":" + elements[2] + ":" + elements[0]);
-				}
-			}
-		} catch (IOException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				reader.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		return counter;
-	}
-
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/AkkaMatcher.java

@@ -1,214 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser2;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Scanner;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import akka.actor.ActorRef;
-import akka.actor.ActorSystem;
-import edu.lu.uni.serval.MultipleThreadsParser.MessageFile;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-import edu.lu.uni.serval.utils.MapSorter;
-
-/**
- * Multi-thread parser of parsing the difference between buggy code file and fixed code file.
- * 
- * @author kui.liu
- *
- */
-public class AkkaMatcher {
-	
-	private static Logger log = LoggerFactory.getLogger(AkkaMatcher.class);
-
-	public static void main(String[] args) {
-		List<Double[]> extractedFeatures = readStringList(Configuration.ROOT_PATH + "TestData/2_CNNinput.csv");
-		int size = extractedFeatures.size();
-		List<Double[]> trainingFeatures = extractedFeatures.subList(0, size - 178);
-		List<Double[]> bugFeatures = extractedFeatures.subList(size - 178, size);
-		
-		
-		for (int index = 0; index < 178; index ++) {
-//			AkkaMatcher computor = new AkkaMatcher();
-//			computor.matchFixPatterns(bugFeatures.get(index), index, trainingFeatures);
-			Map<Integer, Double> similarities = new HashMap<>();
-			for (int i = 0; i < size - 178; i ++) {
-				Double similarity = Math.abs(computeSimilarity(bugFeatures.get(index), trainingFeatures.get(i)));
-				similarities.put(i + 1, similarity);
-			}
-			
-			MapSorter<Integer, Double> mapSorter = new MapSorter<Integer, Double>();
-			Map<Integer, Double> sortedSimilarities = mapSorter.sortByValueDescending(similarities);
-			
-			List<Integer> similarityList = new ArrayList<>();
-			double similarity = 0;
-			int num = 0;
-			for (Map.Entry<Integer, Double> entry : sortedSimilarities.entrySet()) {
-				if (entry.getValue().equals(Double.NaN)) {
-					continue;
-				}
-				if (entry.getValue() == similarity) {
-					continue;
-				}
-				similarityList.add(entry.getKey());
-				similarity = entry.getValue();
-				if (++ num % 100 == 0) {
-					break;
-				}
-			}
-			outputMatchedPatterns(similarityList, index + 1);
-		}
-		
-	}
-	
-	private static Double computeSimilarity(Double[] feature, Double[] trainingFeature) {
-		Double similarity = DistanceCalculator.cosineSimilarityDistance(trainingFeature, feature);
-		return similarity;
-	}
-	
-	private static void outputMatchedPatterns(List<Integer> similarityList, int bugId) {
-		String outputFile = Configuration.ROOT_PATH + "TestData/MatchedFixPatterns/Bug_" + bugId + ".list";
-		StringBuilder builder = new StringBuilder("BugId: " + bugId + "\n\n\n");
-		
-		for (int i = 0, size = similarityList.size(); i < size; i ++) {
-			int patternPosition = similarityList.get(i);
-			builder.append(readPattern(patternPosition));
-		}
-		
-		FileHelper.outputToFile(outputFile, builder, false);
-	}
-	
-	private static String readPattern(int patternPosition) {
-		String patternInfo = "";
-		FileInputStream fis = null;
-		Scanner scanner = null;
-		try {
-			fis = new FileInputStream(Configuration.SELECTED_PATCHES_SOURE_CODE_FILE);
-			scanner = new Scanner(fis);
-			int index = 0;
-			while (scanner.hasNextLine()) {
-				String line = scanner.nextLine();
-				if (line.equals("PATCH###")) {
-					if (patternPosition == index) {
-						break;
-					}
-					index ++;
-					patternInfo = "";
-				}
-				patternInfo += line + "\n";
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				scanner.close();
-				fis.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		return patternInfo;
-	}
-
-	@SuppressWarnings("deprecation")
-	public void matchFixPatterns(Double[] bugFeature, int bugIndex, List<Double[]> trainingFeatures) {
-		ActorSystem system = null;
-		ActorRef parsingActor = null;
-		int numberOfWorkers = 100;
-		final WorkMessage msg = new WorkMessage(bugIndex, bugFeature, trainingFeatures);
-		try {
-			log.info("Akka begins...");
-			system = ActorSystem.create("Matching-FixPattern-System");
-			parsingActor = system.actorOf(MatchFixPatternActor.props(numberOfWorkers), "match-fix-pattern-actor");
-			parsingActor.tell(msg, ActorRef.noSender());
-		} catch (Exception e) {
-			system.shutdown();
-			e.printStackTrace();
-		}
-	}
-	
-
-	/**
-	 * Get bug commit-related files.
-	 * 
-	 * @return
-	 */
-	public static List<MessageFile> getMessageFiles() {
-		String inputPath = Configuration.GUM_TREE_INPUT; //DiffEntries  prevFiles  revFiles
-		File inputFileDirector = new File(inputPath);
-		File[] files = inputFileDirector.listFiles();   // project folders
-		log.info("Projects: " + files.length);
-		List<MessageFile> msgFiles = new ArrayList<>();
-		
-		for (File file : files) {
-			if (!file.isDirectory()) continue;
-//			if (!(file.getName().startsWith("k") || file.getName().startsWith("l"))) continue;
-			if (file.getName().startsWith("a") || file.getName().startsWith("b")
-					|| file.getName().startsWith("c") || file.getName().startsWith("d")
-				|| file.getName().startsWith("e") || file.getName().startsWith("f")
-				|| file.getName().startsWith("g") || file.getName().startsWith("h") 
-				||file.getName().startsWith("h") || file.getName().startsWith("i")
-				|| file.getName().startsWith("k") || file.getName().startsWith("l")
-				|| file.getName().startsWith("j") || file.getName().startsWith("t")) continue;
-//			if (!file.getName().startsWith("j")) continue;
-			log.info("Project name: " + file.getName());
-			String projectFolder = file.getPath();
-			File revFileFolder = new File(projectFolder + "/revFiles/");// revised file folder
-			File[] revFiles = revFileFolder.listFiles();
-			for (File revFile : revFiles) {
-				if (revFile.getName().endsWith(".java")) {
-					File prevFile = new File(projectFolder + "/prevFiles/prev_" + revFile.getName());// previous file
-					File diffentryFile = new File(projectFolder + "/DiffEntries/" + revFile.getName().replace(".java", ".txt")); // DiffEntry file
-					MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile);
-					msgFiles.add(msgFile);
-				}
-			}
-		}
-		
-		return msgFiles;
-	}
-	
-	public static List<Double[]> readStringList(String inputFile) {
-		List<Double[]> list = new ArrayList<>();
-		FileInputStream fis = null;
-		Scanner scanner = null;
-		try {
-			fis = new FileInputStream(inputFile);
-			scanner = new Scanner(fis);
-			while(scanner.hasNextLine()) {
-				String line = scanner.nextLine();
-				Double[] features = doubleParseFeature(line);
-				list.add(features);
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				scanner.close();
-				fis.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		return list;
-	}
-	
-	private static Double[] doubleParseFeature(String feature) {
-		String[] features = feature.split(", ");
-		int length = features.length;
-		Double[] doubleFeatures = new Double[length];
-		for (int i = 0; i < length; i ++) {
-			doubleFeatures[i] = Double.parseDouble(features[i]);
-		}
-		return doubleFeatures;
-	}
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/DistanceCalculator.java

@@ -1,68 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser2;
-
-public class DistanceCalculator {
-	
-	public static double calculateDistance(DistanceFunction distanceType, Double[] targetPoint, Double[] selfPoint) {
-		double distance = 0;
-		switch (distanceType) {
-		case EUCLIDEAN:
-			distance = DistanceCalculator.euclideanDistance(targetPoint, selfPoint);
-			break;
-		case COSINESIMILARITY:
-			distance = DistanceCalculator.cosineSimilarityDistance(targetPoint, selfPoint);
-			break;
-		case MANHATTAN:
-			distance = DistanceCalculator.manhattanDistance(targetPoint, selfPoint);
-			break;
-		default:
-			distance = DistanceCalculator.euclideanDistance(targetPoint, selfPoint);
-			break;
-		}
-		return distance;
-	}
-
-	public static double euclideanDistance(Double[] targetPoint, Double[] selfPoint) {
-		double sum = 0.0;
-
-		for (int i = 0, length = targetPoint.length; i < length; i++) {
-			double diff = targetPoint[i] - selfPoint[i];
-			sum += diff * diff;
-		}
-		return Math.sqrt(sum);
-	}
-
-	public static Double cosineSimilarityDistance(Double[] targetPoint, Double[] selfPoint) {
-		Double sim = 0.0d;
-		int length = targetPoint.length;
-		double dot = 0.0d;
-		double mag1 = 0.0d;
-		double mag2 = 0.0d;
-
-		for (int i = 0; i < length; i ++) {
-			dot += targetPoint[i] * selfPoint[i];
-			mag1 += Math.pow(targetPoint[i], 2);
-			mag2 += Math.pow(selfPoint[i], 2);
-		}
-
-		sim = dot / (Math.sqrt(mag1) * Math.sqrt(mag2));
-		return sim;
-	}
-
-	public static Double manhattanDistance(Double[] targetPoint, Double[] selfPoint) {
-		double result = 0.0;
-		for (int i = 0; i < targetPoint.length; i++) {
-			result += Math.abs(selfPoint[i] - targetPoint[i]);
-		}
-		return result;
-	}
-
-	public static Double minkowskiDistance(Double[] targetPoint, Double[] selfPoint) {
-		return null;
-	}
-	
-	public static Double jaccardSimilarity(Double[] targetPoint, Double[] selfPoint) {
-		return null;
-	}
-
-}
-

src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/DistanceFunction.java

@@ -1,5 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser2;
-
-public enum DistanceFunction {
-	EUCLIDEAN, COSINESIMILARITY, MANHATTAN
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/MatchFixPatternActor.java

@@ -1,172 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser2;
-
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Scanner;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import akka.actor.ActorRef;
-import akka.actor.Props;
-import akka.actor.UntypedActor;
-import akka.japi.Creator;
-import akka.routing.RoundRobinPool;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-import edu.lu.uni.serval.utils.ListSorter;
-import edu.lu.uni.serval.utils.MapSorter;
-
-public class MatchFixPatternActor extends UntypedActor {
-	
-	private static Logger logger = LoggerFactory.getLogger(MatchFixPatternActor.class);
-
-	private ActorRef mineRouter;
-	private final int numberOfWorkers;
-	private int counter = 0;
-	
-	public MatchFixPatternActor(int numberOfWorkers) {
-		mineRouter = this.getContext().actorOf(new RoundRobinPool(numberOfWorkers)
-				.props(MatchFixPatternWorker.props()), "match-fix-pattern-router");
-		this.numberOfWorkers = numberOfWorkers;
-	}
-
-	public static Props props(final int numberOfWorkers) {
-		
-		return Props.create(new Creator<MatchFixPatternActor>() {
-
-			private static final long serialVersionUID = 9207427376110704705L;
-
-			@Override
-			public MatchFixPatternActor create() throws Exception {
-				return new MatchFixPatternActor(numberOfWorkers);
-			}
-			
-		});
-	}
-	
-	@SuppressWarnings("deprecation")
-	@Override
-	public void onReceive(Object message) throws Exception {
-		if (message instanceof WorkMessage) {
-			WorkMessage msg = (WorkMessage) message;
-			List<Double[]> trainingFeatures = msg.getTrainingFeatures();
-			int size = trainingFeatures.size();
-			int average = size / numberOfWorkers;
-			this.bugId = msg.getId();
-			Double[] bugFeature = msg.getBugFeature();
-			
-			for (int i = 0; i < numberOfWorkers; i ++) {
-				int fromIndex = i * average;
-				int toIndex = (i + 1) * average;
-				if (i == numberOfWorkers - 1) {
-					toIndex = size;
-				}
-				
-				List<Double[]> subTrainingFeatures = new ArrayList<>();
-				subTrainingFeatures.addAll(trainingFeatures.subList(fromIndex, toIndex));
-				final WorkMessage workMsg = new WorkMessage(bugId, bugFeature, subTrainingFeatures);
-				workMsg.setNum(i + 1);
-				mineRouter.tell(workMsg, getSelf());
-				logger.info("Assign a task to worker #" + (i + 1) + "...");
-			}
-		} else if (message instanceof ReturnMessage) {
-			counter ++;
-			logger.info(counter + " workers finished their work...");
-			ReturnMessage rMsg = (ReturnMessage) message;
-			returnMessages.add(rMsg);
-			
-			if (counter >= numberOfWorkers) {
-				ListSorter<ReturnMessage> sorter = new ListSorter<ReturnMessage>(returnMessages);
-				returnMessages = sorter.sortAscending();
-				
-				Map<Integer, Double> similarities = new HashMap<>();
-				int index = 0;
-				for (int i = 0; i < numberOfWorkers; i ++) {
-					ReturnMessage returnMessage = returnMessages.get(i);
-					List<Double> similarity = returnMessage.getSimilarities();
-					for (int j = 0, size = similarity.size(); j < size; j ++) {
-						index ++;
-						similarities.put(index, similarity.get(j));
-					}
-				}
-				
-				MapSorter<Integer, Double> mapSorter = new MapSorter<Integer, Double>();
-				Map<Integer, Double> sortedSimilarities = mapSorter.sortByValueDescending(similarities);
-				
-				List<Integer> similarityList = new ArrayList<>();
-				double similarity = 0;
-				int num = 0;
-				for (Map.Entry<Integer, Double> entry : sortedSimilarities.entrySet()) {
-					if (entry.getValue() == similarity) {
-						continue;
-					}
-					similarityList.add(entry.getKey());
-					similarity = entry.getValue();
-					if (++ num % 100 == 0) {
-						break;
-					}
-				}
-				outputMatchedPatterns(similarityList);
-				logger.info("All workers finished their work...");
-				this.getContext().stop(mineRouter);
-				this.getContext().stop(getSelf());
-				this.getContext().system().shutdown();
-			}
-		} else {
-			unhandled(message);
-		}
-	}
-	
-	private void outputMatchedPatterns(List<Integer> similarityList) {
-		String outputFile = Configuration.ROOT_PATH + "TestData/MatchedFixPatterns/Bug_" + bugId + ".list";
-		StringBuilder builder = new StringBuilder("BugId: " + bugId + "\n\n\n");
-		
-		for (int i = 0, size = similarityList.size(); i < size; i ++) {
-			int patternPosition = similarityList.get(i);
-			builder.append(readPattern(patternPosition));
-		}
-		
-		FileHelper.outputToFile(outputFile, builder, false);
-	}
-	
-	private String readPattern(int patternPosition) {
-		String patternInfo = "";
-		FileInputStream fis = null;
-		Scanner scanner = null;
-		try {
-			fis = new FileInputStream(Configuration.SELECTED_PATCHES_SOURE_CODE_FILE);
-			scanner = new Scanner(fis);
-			int index = 0;
-			while (scanner.hasNextLine()) {
-				String line = scanner.nextLine();
-				if (line.equals("PATCH###")) {
-					if (patternPosition == index) {
-						break;
-					}
-					index ++;
-					patternInfo = "";
-				}
-				patternInfo += line + "\n";
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				scanner.close();
-				fis.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		return patternInfo;
-	}
-	
-	private int bugId;
-	private List<ReturnMessage> returnMessages = new ArrayList<>();
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/MatchFixPatternWorker.java

@@ -1,60 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser2;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import akka.actor.Props;
-import akka.actor.UntypedActor;
-import akka.japi.Creator;
-
-public class MatchFixPatternWorker extends UntypedActor {
-	private static Logger log = LoggerFactory.getLogger(MatchFixPatternActor.class);
-	
-	public MatchFixPatternWorker() {
-	}
-
-	public static Props props() {
-		return Props.create(new Creator<MatchFixPatternWorker>() {
-
-			private static final long serialVersionUID = -7615153844097275009L;
-
-			@Override
-			public MatchFixPatternWorker create() throws Exception {
-				return new MatchFixPatternWorker();
-			}
-			
-		});
-	}
-
-	@Override
-	public void onReceive(Object message) throws Exception {
-		if (message instanceof WorkMessage) {
-			WorkMessage msg = (WorkMessage) message;
-			List<Double[]> trainingFeatures = msg.getTrainingFeatures();
-			Double[] bugFeature = msg.getBugFeature();
-			int bugID = msg.getId();
-			int workNum = msg.getNum();
-			
-			List<Double> similarities = new ArrayList<>();
-			for (int i = 0, size = trainingFeatures.size(); i < size; i ++) {
-				Double similarity = Math.abs(computeSimilarity(bugFeature, trainingFeatures.get(i)));
-				similarities.add(similarity);
-			}
-
-			final ReturnMessage rMsg = new ReturnMessage(bugID, workNum, similarities);
-			log.info("Worker #" + workNum + " finished the work...");
-			this.getSender().tell(rMsg, getSelf());
-		} else {
-			unhandled(message);
-		}
-	}
-
-	private Double computeSimilarity(Double[] feature, Double[] trainingFeature) {
-		Double similarity = DistanceCalculator.cosineSimilarityDistance(trainingFeature, feature);
-		return similarity;
-	}
-
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/ReturnMessage.java

@@ -1,35 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser2;
-
-import java.util.List;
-
-public class ReturnMessage implements Comparable<ReturnMessage>{
-	
-	private int bugId;
-	private Integer workerId;
-	private List<Double> similarities;
-	
-	public ReturnMessage(int bugId, int workerId, List<Double> similarities) {
-		super();
-		this.bugId = bugId;
-		this.workerId = workerId;
-		this.similarities = similarities;
-	}
-
-	public int getBugId() {
-		return bugId;
-	}
-
-	public int getWorkerId() {
-		return workerId;
-	}
-
-	public List<Double> getSimilarities() {
-		return similarities;
-	}
-
-	@Override
-	public int compareTo(ReturnMessage o) {
-		return this.workerId.compareTo(o.workerId);
-	}
-	
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/WorkMessage.java

@@ -1,39 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser2;
-
-import java.util.List;
-
-public class WorkMessage {
-
-	private int id;
-	private Double[] bugFeature;
-	private List<Double[]> trainingFeatures;
-	private int num;
-	
-	public WorkMessage(int id, Double[] bugFeature, List<Double[]> trainingFeatures) {
-		super();
-		this.id = id;
-		this.bugFeature = bugFeature;
-		this.trainingFeatures = trainingFeatures;
-	}
-
-	public int getId() {
-		return id;
-	}
-
-	public Double[] getBugFeature() {
-		return bugFeature;
-	}
-
-	public List<Double[]> getTrainingFeatures() {
-		return trainingFeatures;
-	}
-
-	public int getNum() {
-		return num;
-	}
-
-	public void setNum(int num) {
-		this.num = num;
-	}
-
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/AkkaParser.java

@@ -1,90 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser3;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import akka.actor.ActorRef;
-import akka.actor.ActorSystem;
-import edu.lu.uni.serval.MultipleThreadsParser.MessageFile;
-import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-
-/**
- * Multi-thread parser of parsing source code of unfixed violations.
- * 
- * @author kui.liu
- *
- */
-public class AkkaParser {
-	
-	private static Logger log = LoggerFactory.getLogger(AkkaParser.class);
-
-	@SuppressWarnings("deprecation")
-	public static void main(String[] args) {
-		String violationType = Configuration.GUM_TREE_INPUT + "UnfixedViolations/";
-		File file = new File(violationType);
-		File[] violationTypes = file.listFiles();
-		for (File violationT : violationTypes) {
-			if (violationT.isDirectory()) {
-				violationType = violationT.getName();
-				if (//violationType.equals("SF_SWITCH_NO_DEFAULT") ||
-//						violationType.equals("SE_NO_SERIALVERSIONID") ||
-						violationType.equals("DM_DEFAULT_ENCODING")) {
-					// input data
-					log.info("Get the input data...");
-					final List<MessageFile> msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT, violationType);
-					log.info("MessageFiles: " + msgFiles.size());
-					
-					// output path
-					final String sourceCodeFilesPath = Configuration.ROOT_PATH + "UnfixedViolations_RQ3/" + violationType + "/";
-					FileHelper.deleteDirectory(sourceCodeFilesPath);
-
-					ActorSystem system = null;
-					ActorRef parsingActor = null;
-					int numberOfWorkers = 200;
-					final WorkMessage msg = new WorkMessage(0, msgFiles);
-					try {
-						log.info("Akka begins...");
-						system = ActorSystem.create("Mining-Pattern-System-" + violationType);
-						parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, sourceCodeFilesPath, violationType), "mine-pattern-actor-" + violationType);
-						parsingActor.tell(msg, ActorRef.noSender());
-					} catch (Exception e) {
-						system.shutdown();
-						e.printStackTrace();
-					}
-				}
-			}
-		}
-	}
-	
-
-	/**
-	 * Get violation-related files.
-	 * 
-	 * @param gumTreeInput
-	 * @return
-	 */
-	public static List<MessageFile> getMessageFiles(String inputPath, String violationType) {
-		File sourceCodeFilesPath = new File(inputPath + "UnfixedViolations/" + violationType + "/");
-		File[] sourceCodeFiles = sourceCodeFilesPath.listFiles();   // project folders
-		List<MessageFile> msgFiles = new ArrayList<>();
-		
-		for (File sourceCodeFile : sourceCodeFiles) {
-			if (sourceCodeFile.getName().endsWith(".java")) {
-				String fileName = sourceCodeFile.getName();
-				fileName = fileName.substring(8).replace(".java", ".txt");
-				File positionFile = new File(inputPath + "UnFV_positions/" + violationType + "/" + fileName); // position file
-				MessageFile msgFile = new MessageFile(null, sourceCodeFile, null);
-				msgFile.setPositionFile(positionFile);
-				msgFiles.add(msgFile);
-			}
-		}
-		
-		return msgFiles;
-	}
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/AkkaParser2.java

@@ -1,78 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser3;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import akka.actor.ActorRef;
-import akka.actor.ActorSystem;
-import edu.lu.uni.serval.MultipleThreadsParser.MessageFile;
-import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-
-/**
- * Multi-thread parser of parsing source code of fixed violations.
- * 
- * @author kui.liu
- *
- */
-public class AkkaParser2 {
-	
-	private static Logger log = LoggerFactory.getLogger(AkkaParser2.class);
-
-	@SuppressWarnings("deprecation")
-	public static void main(String[] args) {
-		// input data
-		log.info("Get the input data...");
-		final List<MessageFile> msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT);
-		log.info("MessageFiles: " + msgFiles.size());
-		
-		// output path
-		final String sourceCodeFilesPath = Configuration.ROOT_PATH + "fixedViolations/";
-		FileHelper.deleteDirectory(sourceCodeFilesPath);
-
-		ActorSystem system = null;
-		ActorRef parsingActor = null;
-		int numberOfWorkers = 431;
-		final WorkMessage msg = new WorkMessage(0, msgFiles);
-		try {
-			log.info("Akka begins...");
-			system = ActorSystem.create("Mining-Pattern-System");
-			parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, sourceCodeFilesPath, "Type"), "mine-pattern-actor");
-			parsingActor.tell(msg, ActorRef.noSender());
-		} catch (Exception e) {
-			system.shutdown();
-			e.printStackTrace();
-		}
-	}
-	
-
-	/**
-	 * Get violation-related files.
-	 * 
-	 * @param gumTreeInput
-	 * @return
-	 */
-	public static List<MessageFile> getMessageFiles(String inputPath) {
-		File sourceCodeFilesPath = new File(inputPath + "prevFiles/");
-		File[] sourceCodeFiles = sourceCodeFilesPath.listFiles();
-		List<MessageFile> msgFiles = new ArrayList<>();
-		
-		for (File sourceCodeFile : sourceCodeFiles) {
-			if (sourceCodeFile.getName().endsWith(".java")) {
-				String fileName = sourceCodeFile.getName();
-				fileName = fileName.substring(5).replace(".java", ".txt");
-				File positionFile = new File(inputPath + "positions/" + fileName); // position file
-				MessageFile msgFile = new MessageFile(null, sourceCodeFile, null);
-				msgFile.setPositionFile(positionFile);
-				msgFiles.add(msgFile);
-			}
-		}
-		
-		return msgFiles;
-	}
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/ParseFixPatternActor.java

@@ -1,80 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser3;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import akka.actor.ActorRef;
-import akka.actor.Props;
-import akka.actor.UntypedActor;
-import akka.japi.Creator;
-import akka.routing.RoundRobinPool;
-import edu.lu.uni.serval.MultipleThreadsParser.MessageFile;
-import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage;
-
-public class ParseFixPatternActor extends UntypedActor {
-	
-	private static Logger logger = LoggerFactory.getLogger(ParseFixPatternActor.class);
-
-	private ActorRef mineRouter;
-	private final int numberOfWorkers;
-	private int counter = 0;
-	
-	public ParseFixPatternActor(int numberOfWorkers, String sourceCodeFilesPath, String vType) {
-		mineRouter = this.getContext().actorOf(new RoundRobinPool(numberOfWorkers)
-				.props(ParseFixPatternWorker.props(sourceCodeFilesPath)), "mine-pattern-router-" + vType);
-		this.numberOfWorkers = numberOfWorkers;
-	}
-
-	public static Props props(final int numberOfWorkers, final String sourceCodeFilesPath, final String vType) {
-		
-		return Props.create(new Creator<ParseFixPatternActor>() {
-
-			private static final long serialVersionUID = 9207427376110704705L;
-
-			@Override
-			public ParseFixPatternActor create() throws Exception {
-				return new ParseFixPatternActor(numberOfWorkers, sourceCodeFilesPath, vType);
-			}
-			
-		});
-	}
-	
-	@SuppressWarnings("deprecation")
-	@Override
-	public void onReceive(Object message) throws Exception {
-		if (message instanceof WorkMessage) {
-			List<MessageFile> files = ((WorkMessage) message).getMsgFiles();
-			int size = files.size();
-			int average = size / numberOfWorkers;
-			
-			for (int i = 0; i < numberOfWorkers; i ++) {
-				int fromIndex = i * average;
-				int toIndex = (i + 1) * average;
-				if (i == numberOfWorkers - 1) {
-					toIndex = size;
-				}
-				
-				List<MessageFile> filesOfWorkers = new ArrayList<>();
-				filesOfWorkers.addAll(files.subList(fromIndex, toIndex));
-				final WorkMessage workMsg = new WorkMessage(i + 1, filesOfWorkers);
-				mineRouter.tell(workMsg, getSelf());
-				logger.info("Assign a task to worker #" + (i + 1) + "...");
-			}
-		} else if ("STOP".equals(message.toString())) {
-			counter ++;
-			logger.info(counter + " workers finished their work...");
-			if (counter >= numberOfWorkers) {
-				logger.info("All workers finished their work...");
-				this.getContext().stop(mineRouter);
-				this.getContext().stop(getSelf());
-				this.getContext().system().shutdown();
-			}
-		} else {
-			unhandled(message);
-		}
-	}
-
-}

src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/ParseFixPatternWorker.java

@@ -1,122 +0,0 @@
-package edu.lu.uni.serval.MultipleThreadsParser3;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import akka.actor.Props;
-import akka.actor.UntypedActor;
-import akka.japi.Creator;
-import edu.lu.uni.serval.MultipleThreadsParser.MessageFile;
-import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-import edu.lu.uni.serval.violation.code.parser.ViolationCodeParser;
-
-public class ParseFixPatternWorker extends UntypedActor {
-	private static Logger log = LoggerFactory.getLogger(ParseFixPatternActor.class);
-	
-	private String sourceCodeFilesPath;
-	
-	public ParseFixPatternWorker(String sourceCodeFilesPath) {
-		this.sourceCodeFilesPath = sourceCodeFilesPath;
-	}
-
-	public static Props props(final String sourceCodeFilesPath) {
-		return Props.create(new Creator<ParseFixPatternWorker>() {
-
-			private static final long serialVersionUID = -7615153844097275009L;
-
-			@Override
-			public ParseFixPatternWorker create() throws Exception {
-				return new ParseFixPatternWorker(sourceCodeFilesPath);
-			}
-			
-		});
-	}
-
-	@Override
-	public void onReceive(Object message) throws Exception {
-		if (message instanceof WorkMessage) {
-			WorkMessage msg = (WorkMessage) message;
-			List<MessageFile> files = msg.getMsgFiles();
-			StringBuilder sourceCode = new StringBuilder();
-			StringBuilder sizes = new StringBuilder();
-			StringBuilder tokens = new StringBuilder();
-			
-			List<String> violationTypes = readTypes();
-
-			int id = msg.getId();
-			int counter = 0;
-			
-			for (MessageFile msgFile : files) {
-				File prevFile = msgFile.getPrevFile();
-				File positionFile = msgFile.getPositionFile();
-				if (prevFile.getName().toLowerCase().contains("test")) {
-					continue;
-				}
-				ViolationCodeParser parser =  new ViolationCodeParser();
-				parser.parse(prevFile, positionFile);
-				parser.setTypes(violationTypes);
-				
-				String sourceCodeStr = parser.sourceCode;
-				if ("".equals(sourceCodeStr)) {
-				} else {
-					sourceCode.append(sourceCodeStr);
-					sizes.append(parser.sizes);
-					tokens.append(parser.tokens);
-					
-					counter ++;
-					if (counter % 100 == 0) {
-						FileHelper.outputToFile(sourceCodeFilesPath + "SourceCode/worker_" + id + ".list", sourceCode, true);
-						FileHelper.outputToFile(sourceCodeFilesPath + "Sizes/worker_" + id + ".list", sizes, true);
-						FileHelper.outputToFile(sourceCodeFilesPath + "Tokens/worker_" + id + ".list", tokens, true);
-						sourceCode.setLength(0);
-						sizes.setLength(0);
-						tokens.setLength(0);
-					}
-				}
-			}
-			
-			if (sizes.length() > 0) {
-				FileHelper.outputToFile(sourceCodeFilesPath + "SourceCode/worker_" + id + ".list", sourceCode, true);
-				FileHelper.outputToFile(sourceCodeFilesPath + "Sizes/worker_" + id + ".list", sizes, true);
-				FileHelper.outputToFile(sourceCodeFilesPath + "Tokens/worker_" + id + ".list", tokens, true);
-				sourceCode.setLength(0);
-				sizes.setLength(0);
-				tokens.setLength(0);
-			}
-
-			log.info("Worker #" + id +"Finish of parsing " + counter + " files...");
-			log.info("Worker #" + id + " finished the work...");
-			this.getSender().tell("STOP", getSelf());
-		} else {
-			unhandled(message);
-		}
-	}
-
-	private List<String> readTypes() {
-		String fileName = Configuration.ROOT_PATH + "fixedViolations/types.list";
-		String content = FileHelper.readFile(fileName);
-		List<String> types = new ArrayList<>();
-		BufferedReader reader = new BufferedReader(new StringReader(content));
-		try {
-			String line = null;
-			while ((line = reader.readLine()) != null) {
-				types.add(line);
-			}
-			reader.close();
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
-//		System.err.println(types.size());
-		return types;
-	}
-
-}

src/main/java/edu/lu/uni/serval/TreeToString.java

@@ -1,47 +0,0 @@
-package edu.lu.uni.serval;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap;
-
-public class TreeToString {
-	
-	private List<String> strList = new ArrayList<>();
-
-	public String toString(ITree tree) {
-		List<ITree> children = tree.getChildren();
-		String str = ASTNodeMap.map.get(tree.getType());
-		if (strList.size() == 0) {
-			strList.add(str);
-			for (ITree child : children) {
-				TreeToString t2s = new TreeToString();
-				t2s.toString(child);
-				List<String> strList1 = t2s.strList;
-				for (String str1 : strList1) {
-					strList.add("---" + str1);
-				}
-			}
-		} else {
-			strList.clear();
-			strList.add(str);
-			for (ITree child : children) {
-				TreeToString t2s = new TreeToString();
-				t2s.toString(child);
-				List<String> strList1 = t2s.strList;
-				for (String str1 : strList1) {
-					strList.add("---" + str1);
-				}
-			}
-		}
-		
-		str = "";
-		for (String str1 : strList) {
-			str += str1 + "\n";
-		}
-		 
-		return str;
-	}
-}

src/main/java/edu/lu/uni/serval/config/Configuration.java

@@ -4,88 +4,4 @@ public class Configuration {
 	
 	public static final long SECONDS_TO_WAIT = 900L;
 
-//	public static String ROOT_PATH = "/Volumes/data/bugStudy/dataset/"; // The root path of all output data.
-	public static String ROOT_PATH = "/Users/anilkoyuncu/bugStudy/dataset/"; // The root path of all output data.
-
-	public static int HUNK_SIZE = 10; // The limitation of source code lines of each DiffEntry, which will be selected as training data.
-	public static final String BUGGY_TREE_SIGNAL = "BUGGY_TREE###"; // The starting signal of the tree of buggy source code .
-	public static final String PATCH_SIGNAL = "PATCH###"; // Th starting signal of each patch.
-	
-	// input path of GumTree. (i.e., Fix patterns parser)
-	public static final String GUM_TREE_INPUT = ROOT_PATH + "GumTreeInput/";// Buggy version file VS. Fixing version file, (DiffEntry File)
-	
-
-	// the output path of GumTree results.
-	public static final String GUM_TREE_OUTPUT = ROOT_PATH + "GumTreeResults/";
-	public static final String EDITSCRIPTS_FILE_PATH = GUM_TREE_OUTPUT + "editScripts/";
-	public static final String PATCH_SOURCECODE_FILE_PATH = GUM_TREE_OUTPUT + "sourceCode/";
-	public static final String BUGGYTREE_FILE_PATH = GUM_TREE_OUTPUT + "buggyTrees/";
-	public static final String BUGGY_CODE_TOKEN_FILE_PATH = GUM_TREE_OUTPUT + "tokens/";
-	public static final String EDITSCRIPT_SIZES_FILE_PATH = GUM_TREE_OUTPUT + "editScriptSizes/";
-	public static final String ALARM_TYPES_FILE_PATH = GUM_TREE_OUTPUT + "alarmTypes/";
-
-	public static final String EDITSCRIPTS_FILE = GUM_TREE_OUTPUT + "editScripts.list";
-	public static final String PATCH_SOURCECODE_FILE = GUM_TREE_OUTPUT + "patchSourceCode.list";
-	public static final String BUGGYTREES_FILE = GUM_TREE_OUTPUT + "buggyTrees.list";
-	public static final String BUGGY_CODE_TOKENS_FILE = GUM_TREE_OUTPUT + "tokens.list";
-	public static final String EDITSCRIPT_SIZES_FILE = GUM_TREE_OUTPUT + "editScriptSizes.csv";
-	public static final String ALARM_TYPES_FILE = GUM_TREE_OUTPUT + "alarmTypes.list";
-	
-	public static final int VECTOR_SIZE_OF_EMBEDED_TOKEN1 = 100; // tokens of edit scripts.
-	public static final int VECTOR_SIZE_OF_EMBEDED_TOKEN2 = 200; // tokens of source code
-	
-	// the input path of fix patterns mining.
-	private static final String MINING_INPUT = ROOT_PATH + "MiningInput/";
-	public static final String MAX_TOKEN_VECTORS_SIZE_OF_EDIT_SCRIPTS = MINING_INPUT + "/MaxTokenVectorSizeOfEditScripts.list"; // The max size of edit scripts: upper limitation of max size.
-	public static final String MAX_TOKEN_VECTORS_SIZE_OF_SOURCE_CODE = MINING_INPUT + "/MaxTokenVectorSizeOfBuggySourceCode.list"; // The max size of all buggy source code token vectors.
-	// the input path of token embedding.
-	public static final String EMBEDDING_INPUT = MINING_INPUT + "Embedding/";
-	public static final String SELECTED_PATCHES_SOURE_CODE_FILE = EMBEDDING_INPUT + "patchSourceCode.list";// Selected patches.
-	public static final String SELECTED_BUGGY_TREE_FILE = EMBEDDING_INPUT + "buggyTrees.list";
-	public static final String SELECTED_BUGGY_TOKEN_FILE = EMBEDDING_INPUT + "tokens.list"; // Selected token vectors of buggy source code.
-	public static final String SELECTED_EDITSCRIPTES_FILE = EMBEDDING_INPUT + "editScripts.list"; // Selected edit script vectors.
-	public static final String SELECTED_ALARM_TYPES_FILE = EMBEDDING_INPUT + "alarmTypes.list"; // Selected edit script vectors.
-	// the input path of feature learning.
-	public static final String FEATURE_LEARNING_INPUT = MINING_INPUT + "FeatureLearning/";
-	public static final String EMBEDDED_EDIT_SCRIPT_TOKENS = FEATURE_LEARNING_INPUT + "embeddedEditScriptTokens.list"; // All embedded tokens of selected edit scripts.
-	public static final String VECTORIED_EDIT_SCRIPTS = FEATURE_LEARNING_INPUT + "vectorizedEditScripts.csv"; // Embedded and vectorized edit script vectors.
-	// the input path of clustering.
-	public static final String EXTRACTED_FEATURES = MINING_INPUT + "ExtractedFeatures/"; // Extracted features of all edit scripts.
-	public static final String CLUSTER_INPUT = MINING_INPUT + "ClusteringInput/input.arff";
-
-	// the output path of fix patterns mining.
-	private static final String MINING_OUTPUT = ROOT_PATH + "MiningOutput/";
-	public static final String CLUSTER_OUTPUT = MINING_OUTPUT + "ClusteringOutput/clusterResults.list";
-	public static final String CLUSTERED_PATCHES_FILE = MINING_OUTPUT + "ClusteredPatches/";
-	public static final String CLUSTERED_TOKENSS_FILE = MINING_OUTPUT + "ClusteredTokens/"; // Token vectors of buggy source code.
-	public static final String COMMON_CLUSTERS_SIZES = MINING_OUTPUT + "ClusteringOutput/CommonClusterSizes.list";
-	
-	// evaluation data
-	public static final String TEST_INPUT = ROOT_PATH + "TestProjects/";
-	public static final String TEST_POSITION_FILE = ROOT_PATH + "TestData/Positions/"; // Positions of all test statements.
-	public static final String TEST_DATA_FILE = ROOT_PATH + "TestData/TestStatements/"; // Token vectors of all test statements.
-	
-	public static final String NUMBER_OF_TRAINING_DATA = ROOT_PATH + "TestData/NumberOfTrainingData.list";;
-	
-	// data of unsupervised learning
-	public static final String EMBEDDING_DATA_TOKENS1 = ROOT_PATH + "TestData/AllTokenVectorsForEvaluation.list";
-	public static final String EMBEDDED_ALL_TOKENS1 = ROOT_PATH + "TestData/AllEmbeddedTokens.list";
-	public static final String VECTORIED_ALL_SOURCE_CODE1 = ROOT_PATH + "TestData/AllVectorizedSourceCode/";
-	public static final String EXTRACTED_FEATURES_EVALUATION = ROOT_PATH + "TestDataExtractedFeatures/"; // extracted features of all source code (training data and testing data)
-	
-	// Data of supervised learning
-	public static final String CLUSTERNUMBER_LABEL_MAP = ROOT_PATH + "TestData/clusterMappingLabel.list";
-	public static final String EMBEDDING_DATA_TOKENS2 = ROOT_PATH + "TestData/AllTokenVectorsForSupervisedEvaluation.list";
-	public static final String EMBEDDED_ALL_TOKENS2 = ROOT_PATH + "TestData/AllEmbeddedTokensForSuperVisedEvaluation.list";
-	public static final String TRAINING_DATA = ROOT_PATH + "TestData/TrainingData.csv"; // Training data of supervised learning
-	public static final String TESTING_DATA = ROOT_PATH + "TestData/SupervisedLearning/"; // testing data of supervised learning
-	public static final String FEATURES_OF_TRAINING_DATA = ROOT_PATH + "TestingOutput/TraingFeatures/";
-	public static final String FEATURES_OF_TESTING_DATA = ROOT_PATH + "TestingOutput/TestingFeatures/";
-	public static final String POSSIBILITIES_OF_TESTING_DATA = ROOT_PATH + "TestingOutput/Posibilities/";
-	public static final String PREDICTED_RESULTS_OF_TESTING_DATA = ROOT_PATH + "TestingOutput/Prediction/";
-
-	public static final String SUPERVISED_LEARNING_MODEL = ROOT_PATH + "TestingOutput/SupervisedLearningModel.zip";
-	
-	public static final String FEATURES_OF_COMMON_CLUSTERS = ROOT_PATH + "FeaturesOfCommonClusters/";
-
 }

src/main/java/edu/lu/uni/serval/defects4j/Bug.java

@@ -1,43 +0,0 @@
-package edu.lu.uni.serval.defects4j;
-
-public class Bug {
-	private String project;
-	
-	private String fileName;
-	
-	private int startLine;
-	
-	private int endLine;
-	
-	private String type;
-	
-	public Bug(String project, String fileName, int startLine, int endLine, String type) {
-		super();
-		this.project = project;
-		this.fileName = fileName;
-		this.startLine = startLine;
-		this.endLine = endLine;
-		this.type = type;
-	}
-
-	public String getProject() {
-		return project;
-	}
-
-	public String getFileName() {
-		return fileName;
-	}
-
-	public int getStartLine() {
-		return startLine;
-	}
-
-	public int getEndLine() {
-		return endLine;
-	}
-
-	public String getType() {
-		return type;
-	}
-	
-}

src/main/java/edu/lu/uni/serval/defects4j/BugParser.java

@@ -1,206 +0,0 @@
-package edu.lu.uni.serval.defects4j;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Scanner;
-
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.FixPatternParser.Tokenizer;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.gumtree.regroup.SimpleTree;
-import edu.lu.uni.serval.gumtree.regroup.SimplifyTree;
-import edu.lu.uni.serval.utils.FileHelper;
-import edu.lu.uni.serval.violation.code.parser.ViolationSourceCodeTree;
-
-public class BugParser {
-	
-	public static void main(String[] args) throws IOException {
-		List<Bug> bugs = new ArrayList<>();
-		String bugsFile = "Dataset/Defects4j/Bugs.txt";
-		String content = FileHelper.readFile(bugsFile);
-		BufferedReader reader = new BufferedReader(new StringReader(content));
-		String line = null;
-		
-		StringBuilder tokensBuilder = new StringBuilder();
-		StringBuilder buggyCodeBuilder = new StringBuilder();
-		while ((line = reader.readLine()) != null) {
-			String[] elements = line.split(" : ");
-			String type = elements[0];
-			String project = elements[1];
-			project = project.substring(0, project.lastIndexOf("."));
-			String fileName = elements[2];
-			int startLine = Integer.parseInt(elements[3]);
-			int endLine = Integer.parseInt(elements[4]);
-			
-			Bug bug = new Bug(project, fileName, startLine, endLine, type);
-			bugs.add(bug);
-		}
-		int i = 0;
-		for (Bug bug : bugs) {
-			String type = bug.getType();
-			String project = bug.getProject();
-			String fileName = bug.getFileName();
-			int startLine = bug.getStartLine();
-			int endLine = bug.getEndLine();
-			File buggyFile = null;
-			
-			String[] elements = project.split("_");
-			if (elements.length < 2) System.out.println(type + "-" + project + "-" + fileName  + "-" + startLine  + "-" + endLine);
-			List<File> javaFiles = FileHelper.getAllFiles(Configuration.ROOT_PATH + "Testing/projects1/" + elements[0] + "/" + elements[1] + "-b", ".java");
-			for (File javaFile : javaFiles) {
-				if (javaFile.getPath().endsWith(fileName)) {
-					buggyFile = javaFile;
-					break;
-				}
-			}
-			if (i == 31) {
-				i = i + 1 - 1;
-			}
-			SimpleTree simpleTree = null;
-			if ("EQ_DOESNT_OVERRIDE_EQUALS".equals(type)|| "HE_EQUALS_USE_HASHCODE".equals(type) || "HE_INHERITS_EQUALS_USE_HASHCODE".equals(type)||
-					"SE_NO_SUITABLE_CONSTRUCTOR".equals(type) || "RI_REDUNDANT_INTERFACES".equals(type)
-//					||"CN_IDIOM_NO_SUPER_CALL".equals(type)
-					||"SE_NO_SERIALVERSIONID".equals(type) || "SE_COMPARATOR_SHOULD_BE_SERIALIZABLE".equals(type)) {
-				ViolationSourceCodeTree parser = new ViolationSourceCodeTree(buggyFile, startLine, endLine);
-				ITree classNameTree = parser.getClassNameTokens();
-				simpleTree = new SimplifyTree().canonicalizeSourceCodeTree(classNameTree, null);
-				
-				startLine = parser.getViolationFinalStartLine();
-				endLine = parser.getViolationFinalEndLine();
-			} else {
-				ViolationSourceCodeTree alarmTree = new ViolationSourceCodeTree(buggyFile, startLine, endLine);
-				alarmTree.extract();
-				List<ITree> matchedTrees = alarmTree.getViolationSourceCodeTrees();
-				if (matchedTrees.size() == 0) {
-					System.err.println("#Null_Violation_Hunk: " + buggyFile.getName() + ":" + startLine + ":" + endLine);
-					continue;
-				}
-				simpleTree = new SimpleTree();
-				simpleTree.setLabel("Block");
-				simpleTree.setNodeType("Block");
-				List<SimpleTree> children = new ArrayList<>();
-				
-				for (ITree matchedTree : matchedTrees) {
-					SimpleTree simpleT = new SimplifyTree().canonicalizeSourceCodeTree(matchedTree, null);
-					children.add(simpleT);
-				}
-				simpleTree.setChildren(children);
-				
-				startLine = alarmTree.getViolationFinalStartLine();
-				endLine = alarmTree.getViolationFinalEndLine();
-			}
-			
-			String tokens = Tokenizer.getTokensDeepFirst(simpleTree);
-			String[] tokensArray = tokens.split(" ");
-			int length = tokensArray.length;
-			System.out.println((++ i) + "==" + length);
-//			sizes += length + "\n";
-//			this.tokens += tokens + "\n";
-			String sourceCode = readSourceCode(buggyFile, startLine, endLine, type);
-//			this.sourceCode += sourceCode + "\n";
-//			tokensBuilder.append(type).append(":").append(tokens).append("\n");
-			tokensBuilder.append(tokens).append("\n");
-			buggyCodeBuilder.append(sourceCode).append("\n");
-		}
-		
-		FileHelper.outputToFile("Dataset/Defects4j/buggyTokens.list", tokensBuilder, false);
-		FileHelper.outputToFile("Dataset/Defects4j/buggySourceCode.list", buggyCodeBuilder, false);
-	}
-	
-	private static String readSourceCode(File javaFile, int startLine, int endLine, String violationType) {
-		StringBuilder sourceCode = new StringBuilder("##Source_Code:\n");
-		sourceCode.append(violationType).append("\n");
-		sourceCode.append(javaFile.getName().replaceAll("#", "/")).append("\nPosition: ").append(startLine).append(" : ").append(endLine).append("\n");
-		FileInputStream fis = null;
-		Scanner scanner = null;
-		
-		try {
-			fis = new FileInputStream(javaFile);
-			scanner = new Scanner(fis);
-			int counter = 0;
-			while (scanner.hasNextLine()) {
-				String line = scanner.nextLine();
-				counter ++;
-				if (startLine <= counter && counter <= endLine) {
-					sourceCode.append(line + "\n");
-				}
-				if (counter == endLine) break;
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				scanner.close();
-				fis.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		
-		return sourceCode.toString();
-	}
-}
-
-
-
-/*
-20
-32
-20
-8
-8
-16
-22
-10
-10
-10
-12
-16
-18
-10
-12
-8
-14
-44
-8
-26
-20
-10
-12
-12
-10
-4
-10
-8
-8
-12
-16
-1776
-8
-10
-10
-12
-8
-50
-18
-8
-12
-38
-4
-4
-14
-16
-20
-26
-8
-14
-12
-14
-*/

src/main/java/edu/lu/uni/serval/diffentry/DiffEntryHunk.java

@@ -1,85 +0,0 @@
-package edu.lu.uni.serval.diffentry;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
-
-public class DiffEntryHunk {
-	
-	private int bugLineStartNum;
-	private int fixLineStartNum;
-	private int bugRange;
-	private int fixRange;
-	private String hunk;
-	private int buggyHunkSize;
-	private int fixedHunkSize;
-	private String file;
-	private List<HierarchicalActionSet> actionSets = new ArrayList<>();
-	
-	public DiffEntryHunk(int bugLineStartNum, int fixLineStartNum, int bugRange, int fixRange) {
-		super();
-		this.bugLineStartNum = bugLineStartNum;
-		this.fixLineStartNum = fixLineStartNum;
-		this.bugRange = bugRange;
-		this.fixRange = fixRange;
-	}
-
-	public int getBugLineStartNum() {
-		return bugLineStartNum;
-	}
-
-	public int getFixLineStartNum() {
-		return fixLineStartNum;
-	}
-
-	public int getBugRange() {
-		return bugRange;
-	}
-
-	public int getFixRange() {
-		return fixRange;
-	}
-
-	public String getHunk() {
-		return hunk;
-	}
-
-	public void setHunk(String hunk) {
-		this.hunk = hunk;
-	}
-
-	public int getBuggyHunkSize() {
-		return buggyHunkSize;
-	}
-
-	public void setBuggyHunkSize(int buggyHunkSize) {
-		this.buggyHunkSize = buggyHunkSize;
-	}
-
-	public int getFixedHunkSize() {
-		return fixedHunkSize;
-	}
-
-	public void setFixedHunkSize(int fixedHunkSize) {
-		this.fixedHunkSize = fixedHunkSize;
-	}
-
-	public String getFile() {
-		return file;
-	}
-
-	public void setFile(String file) {
-		this.file = file;
-	}
-	
-	public List<HierarchicalActionSet> getActionSets() {
-		return actionSets;
-	}
-
-	@Override
-	public String toString() {
-		return "@@ -" + this.bugLineStartNum + ", " + this.bugRange + " +" + this.fixLineStartNum + ", " + this.fixRange + "\n" + this.hunk;
-	}
-
-}

src/main/java/edu/lu/uni/serval/diffentry/DiffEntryReader.java

@@ -1,250 +0,0 @@
-package edu.lu.uni.serval.diffentry;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.regex.Pattern;
-
-import edu.lu.uni.serval.utils.FileHelper;
-
-public class DiffEntryReader {
-	
-	public List<DiffEntryHunk> readHunks(File diffentryFile) {
-		List<DiffEntryHunk> diffentryHunks = new ArrayList<>();
-		String content = FileHelper.readFile(diffentryFile);
-		BufferedReader reader = null;
-		try {
-			reader = new BufferedReader(new StringReader(content));
-			String line = null;
-			int startLine = 0;
-			int range = 0;
-			int startLine2 = 0;
-			int range2 = 0;
-			StringBuilder hunk = new StringBuilder();
-			boolean sourceCode = false;
-			
-			while ((line = reader.readLine()) != null) {
-				if (RegExp.filterSignal(line.trim())) {
-					sourceCode = true;
-					if (hunk.length() > 0) {
-						if ((range < 7 && range2 < 7) || range == 0 || range2 == 0) { // filter out big hunks
-							DiffEntryHunk diffEntryHunk = new DiffEntryHunk(startLine, startLine2, range, range2);
-							diffEntryHunk.setHunk(hunk.toString());
-							diffentryHunks.add(diffEntryHunk);
-						}
-						hunk.setLength(0);
-					}
-					int plusIndex = line.indexOf("+");
-					String lineNum = line.substring(4, plusIndex);
-					String[] nums = lineNum.split(",");
-					startLine = Integer.parseInt(nums[0].trim());
-					if (nums.length == 2) {
-						range = Integer.parseInt(nums[1].trim());
-					}
-					
-					String lineNum2 = line.substring(plusIndex) .trim();
-					lineNum2 = lineNum2.substring(1, lineNum2.length() - 2);
-					String[] nums2 = lineNum2.split(",");
-					startLine2 = Integer.parseInt(nums2[0].trim());
-					if (nums2.length == 2) {
-						range2 = Integer.parseInt(nums2[1].trim());
-					}
-					continue;
-				}
-				if (sourceCode) hunk.append(line + "\n");
-			}
-
-			if ((range < 7 && range2 < 7) || range == 0 || range2 == 0) { // filter out big hunks
-				DiffEntryHunk diffEntryHunk = new DiffEntryHunk(startLine, startLine2, range, range2);
-				diffEntryHunk.setHunk(hunk.toString());
-				diffentryHunks.add(diffEntryHunk);
-			}
-			hunk.setLength(0);
-			
-		} catch (IOException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				if (reader != null) {
-					reader.close();
-					reader = null;
-				}
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		
-		return diffentryHunks;
-	}
-
-	/**
-	 * Read all hunks without considering their sizes.
-	 * 
-	 * @param diffentryFile
-	 * @return
-	 */
-	public List<DiffEntryHunk> readHunks2(File diffentryFile) {
-		List<DiffEntryHunk> diffentryHunks = new ArrayList<>();
-		String content = FileHelper.readFile(diffentryFile);
-		BufferedReader reader = null;
-		try {
-			reader = new BufferedReader(new StringReader(content));
-			String line = null;
-			int startLine = 0;
-			int range = 0;
-			int startLine2 = 0;
-			int range2 = 0;
-			StringBuilder hunk = new StringBuilder();
-			boolean sourceCode = false;
-			
-			while ((line = reader.readLine()) != null) {
-				if (RegExp.filterSignal(line.trim())) {
-//					line = Pattern.compile("^@@\\s\\-\\d+,*\\d*\\s\\+\\d+,*\\d*\\s@@").split(line)[1];
-					sourceCode = true;
-					if (hunk.length() > 0) {
-						if (startLine > 0) {
-							DiffEntryHunk diffEntryHunk = new DiffEntryHunk(startLine, startLine2, range, range2);
-							diffEntryHunk.setHunk(hunk.toString());
-							diffentryHunks.add(diffEntryHunk);
-						}
-						hunk.setLength(0);
-					}
-					int plusIndex = line.indexOf("+");
-					String lineNum = line.substring(4, plusIndex);
-					String[] nums = lineNum.split(",");
-					startLine = Integer.parseInt(nums[0].trim());
-					if (nums.length == 2) {
-						range = Integer.parseInt(nums[1].trim());
-					}
-					
-					String lineNum2 = line.substring(plusIndex) .trim();
-					lineNum2 = lineNum2.substring(1, lineNum2.length() - 2);
-					String[] nums2 = lineNum2.split(",");
-					startLine2 = Integer.parseInt(nums2[0].trim());
-					if (nums2.length == 2) {
-						range2 = Integer.parseInt(nums2[1].trim());
-					}
-					continue;
-				}
-				if (sourceCode) hunk.append(line + "\n");
-			}
-
-			if (startLine > 0) {
-				DiffEntryHunk diffEntryHunk = new DiffEntryHunk(startLine, startLine2, range, range2);
-				diffEntryHunk.setHunk(hunk.toString());
-				diffentryHunks.add(diffEntryHunk);
-			}
-			hunk.setLength(0);
-			
-		} catch (IOException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				if (reader != null) {
-					reader.close();
-					reader = null;
-				}
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		
-		return diffentryHunks;
-	}
-
-	/**
-	 * Read all hunks with pure deleted lines and added lines.
-	 * 
-	 * @param diffentryFile
-	 * @return
-	 */
-	public List<DiffEntryHunk> readHunks3(File diffentryFile) {
-		List<DiffEntryHunk> diffentryHunks = new ArrayList<>();
-		String content = FileHelper.readFile(diffentryFile);
-		BufferedReader reader = null;
-		try {
-			reader = new BufferedReader(new StringReader(content));
-			String line = null;
-			int buggyStartLine = 0;
-			int buggyRange = 0;
-			int fixedStartLine = 0;
-			int fixedRange = 0;
-			int buggyHunkSize = 0;
-			int fixedHunkSize = 0;
-			StringBuilder hunk = new StringBuilder();
-			boolean sourceCode = false;
-			
-			while ((line = reader.readLine()) != null) {
-				if (RegExp.filterSignal(line.trim())) {
-					sourceCode = true;
-					if (hunk.length() > 0) {
-						if (buggyStartLine > 0) {
-							DiffEntryHunk diffEntryHunk = new DiffEntryHunk(buggyStartLine, fixedStartLine, buggyRange, fixedRange);
-							diffEntryHunk.setHunk(hunk.toString());
-							diffEntryHunk.setBuggyHunkSize(buggyHunkSize);
-							diffEntryHunk.setFixedHunkSize(fixedHunkSize);
-							diffEntryHunk.setFile(diffentryFile.getPath());
-							diffentryHunks.add(diffEntryHunk);
-						}
-						hunk.setLength(0);
-						buggyStartLine = 0;
-						buggyRange = 0;
-						fixedStartLine = 0;
-						fixedRange = 0;
-						buggyHunkSize = 0;
-						fixedHunkSize = 0;
-					}
-					int plusIndex = line.indexOf("+");
-					String lineNum = line.substring(4, plusIndex);
-					String[] nums = lineNum.split(",");
-					buggyStartLine = Integer.parseInt(nums[0].trim());
-					if (nums.length == 2) {
-						buggyRange = Integer.parseInt(nums[1].trim());
-					}
-					
-					String lineNum2 = line.substring(plusIndex) .trim();
-					lineNum2 = lineNum2.substring(1, lineNum2.length() - 2);
-					String[] nums2 = lineNum2.split(",");
-					fixedStartLine = Integer.parseInt(nums2[0].trim());
-					if (nums2.length == 2) {
-						fixedRange = Integer.parseInt(nums2[1].trim());
-					}
-					continue;
-				} else if (sourceCode) {
-					if (line.startsWith("-")) {
-						buggyHunkSize ++;
-					} else if (line.startsWith("+")) {
-						fixedHunkSize ++;
-					}
-					hunk.append(line + "\n");
-				}
-			}
-
-			if (buggyStartLine > 0 && hunk.length() > 0) {
-				DiffEntryHunk diffEntryHunk = new DiffEntryHunk(buggyStartLine, fixedStartLine, buggyRange, fixedRange);
-				diffEntryHunk.setHunk(hunk.toString());
-				diffEntryHunk.setBuggyHunkSize(buggyHunkSize);
-				diffEntryHunk.setFixedHunkSize(fixedHunkSize);
-				diffEntryHunk.setFile(diffentryFile.getPath());
-				diffentryHunks.add(diffEntryHunk);
-				hunk.setLength(0);
-			}
-		} catch (IOException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				if (reader != null) {
-					reader.close();
-					reader = null;
-				}
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		
-		return diffentryHunks;
-	}
-}

src/main/java/edu/lu/uni/serval/diffentry/RegExp.java

@@ -1,20 +0,0 @@
-package edu.lu.uni.serval.diffentry;
-
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class RegExp {
-	private static final String REGULAR_EXPRESSION = "^@@\\s\\-\\d+,*\\d*\\s\\+\\d+,*\\d*\\s@@$"; //@@ -21,0 +22,2 @@
-	private static Pattern pattern = Pattern.compile(REGULAR_EXPRESSION);
-	
-	public static boolean filterSignal(String string) {
-		boolean flag = false;
-
-		Matcher res = pattern.matcher(string);
-		if (res.matches()) {
-			flag = true;
-		}
-		
-		return flag;
-	}
-}

src/main/java/edu/lu/uni/serval/fixminer/EnhancedASTDiff.java

@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.FixPatternParser.violations;
+package edu.lu.uni.serval.fixminer;
 
 import akka.actor.ActorRef;
 import akka.actor.ActorSystem;
@@ -16,10 +16,10 @@ import java.util.List;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-public class TestHunkParser {
+public class EnhancedASTDiff {
+
+	private static Logger log = LoggerFactory.getLogger(EnhancedASTDiff.class);
 
-	private static Logger log = LoggerFactory.getLogger(TestHunkParser.class);
-//	public static void main(String[] args) {
 	public static void main(String inputPath, String outputPath,String numOfWorkers,String project) {
 
 
@@ -44,29 +44,13 @@ public class TestHunkParser {
                 continue;
 
             String GUM_TREE_OUTPUT = outputPath + "/"+  pjName + "/";
-//            final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts.list";
-//            final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode.list";
-//            final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens.list";
-//            final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes.csv";
-//            final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes.list";
-
 
 			FileHelper.createDirectory(GUM_TREE_OUTPUT + "/UPD");
 			FileHelper.createDirectory(GUM_TREE_OUTPUT + "/INS");
 			FileHelper.createDirectory(GUM_TREE_OUTPUT + "/DEL");
 			FileHelper.createDirectory(GUM_TREE_OUTPUT + "/MOV");
 			FileHelper.createDirectory(GUM_TREE_OUTPUT + "/ALL");
-//            FileHelper.deleteDirectory(editScriptsFilePath);
-//            FileHelper.deleteDirectory(patchesSourceCodeFilePath);
-//            FileHelper.deleteDirectory(buggyTokensFilePath);
-//            FileHelper.deleteDirectory(editScriptSizesFilePath);
-//            FileHelper.deleteDirectory(alarmTypesFilePath);
 
-//            StringBuilder astEditScripts = new StringBuilder();
-//            StringBuilder tokens = new StringBuilder();
-//            StringBuilder sizes = new StringBuilder();
-//            StringBuilder patches = new StringBuilder();
-//            StringBuilder alarmTypes = new StringBuilder();
 
             int a = 0;
 
@@ -76,7 +60,7 @@ public class TestHunkParser {
 			try {
 				log.info("Akka begins...");
 				system = ActorSystem.create("Mining-FixPattern-System");
-				System.out.println(system.settings());
+
 				parsingActor = system.actorOf(ParseFixPatternActor.props(Integer.valueOf(numOfWorkers), project), "mine-fix-pattern-actor");
 				parsingActor.tell(msg, ActorRef.noSender());
 			} catch (Exception e) {
@@ -84,20 +68,6 @@ public class TestHunkParser {
 				e.printStackTrace();
 			}
 
-
-//            FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true);
-//            FileHelper.outputToFile(buggyTokensFilePath, tokens, true);
-//            FileHelper.outputToFile(editScriptSizesFilePath, sizes, true);
-//            FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true);
-//            FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true);
-//            astEditScripts.setLength(0);
-//            tokens.setLength(0);
-//            sizes.setLength(0);
-//            patches.setLength(0);
-//            alarmTypes.setLength(0);
-//            System.out.println(a);
-
-//		classifyByAlarmTypes();
         }
 	}
 	
@@ -109,16 +79,15 @@ public class TestHunkParser {
 		List<MessageFile> msgFiles = new ArrayList<>();
         if (revFiles.length >= 0) {
             for (File revFile : revFiles) {
-//			if (revFile.getName().endsWith(".java")) {
                 String fileName = revFile.getName();
                 File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file
                 fileName = fileName.replace(".java", ".txt");
                 File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file
-//                File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file
+
                 MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile);
-//                msgFile.setPositionFile(positionFile);
+
                 msgFiles.add(msgFile);
-//			}
+
             }
 
             return msgFiles;

src/main/java/edu/lu/uni/serval/fixminer/Launcher.java

@@ -1,6 +1,5 @@
 package edu.lu.uni.serval.fixminer;
 
-import edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser;
 import edu.lu.uni.serval.fixminer.cluster.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -27,34 +26,34 @@ public class Launcher {
         appProps.load(new FileInputStream(appConfigPath));
 
         String portInner = appProps.getProperty("portInner","6380");
-        String serverWait = appProps.getProperty("serverWait", "50000");
+//        String serverWait = appProps.getProperty("serverWait", "50000");
         String numOfWorkers = appProps.getProperty("numOfWorkers", "10");
         String jobType = appProps.getProperty("jobType","ALL");
         String portDumps = appProps.getProperty("portDumps","6399");
         String pythonPath = appProps.getProperty("pythonPath","/Users/anilkoyuncu/bugStudy/code/python");
         String datasetPath = appProps.getProperty("datasetPath","/Users/anilkoyuncu/bugStudy/dataset");
         String pjName = appProps.getProperty("pjName","allDataset");
-        String dbNo = appProps.getProperty("dbNo","0");
+//        String dbNo = appProps.getProperty("dbNo","0");
         String actionType = appProps.getProperty("actionType","ALL");
         String threshold = appProps.getProperty("threshold","1");
         String cursor = appProps.getProperty("cursor","10000000");
         String chunk = appProps.getProperty("chunk","1.txt");
 
         String parameters = String.format("\nportInner %s " +
-                "\nserverWait %s \nnumOfWorkers %s " +
+                "\nnumOfWorkers %s " +
                 "\njobType %s \nport %s " +
                 "\npythonPath %s \ndatasetPath %s" +
-                "\npjName %s \ndbNo %s \nactionType %s \nthreshold %s \ncursor %s"
+                "\npjName %s \nactionType %s \nthreshold %s \ncursor %s"
-                , portInner, serverWait, numOfWorkers, jobType, portDumps, pythonPath,datasetPath,pjName,dbNo,actionType,threshold,cursor);
+                , portInner,  numOfWorkers, jobType, portDumps, pythonPath,datasetPath,pjName,actionType,threshold,cursor);
 
         log.info(parameters);
 
-        mainLaunch(portInner, serverWait, numOfWorkers, jobType, portDumps, pythonPath,datasetPath,pjName,dbNo,actionType,threshold,cursor,chunk);
+        mainLaunch(portInner,  numOfWorkers, jobType, portDumps, pythonPath,datasetPath,pjName,actionType,threshold,cursor,chunk);
 
 
     }
 
-    public static void mainLaunch(String portInner, String serverWait, String numOfWorkers, String jobType, String portDumps, String pythonPath, String datasetPath, String pjName, String dbNo, String actionType, String threshold, String cursor, String chunk){
+    public static void mainLaunch(String portInner, String numOfWorkers, String jobType, String portDumps, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String cursor, String chunk){
 
 
         String dbDir;
@@ -72,43 +71,35 @@ public class Launcher {
         try {
             switch (jobType) {
                 case "ENHANCEDASTDIFF":
-                    TestHunkParser.main(gumInput, gumOutput, numOfWorkers, pjName);
+                    EnhancedASTDiff.main(gumInput, gumOutput, numOfWorkers, pjName);
                     break;
                 case "CACHE":
-                    StoreFile.main(gumOutput, portDumps, serverWait, dbDir, actionType+dumpsName,actionType);
+                    StoreEDiffInCache.main(gumOutput, portDumps, dbDir, actionType+dumpsName,actionType);
                     break;
-                case "COMP":
+                case "SI":
-                    CalculatePairs.main(serverWait, dbDir, actionType+dumpsName, portDumps, pairsPath+actionType, pjName+actionType);
+                    CalculatePairs.main(dbDir, actionType+dumpsName, portDumps, pairsPath+actionType, pjName+actionType);
-
+                    ImportPairs2DB.main(pairsPath+actionType, portInner, dbDir,datasetPath);
-                    ImportPairs2DB.main(pairsPath+actionType, portInner, serverWait, dbDir,datasetPath);
                     break;
-                case "AKKA":
+                case "SIMI":
-                    AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+chunk+".rdb" , portDumps, actionType+dumpsName,pairsPath+actionType,numOfWorkers,cursor);
+                    AkkaTreeLoader.main(portInner,  dbDir, pjName +actionType+chunk+".rdb" , portDumps, actionType+dumpsName,pairsPath+actionType,numOfWorkers,cursor,chunk);
                     break;
 
                 case "LEVEL1":
-                    level1(portInner, serverWait, portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput);
+                    level1(portInner, portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput);
                     break;
                 //CALC python abstractPatch.py to from cluster folder
                 case "LEVEL2":
-                    level2(serverWait, portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput);
+                    level2(portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput);
                     break;
                 //CALC via python
                 case "LEVEL3":
-                    level3(serverWait, portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput);
+                    level3(portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput);
-                    break;
-                case "ALL":
-//                    TestHunkParser.main(gumInput, gumOutput, numOfWorkers, pjName);
-//                    StoreFile.main(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType);
-//                    level1(portInner, serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput);
-//                    level2(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput);
-//                    level3(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput);
                     break;
                 case "EXTRACTPATTERN":
-                    PatternExtractor.mainLaunch(portInner,serverWait,numOfWorkers,jobType,portDumps,pythonPath,datasetPath,pjName,dbNo,actionType,threshold);
+                    PatternExtractor.mainLaunch(portInner,numOfWorkers,jobType,portDumps,pythonPath,datasetPath,pjName,actionType,threshold);
                     break;
                 case "GETPATTERN":
-                    PatternExtractor.mainLaunch(portInner,serverWait,numOfWorkers,jobType,portDumps,pythonPath,datasetPath,pjName,dbNo,actionType,threshold);
+                    PatternExtractor.mainLaunch(portInner,numOfWorkers,jobType,portDumps,pythonPath,datasetPath,pjName,actionType,threshold);
                     break;
             }
         } catch (Exception e) {
@@ -120,63 +111,63 @@ public class Launcher {
 
         }
 
-    private static void level1(String portInner, String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String pairsPath, String dumpsName, String gumInput) throws Exception {
+    private static void level1(String portInner, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String pairsPath, String dumpsName, String gumInput) throws Exception {
 
 
-        TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ actionType+".rdb", dbDir ,pjName + actionType);
+        TreeLoaderClusterL1.main(portInner, port, dbDir, "level1-"+pjName+ actionType+".rdb", dbDir ,pjName + actionType);
 
         CallShell cs1 =new CallShell();
         String db1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
         String db11 = String.format(db1, dbDir,"level1-"+pjName+ actionType+".rdb" ,Integer.valueOf(port));
-        cs1.runShell(db11,serverWait, port);
+        cs1.runShell(db11, port);
         String runpy =  "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s";
         String formatRunPy = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ actionType, port, "matches" + pjName + actionType, threshold);
 
         cs1.runShell(formatRunPy);
         String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s";
         stopServer = String.format(stopServer,Integer.valueOf(port));
-        cs1.runShell(stopServer,serverWait, port);
+        cs1.runShell(stopServer, port);
     }
 
-    private static void level2(String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String dumpsName, String gumInput) throws Exception {
+    private static void level2(String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String dumpsName, String gumInput) throws Exception {
         String stopServer;
         MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ actionType, datasetPath,actionType);
 
-        MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairs"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",serverWait,actionType);
+        MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairs"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",actionType);
 
         CallShell cs3 =new CallShell();
         String db22 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
         String db1b = String.format(db22, dbDir,"clusterl1-"+pjName+actionType+".rdb",Integer.valueOf(port));
-        cs3.runShell(db1b,serverWait, port);
+        cs3.runShell(db1b, port);
         String runpy2 =  "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s";
         String formatRunPy1a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ actionType, port, datasetPath + "/cluster-2l"+pjName+ actionType,threshold);
 
         cs3.runShell(formatRunPy1a);
         String stopServer1a = "bash "+dbDir + "/" + "stopServer.sh" +" %s";
         stopServer = String.format(stopServer1a,Integer.valueOf(port));
-        cs3.runShell(stopServer,serverWait, port);
+        cs3.runShell(stopServer, port);
     }
 
-    private static void level3(String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String dumpsName, String gumInput) throws Exception {
+    private static void level3(String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String dumpsName, String gumInput) throws Exception {
         String stopServer;
         MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ actionType, datasetPath,actionType);
 
-        MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2l"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",serverWait,actionType);
+        MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2l"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",actionType);
 
         CallShell cs5 =new CallShell();
         String dba = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
         String dbaa = String.format(dba, dbDir,"clusterl2-"+pjName+actionType+".rdb",Integer.valueOf(port));
-        cs5.runShell(dbaa,serverWait, port);
+        cs5.runShell(dbaa, port);
         String runpya =  "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s";
         String formatRunPya = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ actionType, port, datasetPath + "/cluster-2l"+pjName+ actionType,threshold);
 
         cs5.runShell(formatRunPya);
         String stopServera = "bash "+dbDir + "/" + "stopServer.sh" +" %s";
         stopServer = String.format(stopServera,Integer.valueOf(port));
-        cs5.runShell(stopServer,serverWait, port);
+        cs5.runShell(stopServer, port);
         return;
     }
-//        System.exit(1);
+
 }
 
 

src/main/java/edu/lu/uni/serval/fixminer/PatternExtractor.java

@@ -1,7 +1,5 @@
 package edu.lu.uni.serval.fixminer;
 
-import com.github.gumtreediff.tree.ITree;
-import com.github.gumtreediff.tree.TreeContext;
 import edu.lu.uni.serval.FixPattern.utils.Checker;
 import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
 import org.slf4j.Logger;
@@ -21,7 +19,6 @@ import java.util.List;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.getASTTree;
 
 /**
  * Created by anilkoyuncu on 02/08/2018.
@@ -30,7 +27,7 @@ public class PatternExtractor {
     private static Logger log = LoggerFactory.getLogger(PatternExtractor.class);
 
 
-    public static void mainLaunch(String portInner,String serverWait, String numOfWorkers,String jobType,String port, String pythonPath, String datasetPath, String pjName, String dbNo, String actionType,String threshold) {
+    public static void mainLaunch(String portInner,String numOfWorkers,String jobType,String port, String pythonPath, String datasetPath, String pjName, String actionType,String threshold) {
 
 
         String dbDir;
@@ -55,7 +52,7 @@ public class PatternExtractor {
 
             switch (jobType) {
                 case "EXTRACTPATTERN":
-                    loadDB(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType,fixes);
+                    loadDB(gumOutput, portInner, dbDir, actionType+dumpsName,actionType,fixes);
                     break;
                 case "GETPATTERN":
                     getPattern(fixes,actionType);
@@ -67,7 +64,7 @@ public class PatternExtractor {
     }
 
 
-    public static void loadDB(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String operation,List<String> fixes) throws Exception {
+    public static void loadDB(String inputPath,String portInner,String dbDir,String chunkName,String operation,List<String> fixes) throws Exception {
 //        String inputPath;
 //        String portInner;
 //        String serverWait;
@@ -246,24 +243,24 @@ public class PatternExtractor {
         }
     }
 
-    public static ITree getSimpliedTree(HierarchicalActionSet actionSet) {
+//    public static ITree getSimpliedTree(HierarchicalActionSet actionSet) {
-
+//
-        ITree tree = null;
+//        ITree tree = null;
-        Jedis inner = null;
+//        Jedis inner = null;
-        try {
+//        try {
-
+//
-            ITree parent = null;
+//            ITree parent = null;
-            ITree children = null;
+//            ITree children = null;
-            TreeContext tc = new TreeContext();
+//            TreeContext tc = new TreeContext();
-            tree = getASTTree(actionSet, parent, children, tc);
+//            tree = getASTTree(actionSet, parent, children, tc);
-//            tree.setParent(null);
+////            tree.setParent(null);
-            tc.validate();
+//            tc.validate();
-
+//
-        } catch (Exception e) {
+//        } catch (Exception e) {
-            e.printStackTrace();
+//            e.printStackTrace();
-        }
+//        }
-        return tree;
+//        return tree;
-    }
+//    }
 
 
 

src/main/java/edu/lu/uni/serval/fixminer/TestHunkParserSingleFile.java

@@ -1,20 +1,18 @@
-package edu.lu.uni.serval.FixPatternParser.violations;
+package edu.lu.uni.serval.fixminer;
 
 import akka.actor.ActorRef;
 import akka.actor.ActorSystem;
 import edu.lu.uni.serval.MultipleThreadsParser.MessageFile;
 import edu.lu.uni.serval.MultipleThreadsParser.ParseFixPatternActor;
 import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage;
-import edu.lu.uni.serval.config.Configuration;
 import edu.lu.uni.serval.utils.FileHelper;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.File;
-import java.io.FileInputStream;
+import java.util.ArrayList;
-import java.io.FileNotFoundException;
+import java.util.Arrays;
-import java.io.IOException;
+import java.util.List;
-import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -232,131 +230,10 @@ public class TestHunkParserSingleFile {
 //		}
 	}
 	
-	public static void classifyByAlarmTypes() {
 
-		final String alarmTypesFilePath = Configuration.ALARM_TYPES_FILE;
-		List<String> alarmTypes = readStringList(alarmTypesFilePath);
-		//edit scripts, sizes of edit scripts, buggy tokens, patches.
-		classifyByAlarmTypes(alarmTypes, Configuration.EDITSCRIPT_SIZES_FILE);
-		classifyByAlarmTypes(alarmTypes, Configuration.EDITSCRIPTS_FILE);
-		classifyByAlarmTypes(alarmTypes, Configuration.BUGGY_CODE_TOKENS_FILE);
-		classifyByAlarmTypes2(alarmTypes, Configuration.PATCH_SOURCECODE_FILE);
-	}
 
-	private static void classifyByAlarmTypes(List<String> alarmTypes, String file) {
-		Map<String, StringBuilder> buildersMap = new HashMap<>();
-		FileInputStream fis = null;
-		Scanner scanner = null;
-		try {
-			fis = new FileInputStream(file);
-			scanner = new Scanner(fis);
-			int counter = 0;
-			while (scanner.hasNextLine()) {
-				String alarmType = alarmTypes.get(counter);
-				StringBuilder builder = getBuilder(buildersMap, alarmType);
-				builder.append(scanner.nextLine() + "\n");
-				counter ++;
-				if (counter % 1000 == 0) {
-					outputBuilders(buildersMap, file);
-				}
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				scanner.close();
-				fis.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		outputBuilders(buildersMap, file);
-	}
 
-	private static void classifyByAlarmTypes2(List<String> alarmTypes, String patchSourcecodeFile) {
-		Map<String, StringBuilder> buildersMap = new HashMap<>();
-		FileInputStream fis = null;
-		Scanner scanner = null;
-		try {
-			fis = new FileInputStream(patchSourcecodeFile);
-			scanner = new Scanner(fis);
-			int counter = 0;
-			String singlePatch = "";
-			while (scanner.hasNextLine()) {
-				String line = scanner.nextLine();
-				if (Configuration.PATCH_SIGNAL.equals(line)) {
-					if (!"".equals(singlePatch)) {
-						String alarmType = alarmTypes.get(counter);
-						StringBuilder builder = getBuilder(buildersMap, alarmType);
-						builder.append(scanner.nextLine() + "\n");
-						counter ++;
-						if (counter % 2000 == 0) {
-							outputBuilders(buildersMap, patchSourcecodeFile);
-						}
-					}
-					singlePatch = line + "\n";
-				}
-				singlePatch += line + "\n";
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				scanner.close();
-				fis.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
 
-		outputBuilders(buildersMap, patchSourcecodeFile);
-	}
 
-	private static void outputBuilders(Map<String, StringBuilder> map, String fileNameStr) {
-		File file = new File(fileNameStr);
-		String fileName = file.getName();
-		String parentPath = file.getParent();
-		for (Map.Entry<String, StringBuilder> entry : map.entrySet()) {
-			String alarmType = entry.getKey();
-			StringBuilder builder = entry.getValue();
 
-			FileHelper.outputToFile(parentPath + "/" + alarmType + "/" + fileName, builder, true);
-			
-			builder.setLength(0);
-			entry.setValue(builder);
-		}
-	}
-
-	public static List<String> readStringList(String inputFile) {
-		List<String> list = new ArrayList<>();
-		FileInputStream fis = null;
-		Scanner scanner = null;
-		try {
-			fis = new FileInputStream(inputFile);
-			scanner = new Scanner(fis);
-			while(scanner.hasNextLine()) {
-				list.add(scanner.nextLine());
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				scanner.close();
-				fis.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		return list;
-	}
-
-	private static StringBuilder getBuilder(Map<String, StringBuilder> buildersMap, String alarmType) {
-		if (buildersMap.containsKey(alarmType)) {
-			return buildersMap.get(alarmType);
-		} else {
-			StringBuilder builder = new StringBuilder();
-			buildersMap.put(alarmType, builder);
-			return builder;
-		}
-	}
 }

src/main/java/edu/lu/uni/serval/fixminer/TestTreeLoader.java

@@ -1,15 +1,16 @@
-package edu.lu.uni.serval.FixPatternParser.violations;
+package edu.lu.uni.serval.fixminer;
 
 import com.github.gumtreediff.actions.ActionGenerator;
 import com.github.gumtreediff.actions.model.Action;
-import com.github.gumtreediff.matchers.Mapping;
 import com.github.gumtreediff.matchers.Matcher;
 import com.github.gumtreediff.matchers.Matchers;
 import com.github.gumtreediff.tree.ITree;
-import edu.lu.uni.serval.gumtree.regroup.SimplifyTree;
 
 import java.io.*;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -132,98 +133,98 @@ public class TestTreeLoader {
 
 
     }
-    public static void compareAll(List<File> folders){
+//    public static void compareAll(List<File> folders){
-        List<ITree> trees = new ArrayList<>();
+//        List<ITree> trees = new ArrayList<>();
-        HashMap<Integer, String> hmap = new HashMap<Integer, String>();
+//        HashMap<Integer, String> hmap = new HashMap<Integer, String>();
-        for (File target : folders) {
+//        for (File target : folders) {
-
+//
-            try {
+//            try {
-                FileInputStream fi = new FileInputStream(new File(target.toString()));
+//                FileInputStream fi = new FileInputStream(new File(target.toString()));
-                ObjectInputStream oi = new ObjectInputStream(fi);
+//                ObjectInputStream oi = new ObjectInputStream(fi);
-                ITree pr1 = (ITree) oi.readObject();
+//                ITree pr1 = (ITree) oi.readObject();
-                oi.close();
+//                oi.close();
-                fi.close();
+//                fi.close();
-                trees.add(pr1);
+//                trees.add(pr1);
-                hmap.put(folders.indexOf(target), target.toString());
+//                hmap.put(folders.indexOf(target), target.toString());
-
+//
-            } catch (FileNotFoundException e) {
+//            } catch (FileNotFoundException e) {
-                System.out.println("File not found");
+//                System.out.println("File not found");
-            } catch (IOException e) {
+//            } catch (IOException e) {
-                System.out.println("Error initializing stream");
+//                System.out.println("Error initializing stream");
-            } catch (ClassNotFoundException e) {
+//            } catch (ClassNotFoundException e) {
-                // TODO Auto-generated catch block
+//                // TODO Auto-generated catch block
-                e.printStackTrace();
+//                e.printStackTrace();
-            }
+//            }
-        }
+//        }
-
+//
-        for (ITree tree : trees) {
+//        for (ITree tree : trees) {
-//            SimplifyTree simplifyTree = new SimplifyTree();
+////            SimplifyTree simplifyTree = new SimplifyTree();
-//            simplifyTree.canonicalizeSourceCodeTree(tree);
+////            simplifyTree.canonicalizeSourceCodeTree(tree);
-            tree.setLabel("");
+//            tree.setLabel("");
-            tree.setParent(null);
+//            tree.setParent(null);
-            List<ITree> descendants = tree.getDescendants();
+//            List<ITree> descendants = tree.getDescendants();
-            for (ITree descendant : descendants) {
+//            for (ITree descendant : descendants) {
-                descendant.setLabel("");
+//                descendant.setLabel("");
-            }
+//            }
-
-        }
-        System.out.println("a");
-
-        try {
-
-
-
-            for (int i = 0; i < trees.size(); i++) {
-                for (int j = i + 1; j < trees.size(); j++) {
-                    // compare list.get(i) and list.get(j)
-                    BufferedWriter writer = new BufferedWriter(new FileWriter("output.txt",true));
-                    ITree oldTree = trees.get(i);
-
-                    ITree newTree = trees.get(j);
-
-                    Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree);
-                    m.match();
-
-                    ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings());
-                    ag.generate();
-                    List<Action> actions = ag.getActions();
-                    writer.write(String.valueOf(i));
-                    writer.write("\t");
-                    writer.write(String.valueOf(j));
-                    writer.write("\t");
-
-                    writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree)));
-                    writer.write("\t");
-                    writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree)));
-                    writer.write("\t");
-                    writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree)));
-                    writer.write("\t");
-                    writer.write(String.valueOf(actions.size()));
-                    writer.write("\t");
-                    writer.write(hmap.get(i));
-                    writer.write("\t");
-                    writer.write(hmap.get(j));
-                    writer.write("\n");
-
-                    writer.close();
-                }
-            }
-
-
-        } catch (FileNotFoundException e) {
-            System.out.println("File not found");
-        } catch (IOException e) {
-            System.out.println("Error initializing stream");
-
-        }
-
-
-//        if (actions.size() > 1) {
-//            Matcher m1 = Matchers.getInstance().getMatcher(actions.get(0).getNode(), actions.get(0).getNode());
-//            m1.match();
-//            Set<Mapping> mappingSet1 = m1.getMappingSet();
 //
 //        }
-    }
+//        System.out.println("a");
+//
+//        try {
+//
+//
+//
+//            for (int i = 0; i < trees.size(); i++) {
+//                for (int j = i + 1; j < trees.size(); j++) {
+//                    // compare list.get(i) and list.get(j)
+//                    BufferedWriter writer = new BufferedWriter(new FileWriter("output.txt",true));
+//                    ITree oldTree = trees.get(i);
+//
+//                    ITree newTree = trees.get(j);
+//
+//                    Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree);
+//                    m.match();
+//
+//                    ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings());
+//                    ag.generate();
+//                    List<Action> actions = ag.getActions();
+//                    writer.write(String.valueOf(i));
+//                    writer.write("\t");
+//                    writer.write(String.valueOf(j));
+//                    writer.write("\t");
+//
+//                    writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree)));
+//                    writer.write("\t");
+//                    writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree)));
+//                    writer.write("\t");
+//                    writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree)));
+//                    writer.write("\t");
+//                    writer.write(String.valueOf(actions.size()));
+//                    writer.write("\t");
+//                    writer.write(hmap.get(i));
+//                    writer.write("\t");
+//                    writer.write(hmap.get(j));
+//                    writer.write("\n");
+//
+//                    writer.close();
+//                }
+//            }
+//
+//
+//        } catch (FileNotFoundException e) {
+//            System.out.println("File not found");
+//        } catch (IOException e) {
+//            System.out.println("Error initializing stream");
+//
+//        }
+//
+//
+////        if (actions.size() > 1) {
+////            Matcher m1 = Matchers.getInstance().getMatcher(actions.get(0).getNode(), actions.get(0).getNode());
+////            m1.match();
+////            Set<Mapping> mappingSet1 = m1.getMappingSet();
+////
+////        }
+//    }
 
 }

src/main/java/edu/lu/uni/serval/fixminer/cluster/AkkaTreeLoader.java

@@ -1,20 +1,17 @@
 package edu.lu.uni.serval.fixminer.cluster;
 
-import com.github.gumtreediff.tree.ITree;
+import edu.lu.uni.serval.FixPattern.utils.PoolBuilder;
-import com.github.gumtreediff.tree.TreeContext;
-import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap;
-import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
-import org.junit.Assert;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import redis.clients.jedis.*;
+import redis.clients.jedis.Jedis;
+import redis.clients.jedis.JedisPool;
 
-import java.io.*;
+import java.io.BufferedReader;
-import java.time.Duration;
+import java.io.FileReader;
-import java.util.*;
+import java.io.IOException;
-import java.util.concurrent.Executors;
+import java.util.HashMap;
-import java.util.function.Consumer;
+import java.util.Map;
-import java.util.stream.Collectors;
+import java.util.regex.Pattern;
 
 import static edu.lu.uni.serval.fixminer.cluster.akka.AkkaTreeParser.akkaCompare;
 
@@ -23,58 +20,13 @@ import static edu.lu.uni.serval.fixminer.cluster.akka.AkkaTreeParser.akkaCompare
  */
 public class AkkaTreeLoader {
 
-    private static class StreamGobbler implements Runnable {
-        private InputStream inputStream;
-        private Consumer<String> consumer;
-
-        public StreamGobbler(InputStream inputStream, Consumer<String> consumer) {
-            this.inputStream = inputStream;
-            this.consumer = consumer;
-        }
-
-        @Override
-        public void run() {
-            new BufferedReader(new InputStreamReader(inputStream)).lines()
-                    .forEach(consumer);
-        }
-    }
-
     private static Logger log = LoggerFactory.getLogger(AkkaTreeLoader.class);
 
 
-    public static void loadRedis(String cmd,String serverWait){
+    public static void main(String portInner, String dbDir, String chunkName, String port, String dumpsName, String pairsPath, String numOfWorkers, String cursor,String chunk) throws Exception {
-        Process process;
-
-        try {
-//            String comd = String.format(cmd, f.getAbsoluteFile());
-            process = Runtime.getRuntime()
-
-                    .exec(cmd);
 
 
-            StreamGobbler streamGobbler =
+        String parameters = String.format("\nportInner %s \nchunkName %s \ndbDir %s \ndumpsName %s",portInner,chunkName,dbDir,dumpsName);
-                    new StreamGobbler(process.getInputStream(), System.out::println);
-            Executors.newSingleThreadExecutor().submit(streamGobbler);
-            int exitCode = process.waitFor();
-            assert exitCode == 0;
-//            Thread.sleep(Integer.valueOf(serverWait));
-
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
-         catch (InterruptedException e) {
-            e.printStackTrace();
-        }
-        log.info("Load done");
-    }
-
-    private static Consumer<String> consumer = Assert::assertNotNull;
-
-
-    public static void main(String portInner, String serverWait, String dbDir, String chunkName, String port, String dumpsName, String pairsPath, String numOfWorkers, String cursor) throws Exception {
-
-
-        String parameters = String.format("\nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s \ndumpsName %s",portInner,serverWait,chunkName,dbDir,dumpsName);
         log.info(parameters);
 
 
@@ -82,243 +34,76 @@ public class AkkaTreeLoader {
         String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
         String cmd1 = String.format(cmd, dbDir,dumpsName,Integer.valueOf(port));
 //
-        cs.runShell(cmd1,serverWait,port);
+        cs.runShell(cmd1,port);
         String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
         String cmd2 = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner));
         log.info(cmd1);
         log.info(cmd2);
 //
-        cs.runShell(cmd2,serverWait, portInner);
+        cs.runShell(cmd2, portInner);
-        JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000);
+        JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(port),20000000);
-        JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000);
+        JedisPool innerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(portInner),20000000);
-
-
-//        Jedis jedis = new Jedis(new URI("redis://localhost:"+port));
-//        while (!jedis.ping().equals("PONG")){
-//            log.info("wait");
-//        }
-//
-//        jedis = new Jedis(new URI("redis://localhost:"+portInner));
-//        while (!jedis.ping().equals("PONG")){
-//            log.info("wait");
-//        }
-
-
-//        String pairsIndexFile = pairsPath + "/"+ chunkName;
-//        pairsIndexFile = pairsIndexFile.replace("csv.rdb","index");
-//
-//
-//        Pattern pattern = Pattern.compile(",");
-//        String csvFile = pairsIndexFile;
-//        try {
-//            try (BufferedReader in = new BufferedReader(new FileReader(csvFile));){
-//                Map<String,String> namefreq = in
-//                        .lines()
-//                        //                                .skip(1)
-//                        .map(x -> pattern.split(x))
-//                        //                                .filter(x -> x[4].equals("CA") && x[3].equals("F"))
-//                        .collect(HashMap::new, (map, x) ->
-//                                        map.put(x[0], x[1]),
-//                                Map::putAll);
-//                //                        namefreq.forEach((k, v) -> System.out.println(k + " => " + v));
-//
-//                Jedis inner = null;
-//                try {
-//                    inner = outerPool.getResource();
-//
-//                    for (Map.Entry<String, String> entry : namefreq.entrySet()) {
-//                        String key = entry.getKey();
-//                        String value = entry.getValue();
-//                        inner.select(1);
-//                        inner.set(key,value);
-//                        // ...
-//                    }
-//
-//
-//                }finally {
-//                    if (inner != null) {
-//                        inner.close();
-//                    }
-//                }
-//
-//
-//            }
-//        } catch (IOException e) {
-//            e.printStackTrace();
-//        }
 
 
 
-//        comparePairs(innerPool,outerPool);
+        String pairsIndexFile = pairsPath + "/"+ chunkName;
-        Thread.sleep(Integer.valueOf(serverWait));
+        //0.txt.rdb
-        akkaCompare(innerPool,outerPool,numOfWorkers,cursor);
+        pairsIndexFile = pairsIndexFile.replace(chunk+".rdb",".index");
-
-//        String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s";
-//        String stopServer1 = String.format(stopServer,Integer.valueOf(portInner));
-//
-//        cs.runShell(stopServer1,serverWait);
-//        stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s";
-//        String stopServer2 = String.format(stopServer,Integer.valueOf(port));
-//
-//        cs.runShell(stopServer2,serverWait);
 
 
-    }
+        Pattern pattern = Pattern.compile(",");
+        String csvFile = pairsIndexFile;
+        try {
+            try (BufferedReader in = new BufferedReader(new FileReader(csvFile));){
+                Map<String,String> namefreq = in
+                        .lines()
+                        .map(x -> pattern.split(x))
+                        .collect(HashMap::new, (map, x) ->
+                                        map.put(x[0], x[1]),
+                                Map::putAll);
 
-    public static void comparePairs(JedisPool innerPool,JedisPool outerPool){
+                Jedis inner = null;
+                try {
+                    inner = outerPool.getResource();
 
-
+                    for (Map.Entry<String, String> entry : namefreq.entrySet()) {
-                ScanResult<String> scan;
+                        String key = entry.getKey();
-
+                        String value = entry.getValue();
-                try (Jedis inner = innerPool.getResource()) {
+                        inner.select(1);
-                    while (!inner.ping().equals("PONG")){
+                        inner.set(key,value);
-                        log.info("wait");
                     }
 
-                    ScanParams sc = new ScanParams();
-                    //150000000
-                    log.info("Scanning ");
-                    sc.count(250000000);
 
-                    sc.match("pair_[0-9]*");
+                }finally {
-
+                    if (inner != null) {
-                    scan = inner.scan("0", sc);
+                        inner.close();
-                    int size = scan.getResult().size();
+                    }
-                    log.info("Scanned " + String.valueOf(size));
                 }
-                List<String> result = scan.getResult();
-                log.info("Getting results");
-                result
-                .parallelStream()
-                .forEach(m ->
-                        {
-                            Compare compare = new Compare();
-                            compare.coreCompare(m, innerPool, outerPool);
-                            ;
-                        }
-                );
 
 
-
-
-//            }
-
-
-
-
-    }
-
-    /** Read the object from Base64 string. */
-    private static Object fromString( String s ) throws IOException ,
-            ClassNotFoundException {
-        byte [] data = Base64.getDecoder().decode( s );
-        ObjectInputStream ois = new ObjectInputStream(
-                new ByteArrayInputStream(  data ) );
-        Object o  = ois.readObject();
-        ois.close();
-        return o;
-    }
-    public static ITree getSimpliedTree(String fn,JedisPool outerPool) {
-
-        ITree tree = null;
-        Jedis inner = null;
-        try {
-            inner = outerPool.getResource();
-            while (!inner.ping().equals("PONG")){
-                log.info("wait");
             }
-            inner.select(1);
-            String dist2load = inner.get(fn);
-            inner.select(0);
-            String s = inner.get(dist2load);
-            HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(s);
-
-            ITree parent = null;
-            ITree children =null;
-            TreeContext tc = new TreeContext();
-            tree = getASTTree(actionSet, parent, children,tc);
-            tree.setParent(null);
-            tc.validate();
-
         } catch (IOException e) {
             e.printStackTrace();
-        } catch (ClassNotFoundException e) {
-            e.printStackTrace();
-        }finally {
-            if (inner != null) {
-                inner.close();
-            }
         }
-        return tree;
+
+
+
+
+        akkaCompare(innerPool,outerPool,numOfWorkers,cursor);
+
+
+
 
     }
 
-    public static <T, E> List<T> getKeysByValue(Map<T, E> map, E value) {
-        return map.entrySet()
-                .stream()
-                .filter(entry -> Objects.equals(entry.getValue(), value))
-                .map(Map.Entry::getKey)
-                .collect(Collectors.toList());
-    }
-
-    public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){
-
-        int newType = 0;
-
-        String astNodeType = actionSet.getAstNodeType();
-        List<Integer> keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType);
-
-        if(keysByValue.size() != 1){
-            log.error("More than 1");
-        }
-        newType = keysByValue.get(0);
-        if(actionSet.getParent() == null){
-            //root
-
-//            parent = new Tree(newType,"");
-            parent = tc.createTree(newType, "", null);
-            tc.setRoot(parent);
-        }else{
-//            children = new Tree(newType,"");
-//            parent.addChild(children);
-            children = tc.createTree(newType, "", null);
-            children.setParentAndUpdateChildren(parent);
-        }
-        List<HierarchicalActionSet> subActions = actionSet.getSubActions();
-        if (subActions.size() != 0){
-            for (HierarchicalActionSet subAction : subActions) {
-
-                if(actionSet.getParent() == null){
-                    children = parent;
-                }
-                getASTTree(subAction,children,null,tc);
-
-            }
 
 
-        }
-        return parent;
-    }
 
 
-    static final JedisPoolConfig poolConfig = buildPoolConfig();
 
 
-    private static JedisPoolConfig buildPoolConfig() {
-        final JedisPoolConfig poolConfig = new JedisPoolConfig();
-        poolConfig.setMaxTotal(128);
-        poolConfig.setMaxIdle(128);
-        poolConfig.setMinIdle(16);
-        poolConfig.setTestOnBorrow(false);
-        poolConfig.setTestOnReturn(false);
-        poolConfig.setTestWhileIdle(true);
-        poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis());
-        poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis());
-//        poolConfig.setNumTestsPerEvictionRun(3);
-        poolConfig.setBlockWhenExhausted(true);
 
-        return poolConfig;
+
-    }
 
 
 

src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java

@@ -1,5 +1,6 @@
 package edu.lu.uni.serval.fixminer.cluster;
 
+import edu.lu.uni.serval.FixPattern.utils.PoolBuilder;
 import edu.lu.uni.serval.utils.FileHelper;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -13,7 +14,6 @@ import java.nio.ByteBuffer;
 import java.nio.channels.FileChannel;
 import java.util.List;
 
-import static edu.lu.uni.serval.fixminer.cluster.TreeLoaderClusterL1.poolConfig;
 
 /**
  * Created by anilkoyuncu on 05/04/2018.
@@ -21,21 +21,21 @@ import static edu.lu.uni.serval.fixminer.cluster.TreeLoaderClusterL1.poolConfig;
 public class CalculatePairs {
     private static Logger log = LoggerFactory.getLogger(CalculatePairs.class);
 
-    public static void main(String serverWait,String dbDir,String chunkName,String port,String outputPath,String pjName) throws Exception {
+    public static void main(String dbDir,String chunkName,String port,String outputPath,String pjName) throws Exception {
 
 
-        String parameters = String.format("\nport %s \nserverWait %s \nchunkName %s \ndbDir %s",port,serverWait,chunkName,dbDir);
+        String parameters = String.format("\nport %s \nchunkName %s \ndbDir %s",port,chunkName,dbDir);
         log.info(parameters);
 
         CallShell cs =new CallShell();
         String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
         cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(port));
 
-        cs.runShell(cmd,serverWait, port);
+        cs.runShell(cmd, port);
         FileHelper.createDirectory(outputPath);
 
 
-        JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000);
+        JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(port),20000000);
 
         ScanResult<String> scan;
         try (Jedis outer = outerPool.getResource()) {

src/main/java/edu/lu/uni/serval/fixminer/cluster/CallShell.java

@@ -26,7 +26,7 @@ public class CallShell {
 
     }
 
-    public static void runShell(String command, String serverWait, String port) throws Exception {
+    public static void runShell(String command, String port) throws Exception {
 
         Process process = Runtime.getRuntime().exec(command);
         BufferedReader reader = new BufferedReader(new InputStreamReader(
@@ -101,7 +101,7 @@ try{
     public static void main(String[] args) throws Exception {
 
 //        runPing("redis-cli -p 6380 ping");
-        runShell("bash /Users/anilkoyuncu/bugStudy/release/code/redis/startServer.sh /Users/anilkoyuncu/bugStudy/release/code/redis Defects4JALL0.txt.rdb 6380","1","6380");
+        runShell("bash /Users/anilkoyuncu/bugStudy/release/code/redis/startServer.sh /Users/anilkoyuncu/bugStudy/release/code/redis Defects4JALL0.txt.rdb 6380","6380");
     }
 
 

src/main/java/edu/lu/uni/serval/fixminer/cluster/Compare.java

@@ -5,6 +5,7 @@ import com.github.gumtreediff.actions.model.Action;
 import com.github.gumtreediff.matchers.Matcher;
 import com.github.gumtreediff.matchers.Matchers;
 import com.github.gumtreediff.tree.ITree;
+import edu.lu.uni.serval.FixPattern.utils.EDiff;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import redis.clients.jedis.Jedis;
@@ -13,7 +14,6 @@ import redis.clients.jedis.JedisPool;
 import java.util.List;
 import java.util.Map;
 
-import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.getSimpliedTree;
 
 /**
  * Created by anilkoyuncu on 03/04/2018.
@@ -44,9 +44,9 @@ public class Compare {
 //            String firstValue = resultMap.get("0");
 //            String secondValue = resultMap.get("1");
 
-            oldTree = getSimpliedTree(i,outerPool);
+            oldTree = EDiff.getSimpliedTree(i,outerPool);
 
-            newTree = getSimpliedTree(j,outerPool);
+            newTree = EDiff.getSimpliedTree(j,outerPool);
 
             Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree);
             m.match();

src/main/java/edu/lu/uni/serval/fixminer/cluster/ImportPairs2DB.java

@@ -9,9 +9,6 @@ import java.util.List;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-//import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis;
-//import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedisWait;
-
 
 /**
  * Created by anilkoyuncu on 05/04/2018.
@@ -19,10 +16,10 @@ import java.util.stream.Stream;
 public class ImportPairs2DB {
     private static Logger log = LoggerFactory.getLogger(ImportPairs2DB.class);
 
-    public static void main(String csvInputPath,String portInner,String serverWait,String dbDir,String datasetPath) throws Exception {
+    public static void main(String csvInputPath,String portInner,String dbDir,String datasetPath) throws Exception {
 
 
-        String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \ndbDir %s",csvInputPath,portInner,serverWait,dbDir);
+        String parameters = String.format("\nInput path %s \nportInner %s \ndbDir %s",csvInputPath,portInner,dbDir);
         log.info(parameters);
 
 
@@ -40,7 +37,7 @@ public class ImportPairs2DB {
             cmd = String.format(cmd, dbDir,pj.getName() +".rdb", portInt);
             log.info(cmd);
             CallShell cs = new CallShell();
-            cs.runShell(cmd,serverWait, portInner);
+            cs.runShell(cmd, portInner);
 
             cmd = "bash "+datasetPath + "/redisSingleImport.sh" +" %s %s";
 
@@ -50,7 +47,7 @@ public class ImportPairs2DB {
 
             String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s";
             String stopServer2 = String.format(stopServer,portInt);
-            cs.runShell(stopServer2,serverWait, portInner);
+            cs.runShell(stopServer2, portInner);
 
             portInt++;
 

src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoader.java

@@ -1,14 +1,13 @@
 package edu.lu.uni.serval.fixminer.cluster;
 
 import com.github.gumtreediff.actions.ActionGenerator;
-import com.github.gumtreediff.actions.model.*;
+import com.github.gumtreediff.actions.model.Action;
 import com.github.gumtreediff.matchers.Matcher;
 import com.github.gumtreediff.matchers.Matchers;
 import com.github.gumtreediff.tree.ITree;
 import com.github.gumtreediff.tree.Tree;
 import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap;
 import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
-import edu.lu.uni.serval.utils.FileHelper;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import redis.clients.jedis.*;
@@ -291,17 +290,17 @@ public class MultiThreadTreeLoader {
         readMessageFiles(fileToCompare,port);
     }
 
-    public static void processMessages(String inputPath, String outputPath) {
+//    public static void processMessages(String inputPath, String outputPath) {
-        File folder = new File(outputPath + "pairs_splitted/");
+//        File folder = new File(outputPath + "pairs_splitted/");
-        File[] listOfFiles = folder.listFiles();
+//        File[] listOfFiles = folder.listFiles();
-        Stream<File> stream = Arrays.stream(listOfFiles);
+//        Stream<File> stream = Arrays.stream(listOfFiles);
-        List<File> pjs = stream
+//        List<File> pjs = stream
-                .filter(x -> !x.getName().startsWith("."))
+//                .filter(x -> !x.getName().startsWith("."))
-                .collect(Collectors.toList());
+//                .collect(Collectors.toList());
-        FileHelper.createDirectory(outputPath + "comparison_splitted/");
+//        FileHelper.createDirectory(outputPath + "comparison_splitted/");
-        pjs.parallelStream()
+//        pjs.parallelStream()
-                .forEach(m -> coreLoop(m, outputPath,inputPath));
+//                .forEach(m -> coreLoop(m, outputPath,inputPath));
-    }
+//    }
 
 
     public static ITree getSimpliedTree(String fn) {
@@ -377,45 +376,45 @@ public class MultiThreadTreeLoader {
         return parent;
     }
 
-    public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children){
+//    public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children){
-
+//
-        int newType = 0;
+//        int newType = 0;
-
+//
-        Action action = actionSet.getAction();
+//        Action action = actionSet.getAction();
-        if (action instanceof Update){
+//        if (action instanceof Update){
-            newType = 101;
+//            newType = 101;
-        }else if(action instanceof Insert){
+//        }else if(action instanceof Insert){
-            newType =100;
+//            newType =100;
-        }else if(action instanceof Move){
+//        }else if(action instanceof Move){
-            newType = 102;
+//            newType = 102;
-        }else if(action instanceof Delete){
+//        }else if(action instanceof Delete){
-            newType=103;
+//            newType=103;
-        }else{
+//        }else{
-            new Exception("unknow action");
+//            new Exception("unknow action");
-        }
+//        }
-        if(actionSet.getParent() == null){
+//        if(actionSet.getParent() == null){
-            //root
+//            //root
-
+//
-            parent = new Tree(newType,"");
+//            parent = new Tree(newType,"");
-        }else{
+//        }else{
-            children = new Tree(newType,"");
+//            children = new Tree(newType,"");
-            parent.addChild(children);
+//            parent.addChild(children);
-        }
+//        }
-        List<HierarchicalActionSet> subActions = actionSet.getSubActions();
+//        List<HierarchicalActionSet> subActions = actionSet.getSubActions();
-        if (subActions.size() != 0){
+//        if (subActions.size() != 0){
-            for (HierarchicalActionSet subAction : subActions) {
+//            for (HierarchicalActionSet subAction : subActions) {
-
+//
-                if(actionSet.getParent() == null){
+//                if(actionSet.getParent() == null){
-                    children = parent;
+//                    children = parent;
-                }
+//                }
-                getActionTree(subAction,children,null);
+//                getActionTree(subAction,children,null);
-
+//
-            }
+//            }
-
+//
-
+//
-        }
+//        }
-        return parent;
+//        return parent;
-    }
+//    }
 
 
 

src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster.java

@@ -1,22 +1,29 @@
 package edu.lu.uni.serval.fixminer.cluster;
 
 import com.github.gumtreediff.actions.ActionGenerator;
-import com.github.gumtreediff.actions.model.*;
+import com.github.gumtreediff.actions.model.Action;
 import com.github.gumtreediff.matchers.Matcher;
 import com.github.gumtreediff.matchers.Matchers;
 import com.github.gumtreediff.tree.ITree;
 import com.github.gumtreediff.tree.TreeContext;
+import edu.lu.uni.serval.FixPattern.utils.EDiff;
+import edu.lu.uni.serval.FixPattern.utils.EDiffHelper;
+import edu.lu.uni.serval.FixPattern.utils.PoolBuilder;
 import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
 import edu.lu.uni.serval.utils.FileHelper;
-
 import org.javatuples.Pair;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import redis.clients.jedis.*;
+import redis.clients.jedis.Jedis;
+import redis.clients.jedis.JedisPool;
+import redis.clients.jedis.ScanParams;
+import redis.clients.jedis.ScanResult;
 
 import java.io.*;
-import java.time.Duration;
+import java.util.ArrayList;
-import java.util.*;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -28,28 +35,27 @@ public class MultiThreadTreeLoaderCluster {
     private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoaderCluster.class);
 
 
-    public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner,String serverWait,String type) throws Exception {
+    public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner,String type) throws Exception {
 
         CallShell cs = new CallShell();
         String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
         cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner));
-//        edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000");
+        cs.runShell(cmd1, port);
-        cs.runShell(cmd1,serverWait, port);
 
 
         String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
         cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port));
-        cs.runShell(cmd2,serverWait, port);
+        cs.runShell(cmd2, port);
-//        edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000");
+
 
 
         String cmd3;
         cmd3 = "bash " + importScript +" %s %s";
 
 
-        JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000);
+        JedisPool jedisPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(portInner),20000000);
 
-        JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000);
+        JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(port),20000000);
 
 
         File folder = new File(pairsCSVPath);
@@ -104,29 +110,16 @@ public class MultiThreadTreeLoaderCluster {
         }
         String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s";
         String stopServer1 = String.format(stopServer,Integer.valueOf(portInner));
-//        loadRedis(stopServer2,serverWait);
+       cs.runShell(stopServer1, port);
-        cs.runShell(stopServer1,serverWait, port);
 
         String stopServer2 = String.format(stopServer,Integer.valueOf(port));
-//        loadRedis(stopServer2,serverWait);
+        cs.runShell(stopServer2, port);
-        cs.runShell(stopServer2,serverWait, port);
 
 
 
     }
 
 
-    /** Read the object from Base64 string. */
-    public static Object fromString( String s ) throws IOException ,
-            ClassNotFoundException {
-        byte [] data = Base64.getDecoder().decode( s );
-        ObjectInputStream ois = new ObjectInputStream(
-                new ByteArrayInputStream(  data ) );
-        Object o  = ois.readObject();
-        ois.close();
-        return o;
-    }
-
 
     public  static Pair<ITree,String> getTree(String firstValue, JedisPool outerPool,String type){
 
@@ -148,13 +141,13 @@ public class MultiThreadTreeLoaderCluster {
             inner = outerPool.getResource();
             String filename = project + "/"+type+"/" + pureFileName + ".txt_" + actionSetPosition;
             String si= inner.get(filename);
-            HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(si);
+            HierarchicalActionSet actionSet = (HierarchicalActionSet) EDiffHelper.fromString(si);
 
 
             ITree parent = null;
             ITree children =null;
             TreeContext tc = new TreeContext();
-            tree = getActionTree(actionSet, parent, children,tc);
+            tree = EDiff.getActionTree(actionSet, parent, children,tc);
             tree.setParent(null);
             tc.validate();
 
@@ -179,50 +172,7 @@ public class MultiThreadTreeLoaderCluster {
     }
 
 
-    public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){
 
-        int newType = 0;
-
-        Action action = actionSet.getAction();
-        if (action instanceof Update){
-            newType = 101;
-        }else if(action instanceof Insert){
-            newType =100;
-        }else if(action instanceof Move){
-            newType = 102;
-        }else if(action instanceof Delete){
-            newType=103;
-        }else{
-            new Exception("unknow action");
-        }
-        if(actionSet.getParent() == null){
-            //root
-
-            parent = tc.createTree(newType, "", null);
-            tc.setRoot(parent);
-
-//            parent = new Tree(newType,"");
-        }else{
-            children = tc.createTree(newType, "", null);
-            children.setParentAndUpdateChildren(parent);
-//            children = new Tree(newType,"");
-//            parent.addChild(children);
-        }
-        List<HierarchicalActionSet> subActions = actionSet.getSubActions();
-        if (subActions.size() != 0){
-            for (HierarchicalActionSet subAction : subActions) {
-
-                if(actionSet.getParent() == null){
-                    children = parent;
-                }
-                getActionTree(subAction,children,null,tc);
-
-            }
-
-
-        }
-        return parent;
-    }
 
 
     private static void coreCompare(String name , JedisPool jedisPool,String clusterName,JedisPool outerPool,String type) {
@@ -383,26 +333,6 @@ public class MultiThreadTreeLoaderCluster {
 
 
 
-    static final JedisPoolConfig poolConfig = buildPoolConfig();
-
-
-    private static JedisPoolConfig buildPoolConfig() {
-        final JedisPoolConfig poolConfig = new JedisPoolConfig();
-        poolConfig.setMaxTotal(128);
-        poolConfig.setMaxIdle(128);
-        poolConfig.setMinIdle(16);
-        poolConfig.setTestOnBorrow(true);
-        poolConfig.setTestOnReturn(true);
-        poolConfig.setTestWhileIdle(true);
-        poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis());
-        poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis());
-        poolConfig.setNumTestsPerEvictionRun(3);
-        poolConfig.setBlockWhenExhausted(true);
-
-        return poolConfig;
-    }
-
-
 
 //        return msgFiles;
 }

src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster3.java

@@ -2,24 +2,26 @@ package edu.lu.uni.serval.fixminer.cluster;
 
 import com.github.gumtreediff.tree.ITree;
 import com.github.gumtreediff.tree.TreeContext;
-import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap;
+import edu.lu.uni.serval.FixPattern.utils.EDiffHelper;
+import edu.lu.uni.serval.FixPattern.utils.PoolBuilder;
 import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
 import edu.lu.uni.serval.utils.FileHelper;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.text.similarity.JaroWinklerDistance;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import redis.clients.jedis.*;
+import redis.clients.jedis.Jedis;
+import redis.clients.jedis.JedisPool;
+import redis.clients.jedis.ScanParams;
+import redis.clients.jedis.ScanResult;
 
 import java.io.*;
-import java.time.Duration;
 import java.util.*;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import static edu.lu.uni.serval.fixminer.cluster.MultiThreadTreeLoader.getKeysByValue;
+
-import static edu.lu.uni.serval.fixminer.cluster.MultiThreadTreeLoaderCluster.fromString;
 
 /**
  * Created by anilkoyuncu on 19/03/2018.
@@ -30,27 +32,24 @@ public class MultiThreadTreeLoaderCluster3 {
     private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoaderCluster3.class);
 
 
-//    public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) {
+    public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner,String type) throws Exception {
-    public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner,String serverWait, String type) throws Exception {
 
         CallShell cs = new CallShell();
         String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
         cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner));
-//        edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000");
+        cs.runShell(cmd1, port);
-        cs.runShell(cmd1,serverWait, port);
 
         String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
         cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port));
-//        edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000");
+        cs.runShell(cmd2, port);
-        cs.runShell(cmd2,serverWait, port);
 
         String cmd3;
         cmd3 = "bash " + importScript +" %s %s";
 
 
-        JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000);
+        JedisPool jedisPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(portInner),20000000);
 
-        JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000);
+        JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(port),20000000);
 
 
 
@@ -79,8 +78,7 @@ public class MultiThreadTreeLoaderCluster3 {
                     if (size == 0) {
                         String comd = String.format(cmd3, f.getPath(), portInner);
                         cs.runShell(comd);
-//                        edu.lu.uni.serval.fixminer.cluster.MultiThreadTreeLoaderCluster.
+
-//                                loadRedis(comd);
 
                         scan = jedis.scan("0", sc);
                         size = scan.getResult().size();
@@ -103,17 +101,10 @@ public class MultiThreadTreeLoaderCluster3 {
 
         String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s";
         String stopServer1 = String.format(stopServer,Integer.valueOf(portInner));
-//        loadRedis(stopServer2,serverWait);
+        cs.runShell(stopServer1, port);
-        cs.runShell(stopServer1,serverWait, port);
 
         String stopServer2 = String.format(stopServer,Integer.valueOf(port));
-//        loadRedis(stopServer2,serverWait);
+        cs.runShell(stopServer2, port);
-        cs.runShell(stopServer2,serverWait, port);
-
-
-
-
-//        }
 
 
 
@@ -151,13 +142,13 @@ public class MultiThreadTreeLoaderCluster3 {
             inner = outerPool.getResource();
             String fn = project + "/"+type+"/" + s + ".txt_" + actionSetPosition;
             String si= inner.get(fn);
-            HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(si);
+            HierarchicalActionSet actionSet = (HierarchicalActionSet) EDiffHelper.fromString(si);
 
 
             ITree parent = null;
             ITree children =null;
             TreeContext tc = new TreeContext();
-            tree = getASTTree(actionSet, parent, children,tc);
+            tree = EDiffHelper.getASTTree(actionSet, parent, children,tc);
 //            tree.setParent(null);
             tc.validate();
 
@@ -176,46 +167,7 @@ public class MultiThreadTreeLoaderCluster3 {
 
     }
 
-    public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){
 
-        int newType = 0;
-
-        String astNodeType = actionSet.getAstNodeType();
-
-        String label = actionSet.getAction().toString();
-        List<Integer> keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType);
-
-        if(keysByValue.size() != 1){
-            log.error("Birden cok astnodemapmapping");
-        }
-        newType = keysByValue.get(0);
-        if(actionSet.getParent() == null){
-            //root
-
-//            parent = new Tree(newType,"");
-            parent = tc.createTree(newType, label, null);
-            tc.setRoot(parent);
-        }else{
-//            children = new Tree(newType,"");
-//            parent.addChild(children);
-            children = tc.createTree(newType, label, null);
-            children.setParentAndUpdateChildren(parent);
-        }
-        List<HierarchicalActionSet> subActions = actionSet.getSubActions();
-        if (subActions.size() != 0){
-            for (HierarchicalActionSet subAction : subActions) {
-
-                if(actionSet.getParent() == null){
-                    children = parent;
-                }
-                getASTTree(subAction,children,null,tc);
-
-            }
-
-
-        }
-        return parent;
-    }
 
 
     public static List<String> getNames(ITree oldTree, List<String> oldTokens){
@@ -489,31 +441,6 @@ public class MultiThreadTreeLoaderCluster3 {
             String firstValue = resultMap.get("0");
             String secondValue = resultMap.get("1");
 
-//            if(firstValue.equals("7/0/7af9e0_e674f1_spring-social-web#src#main#java#org#springframework#social#connect#web#ConnectController.txt_0_SOCIAL") || secondValue.equals("7/0/7af9e0_e674f1_spring-social-web#src#main#java#org#springframework#social#connect#web#ConnectController.txt_0_SOCIAL")){
-//                log.info("");
-//            }
-
-            ///35/1/22b5f7_84bf27_ui#org.eclipse.pde.runtime#src#org#eclipse#pde#internal#runtime#registry#RegistryBrowserLabelProvider.txt_2_PDE
-
-
-
-//            firstValue = inputPath + firstValue;
-//            secondValue = inputPath + secondValue;
-
-//            String[] firstValueSplit = firstValue.split("/");
-//            String[] secondValueSplit = secondValue.split("/");
-//
-//            if (firstValueSplit.length == 1) {
-//                firstValue = inputPath + firstValueSplit[0];
-//            } else {
-//                firstValue = inputPath + firstValueSplit[1];
-//            }
-//
-//            if (secondValueSplit.length == 1) {
-//                secondValue = inputPath + secondValueSplit[0];
-//            } else {
-//                secondValue = inputPath + secondValueSplit[1];
-//            }
 
             try {
                 ITree oldTree = getTree(firstValue,outerPool,type);
@@ -526,30 +453,18 @@ public class MultiThreadTreeLoaderCluster3 {
                     return;
                 }
 
-//                ITree oldTree = oldPair.getValue0();
+
-//                ITree newTree = newPair.getValue0();
-//
-//                String oldProject = oldPair.getValue1();
-//                String newProject = newPair.getValue1();
 
                 List<String> oldTokens = new ArrayList<>();
                 List<String> newTokens = new ArrayList<>();
 
 
-//                if(secondValue.startsWith("/2/")){
-//                    log.info("newss");
-//                }
 
-                // 41 return statement
 
                 oldTokens = getNames(oldTree,oldTokens);
                 newTokens = getNames(newTree,newTokens);
 
-//                if(oldTokens.size() == 0 || newTokens.size() == 0){
+
-//                    log.error("Cluster {} has no tokens on pair {}",clusterName , name);
-//                }
-//                Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree);
-//                m.match();
                 CharSequence[] oldSequences = oldTokens.toArray(new CharSequence[oldTokens.size()]);
                 CharSequence[] newSequences = newTokens.toArray(new CharSequence[newTokens.size()]);
                 JaroWinklerDistance jwd = new JaroWinklerDistance();
@@ -572,14 +487,7 @@ public class MultiThreadTreeLoaderCluster3 {
                 int retval = Double.compare(overallSimi, Double.valueOf(0.8));
                 if(retval >= 0){
 
-//                    log.info("YES");
+
-//                    log.info(name);
-//                    log.info(firstValue);
-//                    log.info(secondValue);
-//                    log.info("************");
-//                    if(!overallSimi.equals(1.0)){
-//                        log.info("");
-//                    }
                     String matchKey = "match-"+clusterName+"_" + (String.valueOf(i)) + "_" + String.valueOf(j);
                     String result = firstValue + "," + secondValue + ","+String.join(",", oldTokens);
                     jedis.select(1);
@@ -705,30 +613,6 @@ public class MultiThreadTreeLoaderCluster3 {
 
 
 
-
-
-    static final JedisPoolConfig poolConfig = buildPoolConfig();
-
-
-    private static JedisPoolConfig buildPoolConfig() {
-        final JedisPoolConfig poolConfig = new JedisPoolConfig();
-        poolConfig.setMaxTotal(128);
-        poolConfig.setMaxIdle(128);
-        poolConfig.setMinIdle(16);
-        poolConfig.setTestOnBorrow(true);
-        poolConfig.setTestOnReturn(true);
-        poolConfig.setTestWhileIdle(true);
-        poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis());
-        poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis());
-        poolConfig.setNumTestsPerEvictionRun(3);
-        poolConfig.setBlockWhenExhausted(true);
-
-        return poolConfig;
-    }
-
-
-
-//        return msgFiles;
 }
 
 

src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreEDiffInCache.java

@@ -1,5 +1,7 @@
 package edu.lu.uni.serval.fixminer.cluster;
 
+import edu.lu.uni.serval.FixPattern.utils.EDiffHelper;
+import edu.lu.uni.serval.FixPattern.utils.PoolBuilder;
 import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -9,50 +11,28 @@ import redis.clients.jedis.JedisPool;
 import java.io.*;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Base64;
 import java.util.List;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import static edu.lu.uni.serval.fixminer.cluster.TreeLoaderClusterL1.poolConfig;
 
 /**
  * Created by anilkoyuncu on 03/04/2018.
  */
-public class StoreFile {
+public class StoreEDiffInCache {
 
-    private static Logger log = LoggerFactory.getLogger(StoreFile.class);
+    private static Logger log = LoggerFactory.getLogger(StoreEDiffInCache.class);
 
-//    public static void main(String[] args) {
+
-    public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String operation) throws Exception {
+    public static void main(String inputPath,String portInner,String dbDir,String chunkName,String operation) throws Exception {
-//        String inputPath;
+
-//        String portInner;
+        String parameters = String.format("\nInput path %s \nportInner %s \nchunkName %s \ndbDir %s \noperation %s",inputPath,portInner,chunkName,dbDir,operation);
-//        String serverWait;
-//        String dbDir;
-//        String chunkName;
-//        String numOfWorkers;
-//        if (args.length > 0) {
-//            inputPath = args[0];
-//            portInner = args[1];
-//            serverWait = args[2];
-//            chunkName = args[3];
-//            numOfWorkers = args[4];
-//            dbDir = args[5];
-//        } else {
-//            inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2";
-//            portInner = "6399";
-//            serverWait = "10000";
-//            chunkName ="dumps.rdb";
-//            dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis";
-//            numOfWorkers = "1";
-//        }
-        String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s \noperation %s",inputPath,portInner,serverWait,chunkName,dbDir,operation);
         log.info(parameters);
         CallShell cs = new CallShell();
         String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
         cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(portInner));
-//        loadRedis(cmd,serverWait);
+
-        cs.runShell(cmd,serverWait, portInner);
+        cs.runShell(cmd, portInner);
 
         File folder = new File(inputPath);
         File[] subFolders = folder.listFiles();
@@ -98,7 +78,7 @@ public class StoreFile {
         }
         log.info(String.valueOf(workList.size()));
 
-        JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000);
+        JedisPool innerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(portInner),20000000);
 
         workList.stream().parallel()
                 .forEach(m -> storeCore(innerPool, m.split(",")[1],m.split(",")[0]));
@@ -107,10 +87,12 @@ public class StoreFile {
 
         String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s";
         String stopServer2 = String.format(stopServer,Integer.valueOf(portInner));
-//        loadRedis(stopServer2,serverWait);
+
-        cs.runShell(stopServer2,serverWait, portInner);
+        cs.runShell(stopServer2, portInner);
     }
 
+
+
     public static void storeCore(JedisPool innerPool,String path,String key){
         try {
 
@@ -141,7 +123,7 @@ public class StoreFile {
 
             try (Jedis inner = innerPool.getResource()) {
 
-                inner.set(key,toString(actionSet));
+                inner.set(key, EDiffHelper.toString(actionSet));
             }
 
 
@@ -155,25 +137,7 @@ public class StoreFile {
     }
 
 
-    /** Read the object from Base64 string. */
-    private static Object fromString( String s ) throws IOException ,
-            ClassNotFoundException {
-        byte [] data = Base64.getDecoder().decode( s );
-        ObjectInputStream ois = new ObjectInputStream(
-                new ByteArrayInputStream(  data ) );
-        Object o  = ois.readObject();
-        ois.close();
-        return o;
-    }
 
-    /** Write the object to a Base64 string. */
-    private static String toString( Serializable o ) throws IOException {
-        ByteArrayOutputStream baos = new ByteArrayOutputStream();
-        ObjectOutputStream oos = new ObjectOutputStream( baos );
-        oos.writeObject( o );
-        oos.close();
-        return Base64.getEncoder().encodeToString(baos.toByteArray());
-    }
 
 
     }

src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeActor.java

@@ -8,13 +8,10 @@ import akka.routing.RoundRobinPool;
 import edu.lu.uni.serval.fixminer.cluster.akka.TreeMessage;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import redis.clients.jedis.Jedis;
 import redis.clients.jedis.JedisPool;
 
 import java.util.List;
 
-import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis;
-
 public class TreeActor extends UntypedActor {
 
 	private static Logger logger = LoggerFactory.getLogger(TreeActor.class);

src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeLoaderClusterL1.java

@@ -1,11 +1,14 @@
 package edu.lu.uni.serval.fixminer.cluster;
 
+import edu.lu.uni.serval.FixPattern.utils.PoolBuilder;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import redis.clients.jedis.*;
+import redis.clients.jedis.Jedis;
+import redis.clients.jedis.JedisPool;
+import redis.clients.jedis.ScanParams;
+import redis.clients.jedis.ScanResult;
 
 import java.io.File;
-import java.time.Duration;
 import java.util.Arrays;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -18,19 +21,19 @@ public class TreeLoaderClusterL1 {
 
     private static Logger log = LoggerFactory.getLogger(TreeLoaderClusterL1.class);
 
-    public static void main(String portInner,String serverWait,String port,String inputPath,String level1DB,String level1Path,String innerTypePrefix) throws Exception {
+    public static void main(String portInner,String port,String inputPath,String level1DB,String level1Path,String innerTypePrefix) throws Exception {
 
 
 
-        String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nport %s",inputPath,portInner,serverWait,port);
+        String parameters = String.format("\nInput path %s \nportInner %s \nport %s",inputPath,portInner,port);
         log.info(parameters);
 
         String cmd = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s";
         cmd = String.format(cmd, inputPath,level1DB,Integer.valueOf(port));
 
         CallShell cs = new CallShell();
-        cs.runShell(cmd,serverWait, port);
+        cs.runShell(cmd, port);
-        JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000);
+        JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(port),20000000);
 
 
         File chunks = new File(level1Path);
@@ -44,8 +47,8 @@ public class TreeLoaderClusterL1 {
             String cmdInner = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s";
             cmdInner = String.format(cmdInner, inputPath,db.getName(),Integer.valueOf(portInner));
 
-            cs.runShell(cmdInner,serverWait, port);
+            cs.runShell(cmdInner, port);
-            JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000);
+            JedisPool innerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(portInner),20000000);
 
             Jedis inner = null;
 
@@ -97,38 +100,21 @@ public class TreeLoaderClusterL1 {
 
             String stopServer = "bash "+inputPath + "/" + "stopServer.sh" +" %s";
             stopServer = String.format(stopServer,Integer.valueOf(portInner));
-//            loadRedis(stopServer,serverWait);
+
-            cs.runShell(stopServer,serverWait, port);
+            cs.runShell(stopServer, port);
         }
 
         String stopServer1 = "bash "+inputPath + "/" + "stopServer.sh" +" %s";
         stopServer1 = String.format(stopServer1,Integer.valueOf(port));
-//            loadRedis(stopServer,serverWait);
+
-        cs.runShell(stopServer1,serverWait, port);
+        cs.runShell(stopServer1, port);
 
 
 
 
     }
-    static final JedisPoolConfig poolConfig = buildPoolConfig();
 
 
-    private static JedisPoolConfig buildPoolConfig() {
-        final JedisPoolConfig poolConfig = new JedisPoolConfig();
-        poolConfig.setMaxTotal(128);
-        poolConfig.setMaxIdle(128);
-        poolConfig.setMinIdle(16);
-        poolConfig.setTestOnBorrow(true);
-        poolConfig.setTestOnReturn(true);
-        poolConfig.setTestWhileIdle(true);
-        poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis());
-        poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis());
-        poolConfig.setNumTestsPerEvictionRun(3);
-        poolConfig.setBlockWhenExhausted(true);
-
-        return poolConfig;
-    }
-
 
 }
 

src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeWorker.java

@@ -8,14 +8,10 @@ import edu.lu.uni.serval.fixminer.cluster.akka.TreeMessage;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import redis.clients.jedis.JedisPool;
-import redis.clients.jedis.JedisPoolConfig;
 
-import java.time.Duration;
 import java.util.List;
 import java.util.concurrent.*;
 
-import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.poolConfig;
-
 public class TreeWorker extends UntypedActor {
 	private static Logger log = LoggerFactory.getLogger(TreeWorker.class);
 

src/main/java/edu/lu/uni/serval/gumtree/regroup/ActionFilter.java

@@ -1,254 +0,0 @@
-package edu.lu.uni.serval.gumtree.regroup;
-
-import java.util.ArrayList;
-import java.util.List;
-
-public class ActionFilter {
-	
-	private List<String> methodNames = new ArrayList<>();
-	private List<String> variableNames = new ArrayList<>();
-	
-	/**
-	 * Filter out the modify actions of changing method names, method parameters, variable names and field names in declaration part.
-	 * 
-	 * @param actionSets
-	 * @return
-	 */
-	public List<HierarchicalActionSet> filterOutUselessActions(List<HierarchicalActionSet> actionSets) {
-		// Filter out modifications of variable names and method names.
-		List<HierarchicalActionSet> uselessActions = findoutUselessActions(actionSets);
-		actionSets.removeAll(uselessActions);
-		uselessActions.clear();
-		
-		// Filter out non-UPD modifications, and modifications of variable names and method names.
-		uselessActions = findoutUselessActionSets(actionSets, true);
-		actionSets.removeAll(uselessActions);
-		uselessActions.clear();
-		return actionSets;
-	}
-
-	private List<HierarchicalActionSet> findoutUselessActionSets(List<HierarchicalActionSet> actionSets, boolean isRoot) {
-		List<HierarchicalActionSet> uselessActions = new ArrayList<>();
-		
-		FindActionSet: {
-			for (HierarchicalActionSet actionSet : actionSets) {
-				if (!isRoot) {
-					String actionStr = actionSet.getActionString();
-					if (actionStr.startsWith("UPD MethodInvocation") || actionStr.startsWith("INS MethodInvocation") || actionStr.startsWith("DEL MethodInvocation")) {
-						String label = actionSet.getAction().getNode().getLabel();
-						for (String methodName : methodNames) {
-							if (actionSet.getActionString().startsWith("UPD MethodInvocation@@" + methodName + "(")
-									|| actionSet.getActionString().startsWith("INS MethodInvocation@@" + methodName + "(")
-									|| actionSet.getActionString().startsWith("DEL MethodInvocation@@" + methodName + "(")
-									|| label.contains("." + methodName + "(")) {
-								addToUselessActions(actionSet, uselessActions);
-								break FindActionSet;
-							}
-						}
-					} else if (actionStr.startsWith("UPD SimpleName") || actionStr.startsWith("INS SimpleName") || actionStr.startsWith("DEL SimpleName")) {
-						String label = actionSet.getAction().getNode().getLabel();
-						for (String variableName : variableNames) {
-							if (label.equals(variableName) || label.equals("Name:" + variableName)) {
-								addToUselessActions(actionSet, uselessActions);
-								break FindActionSet;
-							}
-						}
-					} else if (actionStr.startsWith("UPD StringLiteral") || actionStr.startsWith("INS StringLiteral") 
-							|| actionStr.startsWith("DEL StringLiteral") || actionStr.startsWith("MOV StringLiteral")
-							|| actionStr.startsWith("UPD CharacterLiteral") || actionStr.startsWith("INS CharacterLiteral") 
-							|| actionStr.startsWith("DEL CharacterLiteral") || actionStr.startsWith("MOV CharacterLiteral")) {
-						addToUselessActions(actionSet, uselessActions);
-						break FindActionSet;
-					}
-					
-					List<HierarchicalActionSet> uselessActionSets = findoutUselessActionSets(actionSet.getSubActions(), false);
-					if (uselessActionSets.size() > 0) {
-						uselessActions.addAll(uselessActionSets);
-						break;
-					}
-				} else {
-					if (actionSet.getAstNodeType().endsWith("Statement") || "FieldDeclaration".equals(actionSet.getAstNodeType())) {
-						uselessActions.addAll(findoutUselessActionSets(actionSet.getSubActions(), false));
-					} else {
-						uselessActions.add(actionSet);
-					}
-                }
-			}
-		}
-		
-		return uselessActions;
-	}
-
-	private void addToUselessActions(HierarchicalActionSet actionSet, List<HierarchicalActionSet> uselessActions) {
-		while (actionSet.getParent() != null) {
-			actionSet = actionSet.getParent();
-		}
-		if (!uselessActions.contains(actionSet)) {
-			uselessActions.add(actionSet);
-		}
-	}
-
-	/**
-	 * Identify the the modify actions of changing method names, method parameters, variable names and field names in declaration part.
-	 * 
-	 * @param actionSets
-	 * @return
-	 */
-	private List<HierarchicalActionSet> findoutUselessActions(List<HierarchicalActionSet> actionSets) {
-		List<HierarchicalActionSet> uselessActions = new ArrayList<>();
-		
-		for (HierarchicalActionSet actionSet : actionSets) {
-			String actionType = actionSet.getAstNodeType();
-			if (actionType.equals("MethodDeclaration")) {
-				addToUselessActions(actionSet, uselessActions);// INS, DEL: useful?, UPD, except the modifier actions
-				if (!actionSet.getActionString().startsWith("MOV ")) {
-					String label = actionSet.getNode().getLabel();
-					String methodName = label.substring(label.indexOf("MethodName:"));
-					methodName = methodName.substring(11, methodName.indexOf(","));
-					methodNames.add(methodName); // "MethodName:***"
-					
-					// UPD, DEL, INS parameters.
-					List<HierarchicalActionSet> subActionSets = actionSet.getSubActions();
-					for (HierarchicalActionSet subActionSet : subActionSets) {
-						if (subActionSet.getAstNodeType().equals("SingleVariableDeclaration")) {
-							List<HierarchicalActionSet> subActionSets2 = subActionSet.getSubActions(); // <Type, identifier>
-							if (subActionSets2.size() == 0) { 
-								String actSetStr = subActionSet.getActionString();
-								int index1 = actSetStr.indexOf("@@");
-								int index2 = 0;
-								if (actSetStr.startsWith("DEL")) {
-									index2 = actSetStr.indexOf("@AT@");
-								} else {
-									index2 = actSetStr.indexOf("@TO@");;
-								}
-								actSetStr = actSetStr.substring(index1, index2).trim();
-								String variableName = actSetStr.substring(actSetStr.lastIndexOf(" "));
-								variableNames.add(variableName); // "SimpleName:" + variableName TODO: effect range
-							} else {
-								HierarchicalActionSet actSet = subActionSets2.get(subActionSets2.size() - 1);
-								String actStr = actSet.getActionString();
-								if (actStr.startsWith("UPD SimpleName") || actStr.startsWith("INS SimpleName") || actStr.startsWith("DEL SimpleName")) {
-									String variableName = actSet.getNode().getLabel();
-									variableNames.add(variableName); // "SimpleName:" + variableName TODO: effect range
-								}
-							}
-						}
-					}
-				} 
-			} else if (actionType.equals("FieldDeclaration") || actionType.equals("VariableDeclarationStatement")) { 
-				// UPD VariableDeclarationFragment
-				if (!actionSet.getActionString().startsWith("MOV ")) {
-					List<HierarchicalActionSet> subActionSets = actionSet.getSubActions();
-					if (subActionSets.size() > 0) {
-						for (HierarchicalActionSet subActionSet : subActionSets) { // VariableDeclarationFragments
-							if (identifyUpdateVDF(subActionSet)) {
-								addToUselessActions(actionSet, uselessActions);
-							}
-						}
-					}
-				}
-			} else if (actionType.equals("TryStatement")) {
-				if (actionSet.getActionString().startsWith("UPD ")) {
-					List<HierarchicalActionSet> subActionSets = actionSet.getSubActions();
-					if (subActionSets.size() > 0) {
-						for (HierarchicalActionSet subActionSet : subActionSets) {
-							if (subActionSet.getActionString().startsWith("UPD VariableDeclarationExpression")) {
-								List<HierarchicalActionSet> subActionSets2 = subActionSet.getSubActions(); // VariableDeclarationFragments
-								for (HierarchicalActionSet subActionSet2 : subActionSets2) {
-									if (identifyUpdateVDF(subActionSet2)) {
-										addToUselessActions(actionSet, uselessActions);
-									}
-								}
-							} else {
-								break;
-							}
-						}
-					}
-				}
-			} else if (actionType.equals("EnhancedForStatement")) { // SingleVariableDeclaration
-				if (!actionSet.getActionString().startsWith("MOV ")) {
-					List<HierarchicalActionSet> subActionSets = actionSet.getSubActions();
-					if (subActionSets.size() > 0) {
-						HierarchicalActionSet subActionSet = subActionSets.get(0);
-						if (subActionSet.getActionString().startsWith("UPD SingleVariableDeclaration")) {
-							List<HierarchicalActionSet> subActionSets2 = subActionSet.getSubActions();
-							for (HierarchicalActionSet subActionSet2 : subActionSets2) { // Type or Identifier
-								if (subActionSet2.getActionString().startsWith("UPD SimpleName")) {
-									String variableName = subActionSet2.getNode().getLabel();
-									variableNames.add(variableName); // "SimpleName:" + variableName TODO: effect range
-									addToUselessActions(actionSet, uselessActions);
-								}
-							}
-						}
-					}
-				}
-			} else if (actionType.equals("SingleVariableDeclaration")) {
-				if (!actionSet.getActionString().startsWith("MOV ")) {
-					List<HierarchicalActionSet> subActionSets2 = actionSet.getSubActions(); // <Type, identifier>
-					if (subActionSets2.size() == 0) {
-						String actSetStr = actionSet.getActionString();
-						int index1 = actSetStr.indexOf("@@");
-						int index2 = 0;
-						if (actSetStr.startsWith("DEL")) {
-							index2 = actSetStr.indexOf("@AT@");
-						} else {
-							index2 = actSetStr.indexOf("@TO@");;
-						}
-						actSetStr = actSetStr.substring(index1, index2).trim();
-						String variableName = actSetStr.substring(actSetStr.lastIndexOf(" "));
-						variableNames.add(variableName); // "SimpleName:" + variableName TODO: effect range
-						addToUselessActions(actionSet, uselessActions);
-					} else {
-						HierarchicalActionSet actSet = subActionSets2.get(subActionSets2.size() - 1);
-						String actStr = actSet.getActionString();
-						if (actStr.startsWith("UPD SimpleName") || actStr.startsWith("INS SimpleName") || actStr.startsWith("DEL SimpleName")) {
-							String variableName = actSet.getNode().getLabel();
-							variableNames.add(variableName); // "SimpleName:" + variableName TODO: effect range
-							addToUselessActions(actionSet, uselessActions);
-						}
-					}
-				}
-			}  else {
-				if (actionSet.getParent() != null) {
-					while (actionSet.getParent() != null) {
-						actionSet = actionSet.getParent();
-					}
-					if (uselessActions.contains(actionSet)) {
-						return uselessActions;
-					} else {
-						uselessActions.addAll(findoutUselessActions(actionSet.getSubActions()));
-					}
-				}
-			}
-		}
-		return uselessActions;
-	}
-
-	/**
-	 * Identify the AST node of this ActionSet is VariableDeclarationFragment or not.
-	 * And, whether the action is happened on the Variable name or not.
-	 * 
-	 * @param actionSet
-	 */
-	private boolean identifyUpdateVDF(HierarchicalActionSet actionSet) {
-		String actStr = actionSet.getActionString();
-		if (actStr.startsWith("UPD VariableDeclarationFragment")
-				|| actStr.startsWith("INS VariableDeclarationFragment")
-				|| actStr.startsWith("DEL VariableDeclarationFragment")) {
-			List<HierarchicalActionSet> subActionSets = actionSet.getSubActions();
-			if (subActionSets == null || subActionSets.size() == 0) {
-				// modification of Dimension
-				return true;
-			}
-			HierarchicalActionSet actSet = subActionSets.get(0);
-			String actSetStr = actSet.getActionString();
-			if (actSetStr.startsWith("UPD SimpleName") || actSetStr.startsWith("INS SimpleName") || actSetStr.startsWith("DEL SimpleName")) {
-				String variableName = actSet.getNode().getLabel();
-				variableNames.add(variableName); // "SimpleName:" + variableName TODO: effect range
-				return true;
-			}
-		}
-		return false;
-	}
-
-}

src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java

@@ -1,12 +1,12 @@
 package edu.lu.uni.serval.gumtree.regroup;
 
+import com.github.gumtreediff.actions.model.Action;
+import com.github.gumtreediff.tree.ITree;
+
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
-import com.github.gumtreediff.actions.model.Action;
-import com.github.gumtreediff.tree.ITree;
-
 /**
  * Hierarchical-level results of GumTree results
  * 
@@ -29,10 +29,15 @@ public class HierarchicalActionSet implements Comparable<HierarchicalActionSet>,
 	private List<HierarchicalActionSet>	subActions = new ArrayList<>();
 	
 	private ITree node;
-	private SimpleTree abstractSimpleTree =  null;     // semi-source code tree. and AST node type tree
+         // source code tree.
-	private SimpleTree abstractIdentifierTree = null;  // abstract identifier tree
+
-	private SimpleTree simpleTree = null;  			   // source code tree and AST node type tree
+	public int getBugEndPosition() {
-	private SimpleTree originalTree = null;            // source code tree.
+		return bugEndPosition;
+	}
+
+	public int getFixEndPosition() {
+		return fixEndPosition;
+	}
 
 	private int bugEndPosition;
 	private int fixEndPosition;
@@ -147,49 +152,12 @@ public class HierarchicalActionSet implements Comparable<HierarchicalActionSet>,
 		this.subActions = subActions;
 	}
 
-	public SimpleTree getAbstractSimpleTree() {
-		return abstractSimpleTree;
-	}
-
-	public void setAbstractSimpleTree(SimpleTree simpleTree) {
-		this.abstractSimpleTree = simpleTree;
-	}
-
-	public SimpleTree getAbstractIdentifierTree() {
-		return abstractIdentifierTree;
-	}
-
-	public void setAbstractIdentifierTree(SimpleTree abstractIdentifierTree) {
-		this.abstractIdentifierTree = abstractIdentifierTree;
-	}
-
-	public SimpleTree getSimpleTree() {
-		return simpleTree;
-	}
-
-	public void setSimpleTree(SimpleTree rawTokenTree) {
-		this.simpleTree = rawTokenTree;
-	}
-
-	public SimpleTree getOriginalTree() {
-		return originalTree;
-	}
-
-	public void setOriginalTree(SimpleTree originalTree) {
-		this.originalTree = originalTree;
-	}
-
-	public int getBugEndPosition() {
-		return bugEndPosition;
-	}
 
 	public void setBugEndPosition(int bugEndPosition) {
 		this.bugEndPosition = bugEndPosition;
 	}
 
-	public int getFixEndPosition() {
+
-		return fixEndPosition;
-	}
 
 	public void setFixEndPosition(int fixEndPosition) {
 		this.fixEndPosition = fixEndPosition;
@@ -197,10 +165,7 @@ public class HierarchicalActionSet implements Comparable<HierarchicalActionSet>,
 
 	@Override
 	public int compareTo(HierarchicalActionSet o) {
-//		int result = this.startPosition.compareTo(o.startPosition);
+
-//		if (result == 0) {
-//			result = this.length >= o.length ? -1 : 1;
-//		}
 		return this.startPosition.compareTo(o.startPosition);//this.action.compareTo(o.action);
 	}
 	
@@ -238,28 +203,5 @@ public class HierarchicalActionSet implements Comparable<HierarchicalActionSet>,
 		return str;
 	}
 	
-	public String toASTNodeLevelAction() {
-		if (strList.size() == 0) {
-			toString();
-		}
-		String astNodeStr = "";
-		for (String str : strList) {
-			astNodeStr += str.substring(0, str.indexOf("@@")) + "\n";
-		}
-		return astNodeStr;
-	}
 
-	public String toRawCodeLevelAction() {
-		if (strList.size() == 0) {
-			toString();
-		}
-		String astNodeStr = "";
-		for (String str : strList) {
-			str = str.substring(0, str.indexOf(" @AT@")) + "\n";
-			int index1 = str.indexOf(" ") + 1;
-			int index2 = str.indexOf("@@") + 2;
-			astNodeStr += str.substring(0, index1) + str.substring(index2);
-		}
-		return astNodeStr;
-	}
 }

src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java

@@ -1,22 +1,13 @@
 package edu.lu.uni.serval.gumtree.regroup;
 
-import java.io.File;
+import com.github.gumtreediff.actions.model.*;
+import com.github.gumtreediff.tree.ITree;
+import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap;
+import edu.lu.uni.serval.utils.ListSorter;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import com.github.gumtreediff.actions.model.Action;
-import com.github.gumtreediff.actions.model.Addition;
-import com.github.gumtreediff.actions.model.Delete;
-import com.github.gumtreediff.actions.model.Insert;
-import com.github.gumtreediff.actions.model.Move;
-import com.github.gumtreediff.actions.model.Update;
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap;
-import edu.lu.uni.serval.FixPattern.utils.Checker;
-import edu.lu.uni.serval.gumtree.GumTreeComparer;
-import edu.lu.uni.serval.utils.ListSorter;
-
 /**
  * Regroup GumTree results to a hierarchical construction.
  * 
@@ -209,11 +200,6 @@ public class HierarchicalRegrouper {
 			}
 
 
-//		} else if (parent.getType() == 31) { // method declaration
-//			int type = action.getNode().getType();
-//			if (Checker.isStatement(type)) {// statements
-//				return null;
-//			}
 		}
 		
 		for (Action act : actions) {

src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java

@@ -1,300 +0,0 @@
-package edu.lu.uni.serval.gumtree.regroup;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.github.gumtreediff.actions.model.Action;
-import com.github.gumtreediff.actions.model.Addition;
-import com.github.gumtreediff.actions.model.Delete;
-import com.github.gumtreediff.actions.model.Insert;
-import com.github.gumtreediff.actions.model.Move;
-import com.github.gumtreediff.actions.model.Update;
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.FixPattern.utils.CNodeMap;
-import edu.lu.uni.serval.utils.ListSorter;
-
-/**
- * Regroup GumTree results to a hierarchical construction.
- * 
- * @author kui.liu
- *
- */
-public class HierarchicalRegrouperForC {
-
-//	public static void main(String[] args) {
-//		GumTreeComparer com = new GumTreeComparer();
-//		File cFile1 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/prevFiles/prev_0a3d00_b404bc_drivers#pci#iov.c");
-//		File cFile2 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/revFiles/0a3d00_b404bc_drivers#pci#iov.c");
-//		List<Action> action = com.compareTwoFilesWithGumTreeForCCode(cFile1, cFile2);
-//		List<HierarchicalActionSet> actionSet = new HierarchicalRegrouperForC().regroupGumTreeResults(action);
-//		System.out.println(actionSet);
-//	}
-	
-	List<HierarchicalActionSet> actionSets = new ArrayList<>();
-	
-	public List<HierarchicalActionSet> regroupGumTreeResults(List<Action> actions) {
-		/*
-		 * First, sort actions by their positions.
-		 */
-//		List<Action> actions = new ListSorter<Action>(actionsArgu).sortAscending();
-//		if (actions == null) {
-//			actions = actionsArgu;
-//		}
-		
-		/*
-		 * Second, group actions by their positions.
-		 */
-		HierarchicalActionSet actionSet = null;
-		for(Action act : actions){
-			Action parentAct = findParentAction(act, actions);
-			
-			if (parentAct == null) {
-				actionSet = createActionSet(act, parentAct, null);
-				actionSets.add(actionSet);
-			} else {
-				if (!addToAactionSet(act, parentAct, actionSets)) {
-					// The index of the parent action in the actions' list is larger than the index of this action.
-					actionSet = createActionSet(act, parentAct, null);
-					actionSets.add(actionSet);
-				}
-			}
-		}
-		
-		/*
-		 * Third, add the subActionSet to its parent ActionSet.
-		 */
-		List<HierarchicalActionSet> reActionSets = new ArrayList<>();
-		for (HierarchicalActionSet actSet : actionSets) {
-			Action parentAct = actSet.getParentAction();
-			if (parentAct != null) {
-				addToActionSets(actSet, parentAct, actionSets);
-			} else {
-				// TypeDeclaration, FieldDeclaration, MethodDeclaration, Statement. 
-				// CatchClause, ConstructorInvocation, SuperConstructorInvocation, SwitchCase
-//				String astNodeType = actSet.getAstNodeType();
-//				if (astNodeType.endsWith("TypeDeclaration") || astNodeType.endsWith("FieldDeclaration")  || astNodeType.endsWith("EnumDeclaration") ||
-//						astNodeType.endsWith("MethodDeclaration") || astNodeType.endsWith("Statement") ||
-//						astNodeType.endsWith("ConstructorInvocation") || astNodeType.endsWith("CatchClause") || astNodeType.endsWith("SwitchCase")) {
-					reActionSets.add(actSet);
-//				}
-			}
-		}
-		return reActionSets;
-	}
-
-	private HierarchicalActionSet createActionSet(Action act, Action parentAct, HierarchicalActionSet parent) {
-		HierarchicalActionSet actionSet = new HierarchicalActionSet();
-		actionSet.setAction(act);
-		String actStr = parseAction(act.toString());
-		actionSet.setActionString(actStr);
-		actionSet.setParentAction(parentAct);
-		actionSet.setNode(act.getNode());
-		actionSet.setParent(parent);
-		
-		int bugStartLineNum = 0;
-		int bugEndLineNum = 0;
-		int fixStartLineNum = 0;
-		int fixEndLineNum = 0;
-		if (actStr.startsWith("INS")) {
-			Insert insert = (Insert) act;
-//			int pos = insert.getPos();//index position of the new node in the children array list of its corresponding old parent node.
-			ITree newTree = insert.getNode();
-			fixStartLineNum = newTree.getPos();
-			fixEndLineNum = newTree.getLength();
-		} else {
-			ITree tree = act.getNode();
-			bugStartLineNum = tree.getPos();
-		    bugEndLineNum = tree.getLength();
-		    if (actStr.startsWith("UPD")) {
-		    	Update update = (Update) act;
-		    	ITree newTree = update.getNewNode();
-		    	fixStartLineNum = newTree.getPos();
-		    	fixEndLineNum = newTree.getLength();
-		    } else if (actStr.startsWith("MOV")) {
-		    	Move update = (Move) act;
-		    	ITree newTree = update.getNewNode();
-		    	fixStartLineNum = newTree.getPos();
-		    	fixEndLineNum = newTree.getLength();
-		    }
-		}
-		actionSet.setBugStartLineNum(bugStartLineNum);
-		actionSet.setBugEndLineNum(bugEndLineNum);
-		actionSet.setFixStartLineNum(fixStartLineNum);
-		actionSet.setFixEndLineNum(fixEndLineNum);
-		return actionSet;
-	}
-
-	private String parseAction(String actStr1) {
-		// UPD 25@@!a from !a to isTrue(a) at 69
-		String[] actStrArrays = actStr1.split("@@");
-		String actStr = "";
-		int length = actStrArrays.length;
-		for (int i =0; i < length - 1; i ++) {
-			String actStrFrag = actStrArrays[i];
-			int index = actStrFrag.lastIndexOf(" ") + 1;
-			String nodeType = actStrFrag.substring(index);
-			if (!"".equals(nodeType)) {
-				if (Character.isDigit(nodeType.charAt(0)) || (nodeType.startsWith("-") && Character.isDigit(nodeType.charAt(1)))) {
-					try {
-						int typeInt = Integer.parseInt(nodeType);
-						if (CNodeMap.map.containsKey(typeInt)) {
-							String type = CNodeMap.map.get(Integer.parseInt(nodeType));
-							nodeType = type;
-						}
-					} catch (NumberFormatException e) {
-						nodeType = actStrFrag.substring(index);
-					}
-				}
-			}
-			actStrFrag = actStrFrag.substring(0, index) + nodeType + "@@";
-			actStr += actStrFrag;
-		}
-		actStr += actStrArrays[length - 1];
-		return actStr;
-	}
-	
-	private void addToActionSets(HierarchicalActionSet actionSet, Action parentAct, List<HierarchicalActionSet> actionSets) {
-		Action act = actionSet.getAction();
-		for (HierarchicalActionSet actSet : actionSets) {
-			if (actSet.equals(actionSet)) continue;
-			Action action = actSet.getAction();
-			
-			if (!areRelatedActions(action, act)) continue;
-			if (action.equals(parentAct)) { // actSet is the parent of actionSet.
-				actionSet.setParent(actSet);
-				actSet.getSubActions().add(actionSet);
-				sortSubActions(actSet);
-				break;
-			} else {
-				if (isPossibileSubAction(action, act)) {
-					// SubAction range： startPosition2 <= startPosition && length <= length2
-					addToActionSets(actionSet, parentAct, actSet.getSubActions());
-				}
-			}
-		}
-	}
-
-	private boolean isPossibileSubAction(Action parent, Action child) {
-		if ((parent instanceof Update && !(child instanceof Addition))
-				|| (parent instanceof Delete && child instanceof Delete)
-				|| (parent instanceof Insert && (child instanceof Insert))) {
-				int startPosition = child.getPosition();
-				int length = child.getLength();
-				int startPosition2 = parent.getPosition();
-				int length2 = parent.getLength();
-				
-				if (!(startPosition2 <= startPosition && length <= length2)) {
-					// when act is not the sub-set of action.
-					return false;
-				}
-		}
-		return true;
-	}
-
-	private void sortSubActions(HierarchicalActionSet actionSet) {
-		ListSorter<HierarchicalActionSet> sorter = new ListSorter<HierarchicalActionSet>(actionSet.getSubActions());
-		List<HierarchicalActionSet> subActions = sorter.sortAscending();
-		if (subActions != null) {
-			actionSet.setSubActions(subActions);
-		}
-	}
-
-	private boolean addToAactionSet(Action act, Action parentAct, List<HierarchicalActionSet> actionSets) {
-		for(HierarchicalActionSet actionSet : actionSets) {
-			Action action = actionSet.getAction();
-			
-			if (!areRelatedActions(action, act)) continue;
-			
-			if (action.equals(parentAct)) { // actionSet is the parent of actSet.
-				HierarchicalActionSet actSet = createActionSet(act, actionSet.getAction(), actionSet);
-				actionSet.getSubActions().add(actSet);
-				sortSubActions(actionSet);
-				return true;
-			} else {
-				if (isPossibileSubAction(action, act)) {
-					// SubAction range: startPosition2 <= startPosition && startPosition + length <= startP + length2
-					List<HierarchicalActionSet> subActionSets = actionSet.getSubActions();
-					if (subActionSets.size() > 0) {
-						boolean added = addToAactionSet(act, parentAct, subActionSets);
-						if (added) {
-							return true;
-						} else {
-							continue;
-						}
-					}
-				}
-			}
-		}
-		return false;
-	}
-
-	List<Action> newParentActions = new ArrayList<>();
-	private Action findParentAction(Action action, List<Action> actions) {
-		
-		ITree parent = action.getNode().getParent();
-		if (parent == null) return null;
-		if (action instanceof Addition) {
-			parent = ((Addition) action).getParent(); // parent in the fixed source code tree
-		}
-		
-		for (Action act : actions) {
-			if (act.getNode().equals(parent)) {
-				if (areRelatedActions(act, action)) {
-					return act;
-				}
-			}
-		}
-		for (Action act : newParentActions) {
-			if (act.getNode().equals(parent)) {
-				if (areRelatedActions(act, action)) {
-					return act;
-				}
-			}
-		}
-		
-		ITree tree = action.getNode();
-		Action parentAction = null;
-		if (!isStatement(tree)) {
-			parentAction = new Update(parent, action.getNode().getParent());
-			newParentActions.add(parentAction);
-			
-			Action higherParentAct = findParentAction(parentAction, actions);
-			HierarchicalActionSet actionSet = null;
-			if (higherParentAct == null) {
-				actionSet = createActionSet(parentAction, higherParentAct, null);
-				actionSets.add(actionSet);
-			} else {
-				if (!addToAactionSet(parentAction, higherParentAct, actionSets)) {
-					// The index of the parent action in the actions' list is larger than the index of this action.
-					actionSet = createActionSet(parentAction, higherParentAct, null);
-					actionSets.add(actionSet);
-				}
-			}
-		}
-		return parentAction;
-	}
-	
-	private boolean isStatement(ITree tree) {
-		int nodeType = tree.getType();
-		if (nodeType == 280002 || nodeType == 280001 || nodeType == 310200 || nodeType == 280100
-				|| nodeType == 300100 || nodeType == 280003 || nodeType == 310100 || nodeType == 310300
-				|| 260300 == nodeType || nodeType == 460000) {// TODO
-					return true;
-		}
-		return false;
-	}
-
-	private boolean areRelatedActions(Action parent, Action child) {
-		if (parent instanceof Move && !(child instanceof Move)) {// If action is MOV, its children must be MOV.
-			return false;
-		}
-		if (parent instanceof Delete && !(child instanceof Delete)) {// If action is DEL, its children must be DEL.
-			return false;
-		}
-		if (parent instanceof Insert && !(child instanceof Addition)) {// If action is INS, its children must be MOV or INS.
-			return false;
-		}
-		return true;
-	}
-}

src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java

@@ -1,625 +0,0 @@
-package edu.lu.uni.serval.gumtree.regroup;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.eclipse.jdt.core.dom.CompilationUnit;
-
-import com.github.gumtreediff.actions.model.Move;
-import com.github.gumtreediff.actions.model.Update;
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.FixPattern.utils.Checker;
-import edu.lu.uni.serval.FixPatternParser.CUCreator;
-import edu.lu.uni.serval.FixPatternParser.violations.Violation;
-import edu.lu.uni.serval.diffentry.DiffEntryHunk;
-
-public class HunkActionFilter {
-	
-	/**
-	 * Filter out the modify actions, which are not in the DiffEntry hunks, without considering the same parent node.
-	 * 
-	 * @param hunks
-	 * @param actionSets
-	 * @return
-	 */
-	public List<HierarchicalActionSet> filterActionsByDiffEntryHunk(List<DiffEntryHunk> hunks, 
-			List<HierarchicalActionSet> actionSets, File revFile, File prevFile) {
-		List<HierarchicalActionSet> uselessActions = new ArrayList<>();
-		
-		CUCreator cuCreator = new CUCreator();
-		CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile);
-		CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile);
-		if (prevUnit == null || revUnit == null) {
-			return uselessActions;
-		}
-		
-		for (HierarchicalActionSet actionSet : actionSets) {
-			// position of buggy statements
-			int startPosition = 0;
-			int endPosition = 0;
-			int startLine = 0;
-			int endLine = 0;
-			// position of fixed statements
-			int startPosition2 = 0;
-			int endPosition2 = 0;
-			int startLine2 = 0;
-			int endLine2 = 0;
-			
-			String actionStr = actionSet.getActionString();
-			if (actionStr.startsWith("INS")) {
-				startPosition2 = actionSet.getStartPosition();
-				endPosition2 = startPosition2 + actionSet.getLength();
-
-				List<Move> firstAndLastMov = getFirstAndLastMoveAction(actionSet);
-				if (firstAndLastMov != null) {
-					startPosition = firstAndLastMov.get(0).getNode().getPos();
-					ITree lastTree = firstAndLastMov.get(1).getNode();
-					endPosition = lastTree.getPos() + lastTree.getLength();
-				}
-			} else {
-				startPosition = actionSet.getStartPosition(); // range of actions
-				endPosition = startPosition + actionSet.getLength();
-				if (actionStr.startsWith("UPD")) {
-					Update update = (Update) actionSet.getAction();
-					ITree newNode = update.getNewNode();
-					startPosition2 = newNode.getPos();
-					endPosition2 = startPosition2 + newNode.getLength();
-				}
-			}
-			startLine = startPosition == 0 ? 0 : prevUnit.getLineNumber(startPosition);
-			endLine =  endPosition == 0 ? 0 : prevUnit.getLineNumber(endPosition);
-			startLine2 =  startPosition2 == 0 ? 0 : revUnit.getLineNumber(startPosition2);
-			endLine2 =  endPosition2 == 0 ? 0 : revUnit.getLineNumber(endPosition2);
-			
-			for (DiffEntryHunk hunk : hunks) {
-				int bugStartLine = hunk.getBugLineStartNum();
-				int bugRange = hunk.getBugRange();
-				int fixStartLine = hunk.getFixLineStartNum();
-				int fixRange = hunk.getFixRange();
-				
-				if (actionStr.startsWith("INS")) {
-					if (fixStartLine + fixRange < startLine2)  {
-						continue;
-					} 
-					if (endLine2 < fixStartLine ) {
-						uselessActions.add(actionSet);
-					} 
-				} else {
-					if (bugStartLine + bugRange < startLine)  {
-						continue;
-					} 
-					if (endLine < bugStartLine ) {
-						uselessActions.add(actionSet);
-					} 
-					break;
-				}
-			}
-			actionSet.setBugStartLineNum(startLine);
-			actionSet.setBugEndLineNum(endLine);
-			actionSet.setFixStartLineNum(startLine2);
-			actionSet.setFixEndLineNum(endLine2);
-		}
-		
-		actionSets.removeAll(uselessActions);
-		uselessActions.clear();
-		return actionSets;
-	}
-	
-	/**
-	 * Filter out the modify actions, which are not in the DiffEntry hunks, with considering the same parent node.
-	 * 
-	 * @param hunks
-	 * @param actionSets
-	 * @return
-	 */
-	public List<HunkFixPattern> filterActionsByDiffEntryHunk2(List<DiffEntryHunk> hunks, 
-			List<HierarchicalActionSet> actionSets, File revFile, File prevFile) {
-		List<HunkFixPattern> allHunkFixPatterns = new ArrayList<>();
-		
-		CUCreator cuCreator = new CUCreator();
-		CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile);
-		CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile);
-		if (prevUnit == null || revUnit == null) {
-			return allHunkFixPatterns;
-		}
-		
-		int i = 0;
-		int size = actionSets.size();
-		for (DiffEntryHunk hunk : hunks) {
-			int hunkBugStartLine = hunk.getBugLineStartNum();
-			int hunkBugRange = hunk.getBugRange();
-			int hunkFixStartLine = hunk.getFixLineStartNum();
-			int hunkFixRange = hunk.getFixRange();
-			
-			for (; i < size; i ++) {
-				HierarchicalActionSet actionSet = actionSets.get(i);
-				int actionBugStartLine = actionSet.getBugStartLineNum();
-				if (actionBugStartLine == 0) {
-					actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit);
-				} 
-				int actionBugEndLine = actionSet.getBugEndLineNum();
-				int actionFixStartLine = actionSet.getFixStartLineNum();
-				int actionFixEndLine = actionSet.getFixEndLineNum();
-				
-				String actionStr = actionSet.getActionString();
-				ITree previousParent = null;
-				List<HierarchicalActionSet> hunkActionSets = new ArrayList<>();
-				
-				if (actionStr.startsWith("INS")) {
-					if (hunkFixStartLine + hunkFixRange < actionFixStartLine)  {
-						addHunkActionSets(hunkActionSets, allHunkFixPatterns, hunk);// save the previous non-null hunkFixPattern.
-						break;
-					} 
-					if (actionFixEndLine >= hunkFixStartLine ) {
-						ITree parent = addToHunkActionSets(actionSet, hunkActionSets, allHunkFixPatterns, previousParent, hunk);
-						if (parent != null) {
-							if (parent != previousParent) {
-								hunkActionSets = new ArrayList<>();
-							}
-							hunkActionSets.add(actionSet);
-						} else if (hunkActionSets.size() > 0) {
-							hunkActionSets = new ArrayList<>();
-						}
-						previousParent = parent;
-					} 
-				} else { // UPD, DEL, MOV
-					if (hunkBugStartLine + hunkBugRange < actionBugStartLine)  { 
-						addHunkActionSets(hunkActionSets, allHunkFixPatterns, hunk);// save the previous non-null hunkFixPattern.
-						break;
-					} 
-					if (actionBugEndLine >= hunkBugStartLine ) {
-						ITree parent = addToHunkActionSets(actionSet, hunkActionSets, allHunkFixPatterns, previousParent, hunk);
-						if (parent != null) { // same parent
-							if (parent != previousParent) {
-								hunkActionSets = new ArrayList<>();
-							}
-							hunkActionSets.add(actionSet);
-						} else if (hunkActionSets.size() > 0) {
-							hunkActionSets = new ArrayList<>();
-						}
-						previousParent = parent;
-					} 
-				}
-				addHunkActionSets(hunkActionSets, allHunkFixPatterns, hunk);
-			}
-		}
-		
-		return allHunkFixPatterns;
-	}
-	
-	private int getEndPosition(List<ITree> children) {
-		int endPosition = 0;
-		for (int i = 0, size = children.size(); i < size; i ++) {
-			ITree child = children.get(i);
-			int type = child.getType();
-			if (Checker.isStatement2(type)) {
-				if ( i > 0) {
-					child = children.get(i - 1);
-					endPosition = child.getPos() + child.getLength();
-				} else {
-					endPosition = child.getPos() - 1;
-				}
-				break;
-			}
-		}
-		return endPosition;
-	}
-	
-	private void addHunkActionSets(List<HierarchicalActionSet> hunkActionSets, List<HunkFixPattern> allHunkFixPatterns, DiffEntryHunk hunk) {
-		if (hunkActionSets.size() > 0) {
-			HunkFixPattern hunkFixPattern = new HunkFixPattern(hunk, hunkActionSets);
-			allHunkFixPatterns.add(hunkFixPattern);
-		}
-	}
-
-	private ITree addToHunkActionSets(HierarchicalActionSet actionSet, List<HierarchicalActionSet> hunkActionSets, 
-			List<HunkFixPattern> allHunkFixPatterns, ITree previousParent, DiffEntryHunk hunk) {
-		String astNodeType = actionSet.getAstNodeType();
-		if ("FieldDeclaration".equals(astNodeType)) {
-			addHunkActionSets(hunkActionSets, allHunkFixPatterns, hunk);
-			hunkActionSets = new ArrayList<>();
-			hunkActionSets.add(actionSet);
-			HunkFixPattern hunkFixPattern = new HunkFixPattern(hunk, hunkActionSets);
-			allHunkFixPatterns.add(hunkFixPattern);
-			return null;
-		} else {
-			ITree currentParent = actionSet.getNode().getParent();
-			if (previousParent == null) {
-				previousParent = currentParent;
-			} else {
-				if (!previousParent.equals(currentParent)) {
-					HunkFixPattern hunkFixPattern = new HunkFixPattern(hunk, hunkActionSets);
-					allHunkFixPatterns.add(hunkFixPattern);
-					previousParent = currentParent;
-				} 
-			}
-			return previousParent;
-		}
-	}
-
-	private List<Move> getFirstAndLastMoveAction(HierarchicalActionSet gumTreeResult) {
-		List<Move> firstAndLastMoveActions = new ArrayList<>();
-		List<HierarchicalActionSet> actions = new ArrayList<>();
-		actions.addAll(gumTreeResult.getSubActions());
-		if (actions.size() == 0) {
-			return null;
-		}
-		Move firstMoveAction = null;
-		Move lastMoveAction = null;
-		while (actions.size() > 0) {
-			List<HierarchicalActionSet> subActions = new ArrayList<>();
-			for (HierarchicalActionSet action : actions) {
-				subActions.addAll(action.getSubActions());
-				if (action.toString().startsWith("MOV")) {
-					if (firstMoveAction == null) {
-						firstMoveAction = (Move) action.getAction();
-						lastMoveAction = (Move) action.getAction();
-					} else {
-						int startPosition = action.getStartPosition();
-						int length = action.getLength();
-						int startPositionFirst = firstMoveAction.getPosition();
-						int startPositionLast = lastMoveAction.getPosition();
-						int lengthLast = lastMoveAction.getNode().getLength();
-						if (startPosition < startPositionFirst || (startPosition == startPositionFirst && length > firstMoveAction.getLength())) {
-							firstMoveAction = (Move) action.getAction();
-						}
-						if ((startPosition + length) > (startPositionLast + lengthLast)) {
-							lastMoveAction = (Move) action.getAction();
-						} 
-					}
-				}
-			}
-			
-			actions.clear();
-			actions.addAll(subActions);
-		}
-		if (firstMoveAction == null) {
-			return null;
-		}
-		firstAndLastMoveActions.add(firstMoveAction);
-		firstAndLastMoveActions.add(lastMoveAction);
-		return firstAndLastMoveActions;
-	}
-
-	/**
-	 * Filter out the modify actions, which are not in the DiffEntry hunks, without considering the same parent node.
-	 * 
-	 * @param violations
-	 * @param actionSets
-	 * @param revFile
-	 * @param prevFile
-	 * @return
-	 */
-	public List<Violation> filterActionsByModifiedRange(List<Violation> violations,
-			List<HierarchicalActionSet> actionSets, File revFile, File prevFile) {
-		
-		List<Violation> selectedViolations = new ArrayList<>();
-		
-		CUCreator cuCreator = new CUCreator();
-		CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile);
-		CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile);
-		if (prevUnit == null || revUnit == null) {
-			return selectedViolations;
-		}
-		
-		for (Violation violation : violations) {
-			int startLine = violation.getStartLineNum();
-			int endLine = violation.getEndLineNum();
-			int bugStartLine = violation.getBugStartLineNum();
-			int bugEndLine = violation.getBugEndLineNum();
-			int fixStartLine = violation.getFixStartLineNum();
-			int fixEndLine = violation.getFixEndLineNum();
-			
-			for (HierarchicalActionSet actionSet : actionSets) {
-				int actionBugStartLine = actionSet.getBugStartLineNum();
-				if (actionBugStartLine == 0) {
-					actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit);
-				} 
-				int actionBugEndLine = actionSet.getBugEndLineNum();
-				int actionFixStartLine = actionSet.getFixStartLineNum();
-				int actionFixEndLine = actionSet.getFixEndLineNum();
-
-				String actionStr = actionSet.getActionString();
-				if (actionStr.startsWith("INS")) {
-					if (fixStartLine <= actionFixStartLine && actionFixEndLine <= fixEndLine) {
-						if (actionBugStartLine != 0) {
-							if (startLine <= actionBugEndLine && endLine >= actionBugStartLine) {
-								violation.getActionSets().add(actionSet);
-							}
-						} else {
-							
-							violation.getActionSets().add(actionSet);
-						}
-					}
-				} else {
-//					if (bugEndLine < actionBugStartLine)  {
-//						break;
-//					}
-					if (bugStartLine <= actionBugStartLine && actionBugEndLine <= bugEndLine) {
-						if (startLine <= actionBugEndLine && endLine >= actionBugStartLine) {
-							violation.getActionSets().add(actionSet);
-						}
-					}
-				}
-			}
-			
-			if (violation.getActionSets().size() > 0) {
-				selectedViolations.add(violation);
-			}
-		}
-		return selectedViolations;
-	}
-
-	/**
-	 * Match hierarchical actions with code change diffs for C code.
-	 * 
-	 * @param diffentryHunks
-	 * @param actionSets
-	 * @param revFile
-	 * @param prevFile
-	 * @return
-	 */
-	public List<DiffEntryHunk> matchActionsByDiffEntryForC(List<DiffEntryHunk> diffentryHunks, List<HierarchicalActionSet> actionSets) {
-
-		List<DiffEntryHunk> selectedViolations = new ArrayList<>();
-
-		for (DiffEntryHunk diffentryHunk : diffentryHunks) {
-			int bugHunkStartLine = diffentryHunk.getBugLineStartNum();
-			int bugHunkEndLine = bugHunkStartLine + diffentryHunk.getBugRange() - 1;
-			int fixHunkStartLine = diffentryHunk.getFixLineStartNum();
-			int fixHunkEndLine = fixHunkStartLine + diffentryHunk.getFixedHunkSize() - 1;
-
-			for (HierarchicalActionSet actionSet : actionSets) {
-				String actionStr = actionSet.getActionString();
-				if (actionStr.startsWith("INS")) {
-					int actionFixStartLine = actionSet.getFixStartLineNum();
-					int actionFixEndLine = actionSet.getFixEndLineNum();
-					if (fixHunkStartLine <= actionFixEndLine && actionFixStartLine <= fixHunkEndLine ) {
-						diffentryHunk.getActionSets().add(actionSet);
-					}
-				} else {
-					int actionBugStartLine = actionSet.getBugStartLineNum();
-					int actionBugEndLine = actionSet.getBugEndLineNum();
-					
-					if (bugHunkStartLine <= actionBugEndLine && actionBugStartLine <= bugHunkEndLine) {
-						diffentryHunk.getActionSets().add(actionSet);
-					}
-				}
-			}
-
-			if (diffentryHunk.getActionSets().size() > 0) {
-				selectedViolations.add(diffentryHunk);
-			}
-		}
-		return selectedViolations;
-	}
-
-
-	/**
-	 * Filter out the modify actions, which are not in the DiffEntry hunks, with considering the same parent node.
-	 * 
-	 * @param violations
-	 * @param actionSets
-	 * @param revFile
-	 * @param prevFile
-	 * @return
-	 */
-	public List<DiffEntryHunk> filterActionsByModifiedRange2(List<DiffEntryHunk> diffentryHunks,
-			List<HierarchicalActionSet> actionSets, File revFile, File prevFile) {
-		
-		List<DiffEntryHunk> selectedViolations = new ArrayList<>();
-		
-		CUCreator cuCreator = new CUCreator();
-		CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile);
-		CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile);
-		if (prevUnit == null || revUnit == null) {
-			return selectedViolations;
-		}
-		
-		for (DiffEntryHunk diffentryHunk : diffentryHunks) {
-//			int violationEndLine = violationStartLine + diffentryHunk.getBugRange();
-			int bugHunkStartLine = diffentryHunk.getBugLineStartNum();
-			int bugHunkEndLine = bugHunkStartLine + diffentryHunk.getBugRange() - 1;
-			int fixHunkStartLine = diffentryHunk.getFixLineStartNum();
-			int fixHunkEndLine = fixHunkStartLine + diffentryHunk.getFixedHunkSize() - 1;
-			
-			for (HierarchicalActionSet actionSet : actionSets) {
-				int actionBugStartLine = actionSet.getBugStartLineNum();
-				if (actionBugStartLine == 0) {
-					actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit);
-				} 
-				int actionBugEndLine = actionSet.getBugEndLineNum();
-				int actionFixStartLine = actionSet.getFixStartLineNum();
-				int actionFixEndLine = actionSet.getFixEndLineNum();
-				
-				String actionStr = actionSet.getActionString();
-				if (actionStr.startsWith("INS")) {
-					if (fixHunkStartLine <= actionFixEndLine && fixHunkEndLine >= actionFixStartLine ) {
-						if (actionBugStartLine != 0) {
-							diffentryHunk.getActionSets().add(actionSet);
-						}
-					}
-				} else {
-					if (bugHunkStartLine <= actionBugEndLine && bugHunkEndLine >= actionBugStartLine) {
-						diffentryHunk.getActionSets().add(actionSet);
-					}
-				}
-			}
-				
-			
-			if (diffentryHunk.getActionSets().size() > 0) {
-				selectedViolations.add(diffentryHunk);
-			}
-		}
-		return selectedViolations;
-	}
-	
-
-	/**
-	 * Filter out the modify actions, which are not in the DiffEntry hunks, without considering DiffEntry hunks.
-	 * 
-	 * @param violations
-	 * @param actionSets
-	 * @param revFile
-	 * @param prevFile
-	 * @return
-	 */
-	public List<Violation> filterActionsByModifiedRange3(List<Violation> violations,
-			List<HierarchicalActionSet> actionSets, File revFile, File prevFile) {
-		
-		List<Violation> selectedViolations = new ArrayList<>();
-		
-		CUCreator cuCreator = new CUCreator();
-		CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile);
-		CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile);
-		if (prevUnit == null || revUnit == null) {
-			return selectedViolations;
-		}
-		
-		for (Violation violation : violations) {
-			int startLine = violation.getStartLineNum();
-			int endLine = violation.getEndLineNum();
-			
-//			ITree parent = null;
-//			List<HierarchicalActionSet> actionSetsWithSameParent = new ArrayList<>(); //TODO
-			for (HierarchicalActionSet actionSet : actionSets) {
-				int actionBugStartLine = actionSet.getStartPosition();
-				int actionBugEndLine = actionSet.getLength();
-				int actionFixStartLine = actionSet.getFixStartLineNum();
-				int actionFixEndLine = actionSet.getFixEndLineNum();
-
-				String actionStr = actionSet.getActionString();
-				if (actionStr.startsWith("INS")) { // FIXME It is impossible to locate the INS action by the buggy line range.
-					if (startLine <= actionFixStartLine && actionFixEndLine <= endLine) {
-						if (actionBugStartLine != 0) {
-							if (startLine <= actionBugEndLine && endLine >= actionBugStartLine) {
-								violation.getActionSets().add(actionSet);
-							}
-						} else {
-							violation.getActionSets().add(actionSet);
-						}
-					}
-				} else {
-//					if (endLine < actionBugStartLine)  {
-//						break;
-//					}
-					if (startLine <= actionBugStartLine && actionBugEndLine <= endLine) {
-						if (startLine <= actionBugEndLine && endLine >= actionBugStartLine) {
-							violation.getActionSets().add(actionSet);
-						}
-					}
-				}
-			}
-			
-			if (violation.getActionSets().size() > 0) {
-				selectedViolations.add(violation);
-			}
-		}
-		return selectedViolations;
-	}
-
-	private int setLineNumbers(HierarchicalActionSet actionSet, CompilationUnit prevUnit, CompilationUnit revUnit) {
-		int actionBugStartLine;
-		int actionBugEndLine;
-		int actionFixStartLine;
-		int actionFixEndLine;
-		
-		// position of buggy statements
-		int bugStartPosition = 0;
-		int bugEndPosition = 0;
-		// position of fixed statements
-		int fixStartPosition = 0;
-		int fixEndPosition = 0;
-		
-		String actionStr = actionSet.getActionString();
-		if (actionStr.startsWith("INS")) {
-			fixStartPosition = actionSet.getStartPosition();
-			fixEndPosition = fixStartPosition + actionSet.getLength();
-
-			List<Move> firstAndLastMov = getFirstAndLastMoveAction(actionSet);
-			if (firstAndLastMov != null) {
-				bugStartPosition = firstAndLastMov.get(0).getNode().getPos();
-				ITree lastTree = firstAndLastMov.get(1).getNode();
-				bugEndPosition = lastTree.getPos() + lastTree.getLength();
-			}
-		} else {
-			bugStartPosition = actionSet.getStartPosition(); // range of actions
-			bugEndPosition = bugStartPosition + actionSet.getLength();
-			if (actionStr.startsWith("UPD")) {
-				Update update = (Update) actionSet.getAction();
-				ITree newNode = update.getNewNode();
-				fixStartPosition = newNode.getPos();
-				fixEndPosition = fixStartPosition + newNode.getLength();
-				
-				String astNodeType = actionSet.getAstNodeType();
-//				if (Checker.withBlockStatement(newNode.getType())) {
-////					List<ITree> children = update.getNode().getChildren();
-////					bugEndPosition = getEndPosition(children);
-////					List<ITree> newChildren = newNode.getChildren();
-////					fixEndPosition = getEndPosition(newChildren);
-//				} else 
-				if ("TypeDeclaration".equals(astNodeType)) {
-					bugEndPosition = getClassBodyStartPosition(update.getNode());
-					fixEndPosition = getClassBodyStartPosition(newNode);
-				} else if ("MethodDeclaration".equals(astNodeType)) {
-					List<ITree> children = update.getNode().getChildren();
-					bugEndPosition = getEndPosition(children);
-					List<ITree> newChildren = newNode.getChildren();
-					fixEndPosition = getEndPosition(newChildren);
-				}
-				if (fixEndPosition == 0) {
-					fixEndPosition = fixStartPosition + newNode.getLength();
-				}
-			} else if (actionStr.startsWith("DEL")) {
-				ITree buggyTree = actionSet.getNode();
-				int type = buggyTree.getType();
-				if (type == 55) { // TypeDeclaration
-					bugEndPosition = getClassBodyStartPosition(buggyTree);
-				} else if (type == 31 || Checker.withBlockStatement(type)) {//MethodDeclaration && Block-Statements
-					List<ITree> children = buggyTree.getChildren();
-					bugEndPosition = getEndPosition(children);
-				}
-			}
-			if (bugEndPosition == 0) {
-				bugEndPosition = bugStartPosition + actionSet.getLength();
-			}
-		}
-		actionBugStartLine = bugStartPosition == 0 ? 0 : prevUnit.getLineNumber(bugStartPosition);
-		actionBugEndLine = bugEndPosition == 0 ? 0 : prevUnit.getLineNumber(bugEndPosition);
-		actionFixStartLine = fixStartPosition == 0 ? 0 : revUnit.getLineNumber(fixStartPosition);
-		actionFixEndLine = fixEndPosition == 0 ? 0 : revUnit.getLineNumber(fixEndPosition);
-		actionSet.setBugStartLineNum(actionBugStartLine);
-		actionSet.setBugEndLineNum(actionBugEndLine);
-		actionSet.setFixStartLineNum(actionFixStartLine);
-		actionSet.setFixEndLineNum(actionFixEndLine);
-		actionSet.setBugEndPosition(bugEndPosition);
-		actionSet.setFixEndPosition(fixEndPosition);
-		
-		return actionBugStartLine;
-	}
-	
-	private int getClassBodyStartPosition(ITree tree) {
-		List<ITree> children = tree.getChildren();
-		for (int i = 0, size = children.size(); i < size; i ++) {
-			ITree child = children.get(i);
-			int type = child.getType();
-			// Modifier, NormalAnnotation, MarkerAnnotation, SingleMemberAnnotation
-			if (type != 83 && type != 77 && type != 78 && type != 79
-				&& type != 5 && type != 39 && type != 43 && type != 74 && type != 75
-				&& type != 76 && type != 84 && type != 87 && type != 88 && type != 42) {
-				// ArrayType, PrimitiveType, SimpleType, ParameterizedType, 
-				// QualifiedType, WildcardType, UnionType, IntersectionType, NameQualifiedType, SimpleName
-				if (i > 0) {
-					child = children.get(i - 1);
-					return child.getPos() + child.getLength() + 1;
-				} else {
-					return child.getPos() - 1;
-				}
-			}
-		}
-		return 0;
-	}
-
-}

src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkFixPattern.java

@@ -1,27 +0,0 @@
-package edu.lu.uni.serval.gumtree.regroup;
-
-import java.util.List;
-
-import edu.lu.uni.serval.diffentry.DiffEntryHunk;
-
-public class HunkFixPattern {
-	
-	private DiffEntryHunk hunk;
-	
-	private List<HierarchicalActionSet> hunkActionSets;
-
-	public HunkFixPattern(DiffEntryHunk hunk, List<HierarchicalActionSet> hunkActionSets) {
-		super();
-		this.hunk = hunk;
-		this.hunkActionSets = hunkActionSets;
-	}
-
-	public DiffEntryHunk getHunk() {
-		return hunk;
-	}
-
-	public List<HierarchicalActionSet> getHunkActionSets() {
-		return hunkActionSets;
-	}
-	
-}

src/main/java/edu/lu/uni/serval/gumtree/regroup/SimpleTree.java

@@ -1,68 +0,0 @@
-package edu.lu.uni.serval.gumtree.regroup;
-
-import java.util.ArrayList;
-import java.util.List;
-
-public class SimpleTree {
-
-	private String nodeType;
-	private String label;
-	private SimpleTree parent;
-	private List<SimpleTree> children = new ArrayList<>();
-
-	public String getNodeType() {
-		return nodeType;
-	}
-
-	public void setNodeType(String nodeType) {
-		this.nodeType = nodeType;
-	}
-
-	public String getLabel() {
-		return label;
-	}
-
-	public void setLabel(String label) {
-		this.label = label;
-	}
-
-	public SimpleTree getParent() {
-		return parent;
-	}
-
-	public void setParent(SimpleTree parent) {
-		this.parent = parent;
-	}
-
-	public List<SimpleTree> getChildren() {
-		return children;
-	}
-
-	public void setChildren(List<SimpleTree> children) {
-		this.children = children;
-	}
-
-	private List<String> strList = new ArrayList<>();
-
-	@Override
-	public String toString() {
-		String str = this.nodeType + "@@" + this.label;
-		if (strList.size() == 0) {
-			strList.add(str);
-			for (SimpleTree child : children) {
-				child.toString();
-				List<String> strList1 = child.strList;
-				for (String str1 : strList1) {
-					strList.add("------" + str1);
-				}
-			}
-		}
-
-		str = "";
-		for (String str1 : strList) {
-			str += str1 + "\n";
-		}
-
-		return str;
-	}
-}

src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java

@@ -1,902 +0,0 @@
-package edu.lu.uni.serval.gumtree.regroup;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import com.github.gumtreediff.actions.model.Action;
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap;
-import edu.lu.uni.serval.FixPattern.utils.Checker;
-import edu.lu.uni.serval.utils.ListSorter;
-
-/**
- * Simplify the ITree of source code into a simple tree.
- * 
- * @author kui.liu
- *
- */
-public class SimplifyTree {
-	
-	private static final String ABSTRACT_TYPE = "T";
-	private static final String ABSTRACT_NAME = "N";
-	private static final String ABSTRACT_METHOD = "m";
-	private static final String ABSTRACT_VARIABLE = "v";
-	
-	private Map<String, String> abstractTypeIdentifiers = new HashMap<>();
-	private Map<String, String> abstractMethodIdentifiers = new HashMap<>();
-	private Map<String, String> abstractNameIdentifiers = new HashMap<>();
-	private Map<String, String> abstractVariableIdentifiers = new HashMap<>();
-
-	/**
-	 * Convert ITree to a source code simple tree, an abstract identifier simple tree, and a semi-source code simple tree.
-	 * 
-	 * @param actionSet
-	 */
-	public void abstractTree(HierarchicalActionSet actionSet) {
-		SimpleTree sourceCodeSimpleTree = null;    // source code tree and AST node type tree
-		SimpleTree abstractIdentifierTree = null;  // abstract identifier tree
-		SimpleTree abstractSimpleTree =  null;     // semi-source code tree. and AST node type tree
-		SimpleTree simpleTree = null; // source code tree with canonical variable names.
-		
-		if (actionSet.getActionString().startsWith("INS")) {
-			List<Action> allMoveActions = getAllMoveActions(actionSet);
-			if (allMoveActions != null) {
-				List<Action> actions = new ArrayList<>();
-				for (Action action : allMoveActions) {
-					boolean hasParent = false;
-					ITree parent = action.getNode().getParent();
-					for (Action act : allMoveActions) {
-						if (act == action)  continue;
-						ITree actNode = act.getNode();
-						if (actNode.equals(parent)) {
-							hasParent = true;
-							break;
-						}
-					}
-					if (!hasParent) {
-						actions.add(action);
-					}
-				}
-//				sourceCodeSimpleTree = sourceCodeTree(actions);
-				simpleTree = canonicalizeSourceCodeTree(actions, null);
-			}
-		} else {
-			ITree tree = actionSet.getNode();
-			String astNodeType = actionSet.getAstNodeType();
-			if (Checker.containsBodyBlock(astNodeType)) {
-				// delete the body block.
-				List<ITree> children = tree.getChildren();
-				List<ITree> newChildren = new ArrayList<>();
-				for (ITree child : children) {
-					if (!child.getLabel().endsWith("Body")) {
-						newChildren.add(child);
-					}
-				}
-				tree.setChildren(newChildren);
-			}
-//			sourceCodeSimpleTree = originalSourceCodeTree(tree, null);
-//			abstractIdentifierTree = abstractIdentifierTree(actionSet, tree, null);
-//			abstractSimpleTree = semiSourceCodeTree(actionSet, tree, null);
-			simpleTree = canonicalizeSourceCodeTree(tree, null);
-		}
-		
-		actionSet.setAbstractSimpleTree(abstractSimpleTree);
-		actionSet.setAbstractIdentifierTree(abstractIdentifierTree);
-		actionSet.setSimpleTree(simpleTree);
-		actionSet.setOriginalTree(sourceCodeSimpleTree);
-	}
-	
-	/**
-	 * Convert ITree to a source code simple tree, an abstract identifier simple tree, and a semi-source code simple tree.
-	 * 
-	 * @param actionSet
-	 */
-	public void abstractTree(HierarchicalActionSet actionSet, int bugEndPosition) {
-		SimpleTree sourceCodeSimpleTree = null;    // source code tree and AST node type tree
-		SimpleTree abstractIdentifierTree = null;  // abstract identifier tree
-		SimpleTree abstractSimpleTree =  null;     // semi-source code tree. and AST node type tree
-		SimpleTree simpleTree = null; // source code tree with canonical variable names.
-		
-		if (actionSet.getActionString().startsWith("INS")) {
-			List<Action> allMoveActions = getAllMoveActions(actionSet);
-			if (allMoveActions != null) {
-				List<Action> actions = new ArrayList<>();
-				for (Action action : allMoveActions) {
-					boolean hasParent = false;
-					ITree parent = action.getNode().getParent();
-					for (Action act : allMoveActions) {
-						if (act == action)  continue;
-						ITree actNode = act.getNode();
-						if (actNode.equals(parent)) {
-							hasParent = true;
-							break;
-						}
-					}
-					if (!hasParent) {
-						actions.add(action);
-					}
-				}
-//				sourceCodeSimpleTree = sourceCodeTree(actions);
-				simpleTree = canonicalizeSourceCodeTree(actions, null);
-			}
-		} else {
-			ITree tree = actionSet.getNode();
-//			String astNodeType = actionSet.getAstNodeType();
-//			if (Checker.containsBodyBlock(astNodeType)) {
-//				// delete the body block.
-//				List<ITree> children = tree.getChildren();
-//				List<ITree> newChildren = new ArrayList<>();
-//				for (ITree child : children) {
-//					if (!child.getLabel().endsWith("Body")) {
-//						newChildren.add(child);
-//					}
-//				}
-//				tree.setChildren(newChildren);
-//			}
-//			sourceCodeSimpleTree = originalSourceCodeTree(tree, null);
-//			abstractIdentifierTree = abstractIdentifierTree(actionSet, tree, null);
-//			abstractSimpleTree = semiSourceCodeTree(actionSet, tree, null);
-//			if (actionSet.getActionString().startsWith("UPD")) {
-//				simpleTree = canonicalizeSourceCodeTree(tree, null, bugEndPosition);
-//			} else {
-//				simpleTree = canonicalizeSourceCodeTree(tree, null);
-//			}
-			simpleTree = canonicalizeSourceCodeTree(tree, null, bugEndPosition);
-		}
-		
-		actionSet.setAbstractSimpleTree(abstractSimpleTree);
-		actionSet.setAbstractIdentifierTree(abstractIdentifierTree);
-		actionSet.setSimpleTree(simpleTree);
-		actionSet.setOriginalTree(sourceCodeSimpleTree);
-	}
-	
-	private SimpleTree canonicalizeSourceCodeTree(List<Action> actions, SimpleTree parent) {
-		SimpleTree simpleTree = new SimpleTree();
-		simpleTree.setLabel("Block");
-		simpleTree.setNodeType("Block");
-		simpleTree.setParent(parent);
-		List<SimpleTree> children = new ArrayList<>();
-		for (Action action : actions) {
-			ITree node = action.getNode();
-			children.add(canonicalizeSourceCodeTree(node, simpleTree));
-		}
-		simpleTree.setChildren(children);
-		return simpleTree;
-	}
-
-	public SimpleTree canonicalizeSourceCodeTree(ITree tree, SimpleTree parent) {
-		SimpleTree simpleTree = new SimpleTree();
-
-		String label = tree.getLabel();
-		String astNode = ASTNodeMap.map.get(tree.getType());
-
-		List<ITree> children = tree.getChildren();
-		if (children.size() > 0) {
-			simpleTree.setNodeType(astNode);
-			if (astNode.endsWith("Type")) {
-				simpleTree.setLabel(canonicalizeTypeStr(label).replaceAll(" ", ""));
-			} else {
-				if ((astNode.equals("SimpleName") || astNode.equals("MethodInvocation"))) {
-					if (label.startsWith("MethodName:")) {
-						simpleTree.setNodeType("MethodName");
-						label = label.substring(11);
-						int argusIndex = label.indexOf(":[");
-						if (argusIndex > 0) {
-							label = label.substring(0, argusIndex);
-						}
-					} else if (label.startsWith("ClassName:")) {
-						simpleTree.setNodeType("ClassName");
-						label = label.substring(10);
-					}
-					simpleTree.setLabel(label);
-				} else {
-					simpleTree.setLabel(astNode);
-				}
-				List<SimpleTree> subTrees = new ArrayList<>();
-				for (ITree child : children) {
-					subTrees.add(canonicalizeSourceCodeTree(child, simpleTree));
-				}
-				simpleTree.setChildren(subTrees);
-			}
-		} else {
-			if (astNode.endsWith("Name")) {
-				// variableName, methodName, QualifiedName
-				if (label.startsWith("MethodName:")) { // <MethodName, name>
-					simpleTree.setNodeType("MethodName");
-					label = label.substring(11);
-					int argusIndex = label.indexOf(":[");
-					if (argusIndex > 0) {
-						label = label.substring(0, argusIndex);
-					}
-					simpleTree.setLabel(label);
-				} else if (label.startsWith("ClassName:")) {
-					simpleTree.setNodeType("ClassName");
-					label = label.substring(10);
-					simpleTree.setLabel(label);
-				} else if (label.startsWith("Name:")) {
-					label = label.substring(5);
-					char firstChar = label.charAt(0);
-					if (Character.isUpperCase(firstChar)) {
-						simpleTree.setNodeType("Name");
-						simpleTree.setLabel(label);
-					} else {// variableName: <VariableName, canonicalName>
-						simpleTree.setNodeType("VariableName");
-						simpleTree.setLabel(canonicalVariableName(label, tree));
-					}
-				} else {// variableName: <VariableName, canonicalName>
-					simpleTree.setNodeType("VariableName");
-					simpleTree.setLabel(canonicalVariableName(label, tree));
-				}
-			} else {
-				simpleTree.setNodeType(astNode);
-				if (astNode.endsWith("Type")) {
-					simpleTree.setLabel(canonicalizeTypeStr(label).replaceAll(" ", ""));
-				} else if (astNode.startsWith("Type")) {
-					simpleTree.setLabel(canonicalizeTypeStr(label).replaceAll(" ", ""));
-				} else if ((astNode.equals("SimpleName") || astNode.equals("MethodInvocation")) && label.startsWith("MethodName:")) {
-					simpleTree.setNodeType("MethodName");
-					label = label.substring(11);
-					int argusIndex = label.indexOf(":[");
-					if (argusIndex > 0) {
-						label = label.substring(0, argusIndex);
-					}
-					simpleTree.setLabel(label);
-				} else {
-					simpleTree.setLabel(label.replaceAll(" ", ""));
-				}
-			}
-		}
-		
-		simpleTree.setParent(parent);
-		return simpleTree;
-	}
-	
-	public void canonicalizeSourceCodeTree(ITree tree) {
-		String label = tree.getLabel();
-		String astNode = ASTNodeMap.map.get(tree.getType());
-
-		List<ITree> children = tree.getChildren();
-		if (children.size() > 0) {
-			if (astNode.endsWith("Type")) {
-			} else {
-				if ((astNode.equals("SimpleName") || astNode.equals("MethodInvocation"))) {
-					if (label.startsWith("MethodName:")) {
-					} else if (label.startsWith("ClassName:")) {
-					}
-				} else {
-				}
-				for (ITree child : children) {
-					canonicalizeSourceCodeTree(child);
-				}
-			}
-		} else {
-			if (astNode.endsWith("Name")) {
-				// variableName, methodName, QualifiedName
-				if (label.startsWith("MethodName:")) { // <MethodName, name>
-				} else if (label.startsWith("ClassName:")) {
-				} else if (label.startsWith("Name:")) {
-					label = label.substring(5);
-					char firstChar = label.charAt(0);
-					if (Character.isUpperCase(firstChar)) {
-//						simpleTree.setNodeType("Name");
-					} else {// variableName: <VariableName, canonicalName>
-						canonicalVariableName(label, tree);
-					}
-				} else {// variableName: <VariableName, canonicalName>
-					canonicalVariableName(label, tree);
-				}
-			}
-		}
-	}
-	
-	public SimpleTree canonicalizeSourceCodeTree(ITree tree, SimpleTree parent, int bugEndPosition) {
-		SimpleTree simpleTree = new SimpleTree();
-
-		String label = tree.getLabel();
-		String astNode = ASTNodeMap.map.get(tree.getType());
-
-		List<ITree> children = tree.getChildren();
-		if (children.size() > 0) {
-			simpleTree.setNodeType(astNode);
-			if (astNode.endsWith("Type")) {
-				simpleTree.setLabel(canonicalizeTypeStr(label).replaceAll(" ", ""));
-			} else {
-				if ((astNode.equals("SimpleName") || astNode.equals("MethodInvocation"))) {
-					if (label.startsWith("MethodName:")) {
-						simpleTree.setNodeType("MethodName");
-						label = label.substring(11);
-						int argusIndex = label.indexOf(":[");
-						if (argusIndex > 0) {
-							label = label.substring(0, argusIndex);
-						}
-					} else if (label.startsWith("ClassName:")) {
-						simpleTree.setNodeType("ClassName");
-						label = label.substring(10);
-					}
-					simpleTree.setLabel(label);
-				} else {
-					simpleTree.setLabel(astNode);
-				}
-				List<SimpleTree> subTrees = new ArrayList<>();
-				for (ITree child : children) {
-					if (child.getPos() > bugEndPosition) continue;
-					subTrees.add(canonicalizeSourceCodeTree(child, simpleTree));
-				}
-				simpleTree.setChildren(subTrees);
-			}
-		} else {
-			if (astNode.endsWith("Name")) {
-				// variableName, methodName, QualifiedName
-				if (label.startsWith("MethodName:")) { // <MethodName, name>
-					simpleTree.setNodeType("MethodName");
-					label = label.substring(11);
-					int argusIndex = label.indexOf(":[");
-					if (argusIndex > 0) {
-						label = label.substring(0, argusIndex);
-					}
-					simpleTree.setLabel(label);
-				} else if (label.startsWith("ClassName:")) {
-					simpleTree.setNodeType("ClassName");
-					label = label.substring(10);
-					simpleTree.setLabel(label);
-				} else if (label.startsWith("Name:")) {
-					label = label.substring(5);
-					char firstChar = label.charAt(0);
-					if (Character.isUpperCase(firstChar)) {
-						simpleTree.setNodeType("Name");
-						simpleTree.setLabel(label);
-					} else {// variableName: <VariableName, canonicalName>
-						simpleTree.setNodeType("VariableName");
-						simpleTree.setLabel(canonicalVariableName(label, tree));
-					}
-				} else {// variableName: <VariableName, canonicalName>
-					simpleTree.setNodeType("VariableName");
-					simpleTree.setLabel(canonicalVariableName(label, tree));
-				}
-			} else {
-				simpleTree.setNodeType(astNode);
-				if (astNode.endsWith("Type")) {
-					simpleTree.setLabel(canonicalizeTypeStr(label).replaceAll(" ", ""));
-				} else if (astNode.startsWith("Type")) {
-					simpleTree.setLabel(canonicalizeTypeStr(label).replaceAll(" ", ""));
-				} else if ((astNode.equals("SimpleName") || astNode.equals("MethodInvocation")) && label.startsWith("MethodName:")) {
-					simpleTree.setNodeType("MethodName");
-					label = label.substring(11);
-					int argusIndex = label.indexOf(":[");
-					if (argusIndex > 0) {
-						label = label.substring(0, argusIndex);
-					}
-					simpleTree.setLabel(label);
-				} else {
-					simpleTree.setLabel(label.replaceAll(" ", ""));
-				}
-			}
-		}
-		
-		simpleTree.setParent(parent);
-		return simpleTree;
-	}
-
-	public String canonicalVariableName(String label, ITree tree) {
-		ITree parent = tree.getParent();
-		if (parent == null) {
-			return label;
-		} else {
-			String matchStr = null;
-			int parentType = parent.getType();
-			if (parentType == 44) { // SingleVariableDeclaration
-				matchStr = matchSingleVariableDeclaration(parent, label);
-			} else if (parentType == 23 || parentType == 58 || parentType == 60) {
-				//FieldDeclaration, VariableDeclarationExpression, VariableDeclarationStatement
-				matchStr = matchVariableDeclarationExpression(parent, label);
-			} else if (parentType == 31) { // MethodDeclaration
-				List<ITree> children = parent.getChildren();
-				int index = children.indexOf(tree);
-				for (int i = index - 1; i >=0; i --) {
-					ITree child = children.get(i);
-					int childType = child.getType();
-					if (childType == 60) { // VariableDeclarationStatement
-						matchStr = matchVariableDeclarationExpression(child, label);
-					} else if (childType == 44) { // SingleVariableDeclaration
-						matchStr = matchSingleVariableDeclaration(child, label);
-					}
-					if (matchStr != null) break;
-				}
-			} else if (parentType ==70 || parentType == 24 ||parentType == 12 || parentType == 54) {
-				// EnhancedForStatement, ForStatement, CatchClause, TryStatement
-				matchStr = matchStatements(parentType, parent, label);
-			} else if (parentType == 55) { // TypeDeclaration: Class Declaration
-				List<ITree> children = parent.getChildren();
-				int index = children.indexOf(tree);
-				for (int i = index - 1; i >=0; i --) {
-					ITree child = children.get(i);
-					if (child.getType() == 23) { // FieldDeclaration
-						matchStr = matchVariableDeclarationExpression(child, label);
-						if (matchStr != null) break;
-					}
-				}
-			} else if (parentType == 8) { // Block body
-				List<ITree> children = parent.getChildren();
-				int index = children.indexOf(tree);
-				for (int i = index - 1; i >=0; i --) {
-					ITree child = children.get(i);
-					if (child.getType() == 60) { // VariableDeclarationStatement
-						matchStr = matchVariableDeclarationExpression(child, label);
-						if (matchStr != null) break;
-					}
-				}
-			}
-			
-			if (matchStr != null) {
-				return matchStr;
-			} else {
-				return canonicalVariableName(label, parent);
-			}
-		}
-	}
-	
-	private String matchStatements(int typeInt, ITree tree, String label) {
-		String matchStr = null;
-		if (typeInt == 70) { // EnhancedForStatement
-			matchStr = matchSingleVariableDeclaration(tree.getChild(0), label);
-		} else if (typeInt == 24) { // ForStatement
-			List<ITree> children = tree.getChildren();
-			for (ITree child : children) {
-				if (child.getType() == 58) {
-					matchStr = matchVariableDeclarationExpression(child, label);
-					if (matchStr != null) break;
-				} else {
-					break;
-				}
-			}
-		} else if (typeInt == 12) { // CatchClause
-			matchStr = matchSingleVariableDeclaration(tree.getChild(0), label);
-		} else if (typeInt == 54) { // TryStatement
-			List<ITree> children = tree.getChildren();
-			for (ITree child : children) {
-				if (child.getType() == 58) { //VariableDeclarationExpression
-					matchStr = matchVariableDeclarationExpression(tree, label);
-					if (matchStr != null) break;
-				} else {
-					break;
-				}
-			}
-		}
-		return null;
-	}
-
-	public Map<String, String> canonicalVariableMap = new HashMap<>();
-	public Map<String, Integer> canonicalVariables = new HashMap<>();
-	
-	private String matchVariableDeclarationExpression(ITree variable, String label) {
-		List<ITree> children = variable.getChildren();
-		ITree type = null;
-		for (int i = 0, size = children.size(); i < size; i ++) {
-			ITree child = children.get(i);
-			if (child.getType() == 59) {// VariableDeclarationFragment
-				if (type == null) {
-					type = children.get(i - 1);
-				}
-				ITree simpleName = child.getChild(0);
-				if (simpleName.getLabel().equals(label)) {
-					String typeStr = canonicalizeTypeStr(type.getLabel());
-					return canonicalizeVariable(label, typeStr);
-				}
-			}
-		}
-		return null;
-	}
-
-	private String matchSingleVariableDeclaration(ITree singleVariable, String label) {
-		List<ITree> children = singleVariable.getChildren();
-		for (int i = 0, size = children.size(); i < size; i ++) {
-			ITree child = children.get(i);
-			if (child.getType() == 42) { // SimpleName
-				if (child.getLabel().equals(label)) {
-					ITree type = children.get(i - 1);
-					String typeStr = canonicalizeTypeStr(type.getLabel());
-					return canonicalizeVariable(label, typeStr);
-				}
-				break;
-			}
-		}
-		return null;
-	}
-
-	private String canonicalizeVariable(String label, String typeStr) {
-		String key = label + ":" + typeStr;
-		if (canonicalVariableMap.containsKey(key)) {
-			label = canonicalVariableMap.get(key);
-		} else {
-			label = typeStr.toLowerCase() + "Var";
-			Integer num = canonicalVariables.get(label);
-			if (num == null) {
-				num = 0;
-			}
-			num ++;
-			canonicalVariables.put(label, num);
-			label += "" + num;
-			canonicalVariableMap.put(key, label);
-		}
-		return label;
-	}
-
-	private String canonicalizeTypeStr(String label) {
-		String typeStr = label;
-		int index1 = typeStr.indexOf("<");
-		if (index1 != -1) {
-			typeStr = typeStr.substring(0, index1);
-		}
-		index1 = typeStr.lastIndexOf(".");
-		if (index1 != -1) {
-			typeStr = typeStr.substring(index1 + 1);
-		}
-		return typeStr;
-	}
-
-//	public static String addPrefixByType(Type type) {
-//		String newName = "";
-//		if (type instanceof PrimitiveType) {
-//			// byte,short,char,int,long,float,double,boolean,void
-//			newName = type.toString().toLowerCase();
-//		} else if (type instanceof ArrayType) {
-//			// Type [ ]
-//			ArrayType at = (ArrayType) type;
-//			type = at.getElementType();
-//			if (type instanceof SimpleType || type instanceof PrimitiveType) {
-//				newName = getNewName(type);
-//			} else {
-//				newName = addPrefixByType(type);
-//			}
-//		} else if (type instanceof SimpleType) {
-//			// TypeName
-//			if (type.toString().equals("Integer")) {
-//				newName = "int";
-//			} else {
-//				newName = getNewName(type);
-//			}
-//		} else if (type instanceof QualifiedType) {
-//			// Type.SimpleName
-//			newName = ((QualifiedType) type).getName().toString().toLowerCase();
-//		} else if (type instanceof ParameterizedType) {
-//			// Type < Type { , Type } > 泛型
-//			ParameterizedType t = (ParameterizedType) type;
-//			newName = getNewName(t.getType());
-//		} else if (type instanceof WildcardType) {
-//			newName = "object";
-//		} 
-//		return newName;
-//	}
-//	
-//	private static String getNewName(Type type) {
-//		String newName = "";
-//		String typeName = type.toString();
-//		int dot = typeName.lastIndexOf(".");
-//		if (dot > 0) {
-//			newName = typeName.substring(dot + 1).toString().toLowerCase();
-//		} else {
-//			newName = typeName.toString().toLowerCase();
-//		}
-//		return newName;
-//	}
-	
-	/**
-	 * Convert the Move actions of an INS action into a simple tree with AST nodes and leaf labels.
-	 * 
-	 * @param actions
-	 * @return
-	 */
-	private SimpleTree sourceCodeTree(List<Action> actions) {
-		if (actions.size() > 0) {
-			SimpleTree simpleTree = new SimpleTree();
-			simpleTree.setNodeType("Block");
-			simpleTree.setLabel("Block");
-			simpleTree.setParent(null);
-			List<SimpleTree> subTrees = new ArrayList<>();
-			for (Action action : actions) {
-				ITree node = action.getNode();
-				subTrees.add(sourceCodeTree(node, simpleTree));
-			}
-			simpleTree.setChildren(subTrees);
-			
-			return simpleTree;
-		}
-		return null;
-	}
-
-	/**
-	 * Convert a Move action into a simple tree with AST nodes and leaf labels.
-	 * 
-	 * @param tree
-	 * @param parent
-	 * @return
-	 */
-	private SimpleTree sourceCodeTree(ITree tree, SimpleTree parent) {
-		SimpleTree simpleTree = new SimpleTree();
-		String astNode = ASTNodeMap.map.get(tree.getType());
-		do {
-			if (astNode.endsWith("Statement") || astNode.equals("FieldDeclaration")) break;
-			
-			tree = tree.getParent();
-			astNode = ASTNodeMap.map.get(tree.getType());// FIXME if the ASTNode is a method declaration or class declaration?
-		} while (!astNode.endsWith("Statement") && !astNode.equals("FieldDeclaration"));
-
-		String label = tree.getLabel();
-		List<ITree> children = tree.getChildren();
-		if (children.size() > 0) {
-			List<SimpleTree> subTrees = new ArrayList<>();
-			for (ITree child : children) {
-				subTrees.add(sourceCodeTree(child, simpleTree));
-			}
-			simpleTree.setChildren(subTrees);
-			simpleTree.setLabel(astNode);
-		} else {
-			simpleTree.setLabel(label);
-		}
-		simpleTree.setNodeType(astNode);
-		simpleTree.setParent(parent);
-		return simpleTree;
-	}
-
-	/**
-	 * Convert an UPD/DEL/MOV action into a simple tree with AST nodes and leaf labels.
-	 * 
-	 * @param tree
-	 * @param parent
-	 * @return
-	 */
-	private SimpleTree originalSourceCodeTree(ITree tree, SimpleTree parent) {
-		SimpleTree simpleTree = new SimpleTree();
-
-		String label = tree.getLabel();
-		String astNode = ASTNodeMap.map.get(tree.getType());
-
-		simpleTree.setNodeType(astNode);
-		List<ITree> children = tree.getChildren();
-		if (children.size() > 0) {
-			List<SimpleTree> subTrees = new ArrayList<>();
-			for (ITree child : children) {
-				subTrees.add(originalSourceCodeTree(child, simpleTree));
-			}
-			simpleTree.setChildren(subTrees);
-			simpleTree.setLabel(astNode);
-		} else {
-			simpleTree.setLabel(label);
-		}
-		
-		simpleTree.setParent(parent);
-		return simpleTree;
-	}
-
-	/**
-	 * Convert an UPD/DEL/MOV action into a simple tree with abstract identifiers of AST nodes and abstract identifiers of leaf labels.
-	 * 
-	 * @param actionSet
-	 * @param tree
-	 * @param parent
-	 * @return
-	 */
-	private SimpleTree abstractIdentifierTree(ITree tree, SimpleTree parent) {
-		SimpleTree simpleTree = new SimpleTree();
-
-		String label = tree.getLabel();
-		String astNode = ASTNodeMap.map.get(tree.getType());
-
-		simpleTree.setNodeType(astNode);
-		List<ITree> children = tree.getChildren();
-		if (children.size() > 0) {
-			if (astNode.endsWith("Type")) {
-				simpleTree.setNodeType("Type");
-				simpleTree.setLabel(getAbstractLabel(abstractTypeIdentifiers, label, ABSTRACT_TYPE)); // abstract Type identifier
-			} else {
-				List<SimpleTree> subTrees = new ArrayList<>();
-				for (ITree child : children) {
-					subTrees.add(abstractIdentifierTree(child, simpleTree));
-				}
-				simpleTree.setChildren(subTrees);
-				simpleTree.setLabel(astNode);
-			}
-		} else {
-			if (astNode.endsWith("Type")) {
-				simpleTree.setNodeType("Type");
-				if (astNode.equals("WildcardType")) {
-					simpleTree.setLabel("?");
-				} else {
-					simpleTree.setLabel(getAbstractLabel(abstractTypeIdentifiers, label, ABSTRACT_TYPE)); // abstract Type identifier
-				}
-			} else if (astNode.endsWith("Name")) {
-				// variableName, methodName, QualifiedName
-				if (label.startsWith("MethodName:")) { // <Method, name>
-					label = label.substring(11);
-					simpleTree.setNodeType("Method");
-					simpleTree.setLabel(getAbstractLabel(abstractMethodIdentifiers, label, ABSTRACT_METHOD)); // abstract method identifier
-				} else if (label.startsWith("Name:")) {
-					label = label.substring(5);
-					String firstChar = label.substring(0, 1);
-					if (firstChar.equals(firstChar.toUpperCase())) {
-						simpleTree.setNodeType("Name");
-						simpleTree.setLabel(getAbstractLabel(abstractNameIdentifiers, label, ABSTRACT_NAME)); // abstract Name identifier
-					} else {// variableName: <Variable, var>
-						simpleTree.setNodeType("Variable");
-						simpleTree.setLabel(getAbstractLabel(abstractVariableIdentifiers, label, ABSTRACT_VARIABLE));// abstract Variable identifier
-					}
-				} else {// variableName: <Variable, var>
-					simpleTree.setNodeType("Variable");
-					simpleTree.setLabel(getAbstractLabel(abstractVariableIdentifiers, label, ABSTRACT_VARIABLE));// abstract Variable identifier
-				}
-			} else if (astNode.equals("BooleanLiteral") || astNode.equals("CharacterLiteral") || astNode.equals("NullLiteral")
-						|| astNode.equals("NumberLiteral") || astNode.equals("StringLiteral") || astNode.equals("ThisExpression")
-						|| astNode.equals("Modifier") || astNode.equals("Operator")) {
-				simpleTree.setNodeType(astNode);
-				simpleTree.setLabel(label);
-			}
-		}
-		
-		simpleTree.setParent(parent);
-		return simpleTree;
-	}
-	
-	/**
-	 * Convert an UPD/DEL/MOV action into a semi-source code simple tree by abstracting the non-buggy code.
-	 * 
-	 * @param actionSet
-	 * @param tree
-	 * @param parent
-	 * @return
-	 */
-	private SimpleTree semiSourceCodeTree(HierarchicalActionSet actionSet, ITree tree, SimpleTree parent) {
-		SimpleTree simpleTree = new SimpleTree();
-		simpleTree.setParent(parent);
-		// deep first
-		abstractBuggyTreeDeepFirst(actionSet, tree, simpleTree);
-		
-		return simpleTree;
-	}
-	
-	private void abstractBuggyTreeDeepFirst(HierarchicalActionSet actionSet, ITree tree, SimpleTree simpleTree) {
-		List<ITree> children = tree.getChildren();
-		HierarchicalActionSet modifyAction = findHierarchicalActionSet(tree.getPos(), tree.getLength(), actionSet);
-		String label = tree.getLabel();
-		String astNode = ASTNodeMap.map.get(tree.getType());
-
-		if (Checker.isExpressionType(astNode)) {
-			if (modifyAction == null || !modifyAction.getActionString().contains("@@" + label)) {
-				simpleTree.setNodeType("Expression");
-				simpleTree.setLabel("EXP"); // astNode
-			}
-		} else {
-			if (astNode.endsWith("Type")) { // <Type, ?> TODO: sub Type
-				simpleTree.setNodeType("Type");
-				// simpleTree.setLabel("?");
-				if (astNode.equals("WildcardType")) {
-					simpleTree.setLabel("?");
-				} else { // ArrayType, PrimitiveType, SimpleType, ParameterizedType, QualifiedType, WildcardType, UnionType,NameQualifiedType, IntersectionType
-					simpleTree.setLabel(astNode + "@@" + label);
-				}
-			} else if (astNode.endsWith("Name")) { // variableName, methodName, QualifiedName
-				if (label.startsWith("MethodName:")) { // <Method, name>
-					label = label.substring(11);
-					simpleTree.setNodeType("Method");
-					simpleTree.setLabel(label);
-				} else if (label.startsWith("Name:")) {
-					label = label.substring(5);
-					String firstChar = label.substring(0, 1);
-					if (firstChar.equals(firstChar.toUpperCase())) {
-						simpleTree.setNodeType("Name");
-						simpleTree.setLabel(label); // <Name, name>
-					} else {// variableName: <Variable, var>
-						simpleTree.setNodeType("Variable");
-						simpleTree.setLabel(getAbstractLabel(abstractVariableIdentifiers, label, ABSTRACT_VARIABLE));
-					}
-				} else {// variableName: <Variable, var>
-					simpleTree.setNodeType("Variable");
-					simpleTree.setLabel(getAbstractLabel(abstractVariableIdentifiers, label, ABSTRACT_VARIABLE));
-				}
-			} else if (astNode.equals("BooleanLiteral") ||astNode.equals("CharacterLiteral") || astNode.equals("ThisExpression")
-						|| astNode.equals("NullLiteral") || astNode.equals("NumberLiteral") || astNode.equals("StringLiteral")
-						|| astNode.equals("Modifier") || astNode.equals("Operator")) {
-				simpleTree.setNodeType(astNode);
-				simpleTree.setLabel(label);
-			} else {
-				simpleTree.setNodeType(astNode);
-				simpleTree.setLabel(astNode);
-			}
-		}
-		
-		List<SimpleTree> simpleChildren = new ArrayList<>();
-		if (children != null && !astNode.endsWith("Type")) {
-			for (ITree child : children) {
-				simpleChildren.add(semiSourceCodeTree(actionSet, child, simpleTree));
-			}
-		}
-		simpleTree.setChildren(simpleChildren);
-	}
-	
-	private List<Action> getAllMoveActions(HierarchicalActionSet actionSet) {
-		String astNodeType = actionSet.getAstNodeType();
-		if (Checker.containsBodyBlock(astNodeType)) {
-			List<Action> allMoveActions = getAllMoveActions2(actionSet);
-			if (allMoveActions != null && allMoveActions.size() > 0) {
-				ListSorter<Action> sorter = new ListSorter<Action>(allMoveActions);
-				List<Action> moveActions = sorter.sortAscending();
-				if (moveActions != null) {
-					allMoveActions = moveActions;
-				}
-				return allMoveActions;
-			} else {// FIXME: pure INS actions.
-				return null;
-			}
-		} else {// FIXME: pure INS actions.
-			return null;
-		}
-		/**
-		 * Variables, non-new and used in the inserted statements, could be selected to localize buggy code
-		 */
-	}
-
-	private List<Action> getAllMoveActions2(HierarchicalActionSet actionSet) {
-		List<Action> allMoveActions = new ArrayList<>();
-		List<HierarchicalActionSet> actions = new ArrayList<>();
-		actions.addAll(actionSet.getSubActions());
-		if (actions.size() == 0) {
-			return null;
-		}
-		while (actions.size() > 0) {
-			List<HierarchicalActionSet> subActions = new ArrayList<>();
-			for (HierarchicalActionSet action : actions) {
-				subActions.addAll(action.getSubActions());
-				if (action.toString().startsWith("MOV")) {
-					allMoveActions.add(action.getAction());
-				}
-			}
-			
-			actions.clear();
-			actions.addAll(subActions);
-		}
-		return allMoveActions;
-	}
-	
-	private String getAbstractLabel(Map<String, String> map, String label, String nameType) {
-		if (map.containsKey(label)) {
-			return map.get(label);
-		} else {
-			String name = nameType + map.size();
-			map.put(label, name);
-			return name;
-		}
-	}
-
-	private HierarchicalActionSet findHierarchicalActionSet(int position, int length, HierarchicalActionSet actionSet) {
-		if (actionSet.getStartPosition() == position && actionSet.getLength() == length && !actionSet.getActionString().startsWith("INS")) {
-			return actionSet;
-		} else {
-			for (HierarchicalActionSet subActionSet : actionSet.getSubActions()) {
-				HierarchicalActionSet actSet = findHierarchicalActionSet(position, length, subActionSet);
-				if (actSet != null) {
-					return actSet;
-				}
-			}
-		}
-		return null;
-	}
-
-	public Map<String, String> getAbstractTypeIdentifiers() {
-		return abstractTypeIdentifiers;
-	}
-
-	public Map<String, String> getAbstractMethodIdentifiers() {
-		return abstractMethodIdentifiers;
-	}
-
-	public Map<String, String> getAbstractNameIdentifiers() {
-		return abstractNameIdentifiers;
-	}
-
-	public Map<String, String> getAbstractVariableIdentifiers() {
-		return abstractVariableIdentifiers;
-	}
-
-}

src/main/java/edu/lu/uni/serval/gumtree/regroup/Traveler.java

@@ -1,140 +0,0 @@
-package edu.lu.uni.serval.gumtree.regroup;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap;
-
-/**
- * A traveler to travel a tree-constructed object.
- * 
- * @author kui.liu
- *
- */
-public class Traveler {
-
-	public List<List<String>> list = new ArrayList<>();
-	
-	/**
-	 * Get all action string by traveling HierarchicalActionSet in a deep-first way.
-	 *  
-	 * @param actionSet
-	 * @param astNodeTypeActionQueue
-	 */
-	public void travelActionSetDeepFirstToASTNodeQueue(HierarchicalActionSet actionSet, List<String> astNodeTypeActionQueue) {
-		if (actionSet == null) {
-			System.err.println("Null Action set!");
-		} else {
-			if (astNodeTypeActionQueue == null) {
-				astNodeTypeActionQueue = new ArrayList<>();
-			}
-			
-			String actionStr = actionSet.getActionString();
-			actionStr = actionStr.substring(0, actionStr.indexOf("@@"));
-			astNodeTypeActionQueue.add(actionStr); // RawToken: TODO
-			
-			if (actionStr.startsWith("DEL")) {
-				list.add(astNodeTypeActionQueue); // FIXME BUG: Change AST node type 1 to AST node type 2. Solve method: a list is one pattern.
-			} else {
-				List<HierarchicalActionSet> subActionSet = actionSet.getSubActions();
-				int size = subActionSet.size();
-				if (size > 0) {
-					for (HierarchicalActionSet subAction : subActionSet) {
-						List<String> astNodeTypeActionQueue_ = new ArrayList<>();
-						astNodeTypeActionQueue_.addAll(astNodeTypeActionQueue);
-						travelActionSetDeepFirstToASTNodeQueue(subAction, astNodeTypeActionQueue_);
-					}
-				} else {
-					list.add(astNodeTypeActionQueue);
-				}
-			}
-		}
-	}
-	
-	/**
-	 * Get all AST node types of a root tree by traveling the root tree in a deep-first way.
-	 * 
-	 * @param root
-	 * @return
-	 */
-	public static List<String> travelTreeDeepFirstToASTNodeQueue(ITree root) {
-		if (root == null) {
-			System.err.println("Null tree!");
-			return null;
-		}
-		
-		List<String> astNodeTypeQueue = new ArrayList<>();
-		astNodeTypeQueue.add(ASTNodeMap.map.get(root.getType())); // RawToken: root.getLabel();
-		
-		List<ITree> childrenTreeList = root.getChildren();
-		
-		if (childrenTreeList != null && childrenTreeList.size() > 0) {
-			for (ITree childTree : childrenTreeList) {
-				astNodeTypeQueue.addAll(travelTreeDeepFirstToASTNodeQueue(childTree));
-			}
-		}
-		return astNodeTypeQueue;
-	}
-	
-	/**
-	 *  Get all AST node types of a root tree by traveling the root tree in a breadth-first way.
-	 *  
-	 * @param root
-	 * @return
-	 */
-	public static List<String> travelTreeBreadthFirstToASTNodeQueue(ITree root) {
-		if (root == null) {
-			System.err.println("Null tree.");
-			return null;
-		}
-		
-		List<String> astNodeTypeQueue = new ArrayList<>();
-		astNodeTypeQueue.add(ASTNodeMap.map.get(root.getType())); // RawToken: root.getLabel();
-		
-		List<ITree> treeList = new ArrayList<>();
-		treeList.add(root);
-		while (!treeList.isEmpty()) {
-			List<ITree> childrenTreeList = new ArrayList<>();
-			for (ITree tree : treeList) {
-				astNodeTypeQueue.addAll(travelTreeBreadthFirstToASTNodeQueue(tree));
-				childrenTreeList.addAll(tree.getChildren());
-			}
-			
-			treeList.clear();
-			treeList.addAll(childrenTreeList);
-		}
-		return astNodeTypeQueue;
-	}
-	
-	/**
-	 * Convert a root ITree into a SimpleTree by traveling the root tree in a deep-first way.
-	 * 
-	 * SimpleTree node label is root.toShortString().
-	 * 
-	 * @param root
-	 * @param parent
-	 * @return
-	 */
-	public static SimpleTree travelITreeDeepFirstToSimpleTree(ITree root, SimpleTree parent) {
-		if (root == null) {
-			System.err.println("Null tree!");
-			return null;
-		}
-		SimpleTree simpleTree = new SimpleTree();
-		simpleTree.setLabel(root.toShortString());
-		simpleTree.setParent(parent);
-		List<SimpleTree> children = new ArrayList<>();
-		
-		List<ITree> childrenTreeList = root.getChildren();
-		if (childrenTreeList != null && childrenTreeList.size() > 0) {
-			for (ITree childTree : childrenTreeList) {
-				children.add(travelITreeDeepFirstToSimpleTree(childTree, simpleTree));
-			}
-		}
-		simpleTree.setChildren(children);
-		return simpleTree;
-	}
-	
-}

src/main/java/edu/lu/uni/serval/livestudy/Alarm.java

@@ -1,33 +0,0 @@
-package edu.lu.uni.serval.livestudy;
-
-public class Alarm {
-	private String alarmType;
-	private String fileName;
-	private int startLine;
-	private int endLine;
-
-	public String getAlarmType() {
-		return alarmType;
-	}
-
-	public String getFileName() {
-		return fileName;
-	}
-
-	public int getStartLine() {
-		return startLine;
-	}
-
-	public int getEndLine() {
-		return endLine;
-	}
-
-	public Alarm(String alarmType, String fileName, int startLine, int endLine) {
-		super();
-		this.alarmType = alarmType;
-		this.fileName = fileName;
-		this.startLine = startLine;
-		this.endLine = endLine;
-	}
-	
-}

src/main/java/edu/lu/uni/serval/livestudy/ParseViolations.java

@@ -1,212 +0,0 @@
-package edu.lu.uni.serval.livestudy;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Scanner;
-
-import edu.lu.uni.serval.FixPatternParser.Tokenizer;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.gumtree.regroup.SimpleTree;
-import edu.lu.uni.serval.utils.FileHelper;
-
-public class ParseViolations {
-
-	private static final String OUTPUT_PATH = Configuration.ROOT_PATH + "LiveStudy/BugsInfo/";
-	private static int i = 0;
-	private static int j = 0;
-	
-	public static void main(String[] args) {
-		// output path
-//		FileHelper.deleteDirectory(OUTPUT_PATH);
-		List<String> projects = new ArrayList<>();
-		File[] files = new File(OUTPUT_PATH).listFiles();
-		for (File file : files) {
-			if (file.isDirectory()) {
-				projects.add(file.getName());
-			}
-		}
-		String projectsPath = Configuration.ROOT_PATH + "LiveStudy/projects/";
-		String bugsListPath = Configuration.ROOT_PATH + "LiveStudy/BugsList/";
-		List<File> bugsListFiles = FileHelper.getAllFiles(bugsListPath, ".list");
-		for (File bugsListFile : bugsListFiles) {
-			String fileName = FileHelper.getFileNameWithoutExtension(bugsListFile);
-			if (projects.contains(fileName)) continue;
-			ParseViolations parser = new ParseViolations();
-			Map<String, Violation> violations = new HashMap<>(); // <ProjectName, Violations>, Violation: <projectName, List<Alarm>>.
-			violations = parser.readViolations(bugsListFile);
-			parser.parseViolationToTokens(violations, projectsPath);
-		}
-
-		System.out.println(i);
-		System.out.println(j);
-	}
-
-	/**
-	 * Get the source code tokens of all violation instances by visiting each java project.
-	 * 
-	 * @param violations
-	 * @param projectsPath
-	 */
-	public void parseViolationToTokens(Map<String, Violation> violations, String projectsPath) {
-		for (Map.Entry<String, Violation> entry : violations.entrySet()) {
-			String projectName = entry.getKey();
-			List<Alarm> alarms = entry.getValue().getAlarms();
-			List<File> javaFiles = FileHelper.getAllFiles(projectsPath + projectName, ".java");
-			
-			//Each violation: commons-math : DLS_DEAD_LOCAL_STORE : org/apache/commons/math4/dfp/Dfp.java : 2049 : 2049
-			/**
-			 * @ProjectName
-			 * @ViolationType
-			 * @FileName
-			 * @LineNumber
-			 * @SourceCode
-			 * @Tokens
-			 * @NumberOfTokens
-			 */
-			// sizes file, tokens file, and bugs-info file
-			StringBuilder sizesBuilder = new StringBuilder();
-			StringBuilder tokensBuilder = new StringBuilder();
-			StringBuilder bugsInfoBuilder = new StringBuilder();
-			for (Alarm alarm : alarms) {
-				String fileName = alarm.getFileName();
-//				if (fileName.toLowerCase(Locale.ENGLISH).contains("test")) continue;
-				
-				File sourceCodeFile = locateSourceCodeFile(javaFiles, fileName);
-				if (sourceCodeFile == null) {
-					j ++;
-					continue;
-				}
-				
-				Parser parser = new Parser(alarm, sourceCodeFile);
-				parser.parse();
-				SimpleTree simpleTree = parser.getSimpleTree();
-				
-				if (simpleTree != null) {
-					int finalStartLine = parser.getFinalStartLine();
-					int finalEndLine = parser.getFinalEndLine();
-					String violationType = alarm.getAlarmType();
-					
-					String tokens = Tokenizer.getTokensDeepFirst(simpleTree);
-					String[] tokensArray = tokens.split(" ");
-					int length = tokensArray.length;
-					StringBuilder sourceCode = readSourceCode(sourceCodeFile, finalStartLine, finalEndLine);
-					
-					sizesBuilder.append(length).append("\n");
-					tokensBuilder.append(tokens).append("\n");
-					bugsInfoBuilder.append("###BugInstance###\n##Info:");
-					bugsInfoBuilder.append(violationType).append(":");
-					bugsInfoBuilder.append(projectName).append(":");
-					bugsInfoBuilder.append(fileName).append(":");
-					bugsInfoBuilder.append(finalStartLine).append(":");
-					bugsInfoBuilder.append(finalEndLine).append("\n");
-					bugsInfoBuilder.append(sourceCode).append("\n");
-					i ++;
-				} else {
-					j ++;
-				}
-			}
-
-			FileHelper.outputToFile(OUTPUT_PATH + "sizes.list", sizesBuilder, true);
-			FileHelper.outputToFile(OUTPUT_PATH + "tokens.list", tokensBuilder, true);
-			FileHelper.outputToFile(OUTPUT_PATH + "bugsInfo.list", bugsInfoBuilder, true);
-		}
-	}
-
-	private StringBuilder readSourceCode(File javaFile, int startLine, int endLine) {
-		StringBuilder sourceCode = new StringBuilder("##Source_Code:\n");
-		FileInputStream fis = null;
-		Scanner scanner = null;
-		
-		try {
-			fis = new FileInputStream(javaFile);
-			scanner = new Scanner(fis);
-			int counter = 0;
-			while (scanner.hasNextLine()) {
-				String line = scanner.nextLine();
-				counter ++;
-				if (startLine <= counter && counter <= endLine) {
-					sourceCode.append(line + "\n");
-				}
-				if (counter == endLine) break;
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				scanner.close();
-				fis.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		
-		return sourceCode;
-	}
-
-	private File locateSourceCodeFile(List<File> javaFiles, String fileName) {
-		for (File javaFile : javaFiles) {
-			if (javaFile.getPath().endsWith(fileName)) return javaFile;
-		}
-		return null;
-	}
-
-	public Map<String, Violation> readViolations(String violationFile) {
-		return readViolations(new File(violationFile));
-	}
-	
-	public Map<String, Violation> readViolations(File violationFile) {
-		Map<String, Violation> violations = new HashMap<>();
-		
-		FileInputStream fis = null;
-		Scanner scanner = null;
-		try {
-			fis = new FileInputStream(violationFile);
-			scanner = new Scanner(fis);
-			
-			while (scanner.hasNextLine()) {
-				//commons-math : DLS_DEAD_LOCAL_STORE : org/apache/commons/math4/dfp/Dfp.java : 2049 : 2049
-				String line = scanner.nextLine();
-				String[] elements = line.split(" : ");
-				String projectName = elements[0];
-				String alarmType = elements[1];
-				String fileName = elements[2];
-				int startLine = Integer.parseInt(elements[3]);
-				int endLine = Integer.parseInt(elements[4]);
-				
-				Alarm alarm = new Alarm(alarmType, fileName, startLine, endLine);
-				addAlarmToViolations(projectName, alarm, violations);
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				scanner.close();
-				fis.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		
-		return violations;
-	}
-
-	private void addAlarmToViolations(String projectName, Alarm alarm, Map<String, Violation> violations) {
-		Violation violation = null;
-		if (violations.containsKey(projectName)) {
-			violation = violations.get(projectName);
-		} else {
-			violation = new Violation(projectName);
-			violations.put(projectName, violation);
-		}
-		
-		List<Alarm> alarms = violation.getAlarms();
-		alarms.add(alarm);
-	}
-
-}

src/main/java/edu/lu/uni/serval/livestudy/Parser.java

@@ -1,84 +0,0 @@
-package edu.lu.uni.serval.livestudy;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.gumtree.regroup.SimpleTree;
-import edu.lu.uni.serval.gumtree.regroup.SimplifyTree;
-import edu.lu.uni.serval.violation.code.parser.ViolationSourceCodeTree;
-
-public class Parser {
-	// input
-	private Alarm alarm;
-	private File sourceCodeFile;
-	
-	// output
-	private int finalStartLine = 0;
-	private int finalEndLine = 0;
-	private SimpleTree simpleTree = null;
-	
-	public Parser(Alarm alarm, File sourceCodeFile) {
-		this.alarm = alarm;
-		this.sourceCodeFile = sourceCodeFile;
-	}
-
-	public int getFinalStartLine() {
-		return finalStartLine;
-	}
-
-	public int getFinalEndLine() {
-		return finalEndLine;
-	}
-
-	public SimpleTree getSimpleTree() {
-		return simpleTree;
-	}
-
-	public void parse() {
-		int startLine = this.alarm.getStartLine();
-		int endLine = this.alarm.getEndLine();
-		
-		String violationType = this.alarm.getAlarmType();
-	
-		ViolationSourceCodeTree treeParser = new ViolationSourceCodeTree(this.sourceCodeFile, startLine, endLine);
-		
-		if ("EQ_DOESNT_OVERRIDE_EQUALS".equals(violationType)|| "HE_EQUALS_USE_HASHCODE".equals(violationType)
-				|| "HE_INHERITS_EQUALS_USE_HASHCODE".equals(violationType)|| "SE_NO_SUITABLE_CONSTRUCTOR".equals(violationType)
-				|| "RI_REDUNDANT_INTERFACES".equals(violationType) || "CN_IDIOM".equals(violationType)
-				|| "SE_NO_SERIALVERSIONID".equals(violationType) || "SE_COMPARATOR_SHOULD_BE_SERIALIZABLE".equals(violationType)) {
-			// Class name level, tokens
-			// classStartP <= vS <= vE <= classEndP
-			ITree classNameTree = treeParser.getClassNameTokens();
-			if (classNameTree != null) {
-				this.simpleTree = new SimplifyTree().canonicalizeSourceCodeTree(classNameTree, null);
-			} else {
-				System.err.println("#Null_Violation_Hunk: " + this.alarm.getAlarmType() + ":" + this.sourceCodeFile.getPath() + ":" + startLine + ":" + endLine);
-			}
-		} else {
-			treeParser.extract();
-			List<ITree> matchedTrees = treeParser.getViolationSourceCodeTrees();
-			if (matchedTrees.size() == 0) {
-				System.err.println("#Null_Violation_Hunk: " + this.alarm.getAlarmType() + ":" + this.sourceCodeFile.getPath() + ":" + startLine + ":" + endLine);
-			} else {
-				this.simpleTree = new SimpleTree();
-				this.simpleTree.setLabel("Block");
-				this.simpleTree.setNodeType("Block");
-				List<SimpleTree> children = new ArrayList<>();
-				for (ITree matchedTree : matchedTrees) {
-					SimpleTree simpleT = new SimplifyTree().canonicalizeSourceCodeTree(matchedTree, this.simpleTree);
-					children.add(simpleT);
-				}
-				this.simpleTree.setChildren(children);
-			}
-		}
-		
-		if (this.simpleTree != null) {
-			this.finalStartLine = treeParser.getViolationFinalStartLine();
-			this.finalEndLine = treeParser.getViolationFinalEndLine();
-		}
-	}
-
-}

src/main/java/edu/lu/uni/serval/livestudy/README.md

@@ -1,6 +0,0 @@
-## Parse the violations of Live Study ##
-
-1. Localize bugs with FindBugs.
-2. Parse results of FindBugs.  (bug-type project.)
-
-3. Parse source code of violations. (ParseViolation.java)

src/main/java/edu/lu/uni/serval/livestudy/Violation.java

@@ -1,25 +0,0 @@
-package edu.lu.uni.serval.livestudy;
-
-import java.util.ArrayList;
-import java.util.List;
-
-public class Violation {
-	
-	private String project;
-	private List<Alarm> alarms;
-
-	public String getProject() {
-		return project;
-	}
-
-	public List<Alarm> getAlarms() {
-		return alarms;
-	}
-
-	public Violation(String project) {
-		super();
-		this.project = project;
-		this.alarms = new ArrayList<>();
-	}
-	
-}

src/main/java/edu/lu/uni/serval/parameters/ParseAlarms.java

@@ -1,145 +0,0 @@
-package edu.lu.uni.serval.parameters;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.List;
-
-import com.github.gumtreediff.tree.ITree;
-
-import edu.lu.uni.serval.FixPatternParser.Tokenizer;
-import edu.lu.uni.serval.FixPatternParser.violations.Violation;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.gumtree.regroup.SimpleTree;
-import edu.lu.uni.serval.gumtree.regroup.SimplifyTree;
-import edu.lu.uni.serval.utils.FileHelper;
-import edu.lu.uni.serval.violation.code.parser.ViolationSourceCodeTree;
-
-/**
- * Prepare data for tuning parameters of deep learning models.
- * 
- * @author kui.liu
- *
- */
-public class ParseAlarms {
-
-	public static void main(String[] args) {
-		ParseAlarms parser = new ParseAlarms();
-		
-		String outputPath = Configuration.ROOT_PATH + "TuneParameters/fixedAlarmTokens.list";
-		String outputPath2 = Configuration.ROOT_PATH + "TuneParameters/EmptyStatement/fixedAlarmTokens.list";
-		FileHelper.deleteFile(outputPath);
-		FileHelper.deleteFile(outputPath2);
-		int subIndex = 5;
-		String fixedAlarmFilesPath = Configuration.GUM_TREE_INPUT + "prevFiles/";
-		String positionsFilePath = Configuration.GUM_TREE_INPUT + "positions/";
-		parser.dataPreparation(fixedAlarmFilesPath, positionsFilePath, subIndex, outputPath, outputPath2);
-		
-		outputPath = Configuration.ROOT_PATH + "TuneParameters/unfixedAlarmTokens.list";
-		outputPath2 = Configuration.ROOT_PATH + "TuneParameters/EmptyStatement/unfixedAlarmTokens.list";
-		FileHelper.deleteFile(outputPath);
-		FileHelper.deleteFile(outputPath2);
-		subIndex = 8;
-		String unfixedAlarmFilesPath = Configuration.GUM_TREE_INPUT + "unfixAlarms/";
-		String unfixedPositionsFilePath = Configuration.GUM_TREE_INPUT + "un_positions/";
-		parser.dataPreparation(unfixedAlarmFilesPath, unfixedPositionsFilePath, subIndex, outputPath, outputPath2);
-	}
-
-	public void dataPreparation(String sourceCodeFilePath, String positionFilePath, int subIndex, String outputPath, String outputPath2) {
-		StringBuilder tokensBuilder = new StringBuilder();
-		List<File> javaFiles = FileHelper.getAllFilesInCurrentDiectory(sourceCodeFilePath, ".java");
-		int counter = 0;
-		int a = 0;
-		StringBuilder emptyStatements = new StringBuilder();
-		StringBuilder sizes = new StringBuilder();
-		for (File javaFile : javaFiles) {
-			String fileName = javaFile.getName().replace(".java", ".txt");
-			fileName = fileName.substring(subIndex);
-			
-//			if (fileName.endsWith("apache-commons-configuration_8c42aa_8b26e6src#java#org#apache#commons#configuration#plist#XMLPropertyListConfiguration.txt")) {
-//				System.out.println();
-//			}
-			
-			List<Violation> violations = readViolations(positionFilePath + fileName);
-			
-			for (Violation violation : violations) {
-				int startLine = violation.getStartLineNum();
-				int endLine = violation.getEndLineNum();
-				String alarmType = violation.getViolationType();
-
-				if (endLine > startLine + 5) continue;
-
-				ViolationSourceCodeTree alarmTree = new ViolationSourceCodeTree(javaFile, startLine, endLine);
-				alarmTree.extract(alarmType);
-				List<ITree> matchedTrees = alarmTree.getViolationSourceCodeTrees();
-				if (matchedTrees.size() == 0) {
-					emptyStatements.append(alarmType + "," + fileName + "," + startLine + "," + endLine + "\n");
-					a ++;
-					continue;
-				}
-				SimpleTree simpleTree = new SimpleTree();
-				simpleTree.setLabel("Block");
-				simpleTree.setNodeType("Block");
-				List<SimpleTree> children = new ArrayList<>();
-				
-				for (ITree matchedTree : matchedTrees) {
-					SimpleTree simpleT = new SimplifyTree().canonicalizeSourceCodeTree(matchedTree, null);
-					children.add(simpleT);
-				}
-				simpleTree.setChildren(children);
-				
-				String tokens = Tokenizer.getTokensDeepFirst(simpleTree);
-				String[] tokensArray = tokens.split(" ");
-				int length = tokensArray.length;
-				sizes.append(length + "\n");
-				tokensBuilder.append(alarmType + ":" + fileName + ":" + alarmTree.getViolationFinalStartLine() + ":" + alarmTree.getViolationFinalEndLine() + ":" + tokens + "\n");
-				
-				counter ++;
-				if (counter % 10000 == 0) {
-					FileHelper.outputToFile(outputPath, tokensBuilder, true);
-					tokensBuilder.setLength(0);
-				}
-			}
-		}
-
-		System.out.println("Volidated Instances: " + counter);
-		System.out.println("Empty Instances: " + a);
-		FileHelper.outputToFile(outputPath2, emptyStatements, false);
-		FileHelper.outputToFile(outputPath.replace(".list", "Sizes.csv"), sizes, false);
-		FileHelper.outputToFile(outputPath, tokensBuilder, true);
-	}
-
-	private List<Violation> readViolations(String file) {
-		List<Violation> violations = new ArrayList<>();
-		
-		String fileContent = FileHelper.readFile(file);
-		BufferedReader reader = null;
-		reader = new BufferedReader(new StringReader(fileContent));
-		String line = null;
-		try {
-			while ((line = reader.readLine()) != null) {
-				String[] positionStr = line.split(":");
-				int startLine = Integer.parseInt(positionStr[1]);
-				int endLine = Integer.parseInt(positionStr[2]);
-				
-				if (startLine == -1 || endLine == -1) {
-					continue;
-				}
-				String alarmType = positionStr[0];
-				Violation violation = new Violation(startLine, endLine, alarmType);
-				violations.add(violation);
-			}
-		} catch (IOException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				reader.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		return violations;
-	}
-}

src/main/java/edu/lu/uni/serval/statistics/Categories.java

@@ -1,75 +0,0 @@
-package edu.lu.uni.serval.statistics;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-
-public class Categories {
-
-	public static void main(String[] args) throws IOException {
-		String content = FileHelper.readFile(Configuration.ROOT_PATH + "RQ1/Quantity-per-Fixed_1.0V-Type.csv");//"RQ1/Quantity-per-V-Type.csv");
-		BufferedReader reader = new BufferedReader(new StringReader(content));
-		String line = reader.readLine();
-		int counter = 0;
-//		int size = 400;
-		Map<String, Integer> map = new HashMap<>();
-		map.put("Dodgy code", 0);
-		map.put("Experimental", 0);
-		map.put("Internationalization", 0);
-		map.put("Multithreaded correctness", 0);
-		map.put("Malicious code vulnerability", 0);
-		map.put("Performance", 0);
-		map.put("Correctness", 0);
-		map.put("Security", 0);
-		map.put("Bad practice", 0);
-		map.put("Other", 0);
-//		List<Integer> list = new ArrayList<>();
-		Map<String, List<Integer>> map2 = new HashMap<>();
-		map2.put("Dodgy code", new ArrayList<Integer>());
-		map2.put("Experimental", new ArrayList<Integer>());
-		map2.put("Internationalization", new ArrayList<Integer>());
-		map2.put("Multithreaded correctness", new ArrayList<Integer>());
-		map2.put("Malicious code vulnerability", new ArrayList<Integer>());
-		map2.put("Performance", new ArrayList<Integer>());
-		map2.put("Correctness", new ArrayList<Integer>());
-		map2.put("Security", new ArrayList<Integer>());
-		map2.put("Bad practice", new ArrayList<Integer>());
-		map2.put("Other", new ArrayList<Integer>());
-		while ((line = reader.readLine()) != null) {
-			String type = line.substring(line.lastIndexOf(",") + 1);
-			counter ++;
-			if (map.containsKey(type)) {
-				map.put(type, map.get(type) + 1);
-			} else {
-				map.put(type, 1);
-			}
-			if (counter % 10 == 0) {
-				for (Map.Entry<String, List<Integer>> entry : map2.entrySet()) {
-					String type2 = entry.getKey();
-					Integer integ = map.get(type2);
-					if (integ == null) {
-						map2.get(type2).add(0);
-					} else {
-						map2.get(type2).add(integ);
-					}
-				}
-//				System.out.println();
-			}
-		}
-		reader.close();
-		for (Map.Entry<String, Integer> entry : map.entrySet()) {
-			System.out.println(entry.getKey() + "," + entry.getValue());
-		}
-		for (Map.Entry<String, List<Integer>> entry : map2.entrySet()) {
-			System.out.println(entry.getKey() + "," + entry.getValue());
-		}
-	}
-
-}

src/main/java/edu/lu/uni/serval/statistics/FixedProjects.java

@@ -1,26 +0,0 @@
-package edu.lu.uni.serval.statistics;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.StringReader;
-
-import edu.lu.uni.serval.utils.FileHelper;
-
-public class FixedProjects {
-
-	public static void main(String[] args) throws IOException {
-		String content = FileHelper.readFile("../FPM_Violations/RQ1/Quantity-per-FixedProj.csv");
-		BufferedReader reader = new BufferedReader(new StringReader(content));
-		String line = reader.readLine();
-		StringBuilder builder = new StringBuilder();
-		while ((line = reader.readLine()) != null) {
-			String[] elements = line.split(",");
-//			String projectName = elements[0];
-			builder.append(elements[0] + "\n");
-		}
-		reader.close();
-		
-		FileHelper.outputToFile("../FPM_Violations/RQ1/fixedProjects.list", builder, false);
-	}
-
-}

src/main/java/edu/lu/uni/serval/statistics/FixedVilations.java

@@ -1,47 +0,0 @@
-package edu.lu.uni.serval.statistics;
-
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Scanner;
-
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-
-public class FixedVilations {
-
-	public static void main(String[] args) throws IOException {
-		// projectName,ViolationType,Number.
-		FileInputStream fis = new FileInputStream(Configuration.ROOT_PATH + "RQ1/fixed-alarms-v1.0.list");
-		Scanner scanner = new Scanner(fis);
-		Map<String, Integer> map = new HashMap<>();
-		int counter = 0;
-		while (scanner.hasNextLine()) {
-			String line = scanner.nextLine();
-			String[] elements = line.split(":");
-//			String violationType = elements[0];
-//			String projectName = elements[1];
-			String key = elements[1] + "," + elements[0];
-			if (map.containsKey(key)) {
-				map.put(key, map.get(key)+ 1);
-			} else {
-				map.put(key, 1);
-			}
-			counter ++;
-		}
-		
-		scanner.close();
-		fis.close();
-		
-		System.out.println(counter);
-		StringBuilder builder = new StringBuilder();
-		for (Map.Entry<String, Integer> entry : map.entrySet()) {
-			builder.append(entry.getKey()).append(",").append(entry.getValue()).append("\n");
-			counter -= entry.getValue();
-		}
-		FileHelper.outputToFile(Configuration.ROOT_PATH + "RQ1/fixedViolations-v-1.0.csv", builder, false);
-		System.out.println(counter);
-	}
-
-}

src/main/java/edu/lu/uni/serval/statistics/HunkSizeComputer.java

@@ -1,106 +0,0 @@
-package edu.lu.uni.serval.statistics;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-import edu.lu.uni.serval.utils.ListSorter;
-
-public class HunkSizeComputer {
-
-	public static void main(String[] args) throws IOException {
-		String violationsFilePath = Configuration.ROOT_PATH + "unFixedInstances/";
-		sizes(violationsFilePath, ".list");
-	}
-	
-	public static void sizes(String filePath, String fileType) throws NumberFormatException, IOException {
-		List<File> unfixedAlarmFiles = FileHelper.getAllFilesInCurrentDiectory(filePath, fileType);
-		System.out.println(unfixedAlarmFiles.size());
-		StringBuilder builder = new StringBuilder();
-		int counter = 0;
-		int size = 0;
-		int i = 0;
-		List<Integer> sizes = new ArrayList<>();
-		Map<Integer, Integer> map = new HashMap<>();// <size, amount>
-		for (File file : unfixedAlarmFiles) {
-			String content = FileHelper.readFile(file);
-			BufferedReader reader = new BufferedReader(new StringReader(content));
-			String line = null;
-			while ((line = reader.readLine()) != null) {
-				String[] elements = line.split(",");
-				int startLine = Integer.parseInt(elements[4]);
-				int endLine = Integer.parseInt(elements[5]);
-				i ++;
-				if (startLine == -1 || endLine == -1) continue;
-				
-				int range = endLine - startLine + 1;
-				builder.append(range + "\n");
-				if (range != 1) {
-					counter ++;
-				}
-				size ++;
-				sizes.add(range);
-				if (map.containsKey(range)) {
-					map.put(range, map.get(range) + 1);
-				} else {
-					map.put(range, 1);
-				}
-			}
-			reader.close();
-		}
-		System.out.println(i);
-		
-		String content = FileHelper.readFile("Dataset/fixed-alarms-v1.0.list");
-		BufferedReader reader = new BufferedReader(new StringReader(content));
-		String line = null;
-		while ((line = reader.readLine()) != null) {
-			int arrowIndex = line.indexOf("=>");
-			String buggyInfo = line.substring(0, arrowIndex);
-			String[] buggyElements = buggyInfo.split(":");
-
-			int startLine = Integer.parseInt(buggyElements[4]);
-			int endLine = Integer.parseInt(buggyElements[5]);
-			
-			if (startLine == -1 || endLine == -1) continue;
-			
-			int range = endLine - startLine + 1;
-			if (range != 1) {
-				counter ++;
-			}
-			builder.append(range + "\n");
-			size ++;
-			sizes.add(range);
-			if (map.containsKey(range)) {
-				map.put(range, map.get(range) + 1);
-			} else {
-				map.put(range, 1);
-			}
-		}
-		reader.close();
-		
-		FileHelper.outputToFile("Dataset/sizes.csv", builder, false);
-		
-		System.out.println(size);
-		System.out.println(counter);
-		ListSorter<Integer> sorter = new ListSorter<>(sizes);
-		sizes = sorter.sortAscending();
-		System.out.println(sizes.get((int) (sizes.size() * 0.7)));
-		System.out.println(sizes.get((int) (sizes.size() * 0.8)));
-		System.out.println(sizes.get((int) (sizes.size() * 0.9)));
-		System.out.println(sizes.get((int) (sizes.size() * 0.95)));
-		
-		int sum = 0;
-		for (i = 1; i <= 100; i ++) {
-			sum += map.get(i);
-			System.out.println(i + "," + String.format("%.2f", ((double) sum / size * 100)));
-		}
-	}
- 
-}

src/main/java/edu/lu/uni/serval/statistics/NumberOfFilesAndCodeLines.java

@@ -1,74 +0,0 @@
-package edu.lu.uni.serval.statistics;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.List;
-import java.util.Locale;
-import java.util.Scanner;
-
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-
-/**
- * Statistics of files and code lines of projects in Live Study.
- * 
- * @author kui.liu
- *
- */
-public class NumberOfFilesAndCodeLines {
-
-	public static void main(String[] args) {
-		String projectsPath = Configuration.ROOT_PATH + "LiveStudy/BugsInfo/";
-		File[] projects = new File(projectsPath).listFiles();
-		for (File project : projects) {
-			if (project.isDirectory()) {
-				if (project.getName().equals("poi"))
-				new NumberOfFilesAndCodeLines().statistic(project.getName());
-			}
-		}
-	}
-
-	public void statistic(String project) {
-		List<File> javaFiles = FileHelper.getAllFiles(Configuration.ROOT_PATH + "LiveStudy/projects/" + project, ".java");
-		int numberOfFiles = 0;
-		int LOC = 0;
-		for (File javaFile : javaFiles) {
-			if (!javaFile.getPath().toLowerCase(Locale.ENGLISH).contains("test")) {
-				numberOfFiles ++;
-				LOC += readLinesOfCode(javaFile);
-			}
-//			numberOfFiles ++;
-//			LOC += readLinesOfCode(javaFile);
-		}
-		System.out.println(project + " : Files = " + numberOfFiles + ", LOC = " + LOC);
-	}
-
-	private int readLinesOfCode(File javaFile) {
-		int LOC = 0;
-		Scanner scanner = null;
-		FileInputStream fis = null;
-		try {
-			fis = new FileInputStream(javaFile);
-			scanner = new Scanner(fis);
-			
-			while (scanner.hasNextLine()) {
-				scanner.nextLine();
-				LOC ++;
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				scanner.close();
-				fis.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		
-		return LOC;
-	}
-
-}

src/main/java/edu/lu/uni/serval/statistics/ReadSpearmanResults.java

@@ -1,104 +0,0 @@
-package edu.lu.uni.serval.statistics;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.StringReader;
-
-import edu.lu.uni.serval.utils.FileHelper;
-
-public class ReadSpearmanResults {
-
-	public static void main(String[] args) throws IOException {
-		String fileName = "../FPM_Violations/RQ1/SpearmanResults.list";
-		String content = FileHelper.readFile(fileName);
-		BufferedReader reader = new BufferedReader(new StringReader(content));
-		String line = null;
-		String str1 = "1";
-		String str2 = "2";
-		String str3 = "3";
-		String str4 = "4";
-		String str5 = "5";
-		String str6 = "6";
-		String str7 = "7";
-		String str8 = "8";
-		String str9 = "9";
-		String str10 = "10";
-		int counter = 0;
-		while ((line = reader.readLine()) != null) {
-//			String[] elements = line.split("");
-			
-			counter ++;
-			
-			if ((counter / 10 == 2 || counter / 10 == 4) && counter % 10 == 1) {
-				str1 += "@@@@1";
-				str2 += "@@@@2";
-				str3 += "@@@@3";
-				str4 += "@@@@4";
-				str5 += "@@@@5";
-				str6 += "@@@@6";
-				str7 += "@@@@7";
-				str8 += "@@@@8";
-				str9 += "@@@@9";
-				str10 += "@@@@10";
-			}
-			
-			
-			int n = counter % 10;
-			switch (n) {
-			case 1:
-				str1 += "@" + line;
-				break;
-			case 2:
-				str2 += "@" + line;
-				break;
-			case 3:
-				str3 += "@" + line;
-				break;
-			case 4:
-				str4 += "@" + line;
-				break;
-			case 5:
-				str5 += "@" + line;
-				break;
-			case 6:
-				str6 += "@" + line;
-				break;
-			case 7:
-				str7 += "@" + line;
-				break;
-			case 8:
-				str8 += "@" + line;
-				break;
-			case 9:
-				str9 += "@" + line;
-				break;
-			case 0:
-				str10 += "@" + line;
-				break;
-			}
-		}
-		reader.close();
-
-		str1 = str1.replace(".", ",");
-		str2 = str2.replace(".", ",");
-		str3 = str3.replace(".", ",");
-		str4 = str4.replace(".", ",");
-		str5 = str5.replace(".", ",");
-		str6 = str6.replace(".", ",");
-		str7 = str7.replace(".", ",");
-		str8 = str8.replace(".", ",");
-		str9 = str9.replace(".", ",");
-		str10 = str10.replace(".", ",");
-		System.out.println(str1);
-		System.out.println(str2);
-		System.out.println(str3);
-		System.out.println(str4);
-		System.out.println(str5);
-		System.out.println(str6);
-		System.out.println(str7);
-		System.out.println(str8);
-		System.out.println(str9);
-		System.out.println(str10);
-	}
-
-}

src/main/java/edu/lu/uni/serval/statistics/Spearman.R

@@ -1,362 +0,0 @@
-a <- read.csv("~/Public/git/FPM_Violations/RQ1/TenFolds-Q/Ten-fold-all-fixed-violation-type1-70.csv", header=T)
-d<-cor.test( ~ X0 + X0.T, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = FALSE, sep = "@")
-
-d<-cor.test( ~ X1 + X1.T, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X2 + X2.T, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X3 + X3.T, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X4 + X4.T, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X5 + X5.T, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X6 + X6.T, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X7 + X7.T, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X8 + X8.T, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X9 + X9.T, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X0.R + X0.T.R, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X1.R + X1.T.R, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X2.R + X2.T.R, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X3.R + X3.T.R, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X4.R + X4.T.R, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X5.R + X5.T.R, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X6.R + X6.T.R, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X7.R + X7.T.R, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X8.R + X8.T.R, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X9.R + X9.T.R, 
-          data=a,          method = "spearman",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X0 + X0.T, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X1 + X1.T, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X2 + X2.T, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X3 + X3.T, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X4 + X4.T, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X5 + X5.T, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X6 + X6.T, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X7 + X7.T, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X8 + X8.T, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X9 + X9.T, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X0.R + X0.T.R, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X1.R + X1.T.R, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X2.R + X2.T.R, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X3.R + X3.T.R, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X4.R + X4.T.R, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X5.R + X5.T.R, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X6.R + X6.T.R, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X7.R + X7.T.R, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X8.R + X8.T.R, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X9.R + X9.T.R, 
-          data=a,          method = "pearson",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X0 + X0.T, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X1 + X1.T, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X2 + X2.T, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X3 + X3.T, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X4 + X4.T, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X5 + X5.T, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X6 + X6.T, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X7 + X7.T, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X8 + X8.T, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X9 + X9.T, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X0.R + X0.T.R, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X1.R + X1.T.R, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X2.R + X2.T.R, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X3.R + X3.T.R, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X4.R + X4.T.R, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X5.R + X5.T.R, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X6.R + X6.T.R, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X7.R + X7.T.R, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X8.R + X8.T.R, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-d<-cor.test( ~ X9.R + X9.T.R, 
-          data=a,          method = "kendall",
-          continuity = FALSE,
-          conf.level = 0.95)
-write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@")
-
-a=1

src/main/java/edu/lu/uni/serval/statistics/SpearmanCodeGenerator.java

@@ -1,81 +0,0 @@
-package edu.lu.uni.serval.statistics;
-
-
-public class SpearmanCodeGenerator {
-
-	public static void main(String[] args) {
-		generateSpearmanCode();
-	}
-
-	public static void generateSpearmanCode() {
-		for (int i = 0; i < 10; i ++) {
-			String s = "d<-cor.test( ~ X" + i + " + X" + i + ".T, \n";
-			s += "          data=a,";
-			s += "          method = \"spearman\",\n";
-			s += "          continuity = FALSE,\n";
-			s += "          conf.level = 0.95)\n";
-			if (i == 0) {
-				s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," +
-						"append = FALSE, sep = \"@\")\n";
-			} else {
-				s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," +
-						"append = TRUE, sep = \"@\")\n";
-			}
-			
-			System.out.println(s);
-		}
-		for (int i = 0; i < 10; i ++) {
-			String s = "d<-cor.test( ~ X" + i + ".R + X" + i + ".T.R, \n";
-			s += "          data=a,";
-			s += "          method = \"spearman\",\n";
-			s += "          continuity = FALSE,\n";
-			s += "          conf.level = 0.95)\n";
-			s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," +
-					"append = TRUE, sep = \"@\")\n";
-			System.out.println(s);
-		}
-		
-		for (int i = 0; i < 10; i ++) {
-			String s = "d<-cor.test( ~ X" + i + " + X" + i + ".T, \n";
-			s += "          data=a,";
-			s += "          method = \"pearson\",\n";
-			s += "          continuity = FALSE,\n";
-			s += "          conf.level = 0.95)\n";
-			s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," +
-							"append = TRUE, sep = \"@\")\n";
-			System.out.println(s);
-		}
-		for (int i = 0; i < 10; i ++) {
-			String s = "d<-cor.test( ~ X" + i + ".R + X" + i + ".T.R, \n";
-			s += "          data=a,";
-			s += "          method = \"pearson\",\n";
-			s += "          continuity = FALSE,\n";
-			s += "          conf.level = 0.95)\n";
-			s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," +
-					"append = TRUE, sep = \"@\")\n";
-			System.out.println(s);
-		}
-		
-		for (int i = 0; i < 10; i ++) {
-			String s = "d<-cor.test( ~ X" + i + " + X" + i + ".T, \n";
-			s += "          data=a,";
-			s += "          method = \"kendall\",\n";
-			s += "          continuity = FALSE,\n";
-			s += "          conf.level = 0.95)\n";
-			s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," +
-							"append = TRUE, sep = \"@\")\n";
-			System.out.println(s);
-		}
-		for (int i = 0; i < 10; i ++) {
-			String s = "d<-cor.test( ~ X" + i + ".R + X" + i + ".T.R, \n";
-			s += "          data=a,";
-			s += "          method = \"kendall\",\n";
-			s += "          continuity = FALSE,\n";
-			s += "          conf.level = 0.95)\n";
-			s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," +
-					"append = TRUE, sep = \"@\")\n";
-			System.out.println(s);
-		}
-	}
-
-}

src/main/java/edu/lu/uni/serval/statistics/Statistic.java

@@ -1,947 +0,0 @@
-package edu.lu.uni.serval.statistics;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Scanner;
-
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-import edu.lu.uni.serval.utils.ListSorter;
-import edu.lu.uni.serval.utils.MapSorter;
-
-public class Statistic {
-	private static Map<String, Integer> map1 = new HashMap<String, Integer>();
-	private static Map<String, Integer> map2 = new HashMap<>();
-	
-	public static void main(String[] args) throws IOException {
-		/*
-		 * DM_DEFAULT_ENCODING
-		 * NP_NONNULL_RETURN_VIOLATION
-		 * NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE
-		 * NP_PARAMETER_MUST_BE_NONNULL_BUT_MARKED_AS_NULLABLE
-		 * ODR_OPEN_DATABASE_RESOURCE
-		 * PZLA_PREFER_ZERO_LENGTH_ARRAYS
-		 * RI_REDUNDANT_INTERFACES
-		 * RV_RETURN_VALUE_IGNORED_BAD_PRACTICE
-		 * RV_RETURN_VALUE_IGNORED_NO_SIDE_EFFECT
-		 * SE_NO_SERIALVERSIONID
-		 * SF_SWITCH_NO_DEFAULT
-		 * SIC_INNER_SHOULD_BE_STATIC
-		 * SQL_PREPARED_STATEMENT_GENERATED_FROM_NONCONSTANT_STRING
-		 * UC_USELESS_CONDITION
-		 * UC_USELESS_OBJECT
-		 * UCF_USELESS_CONTROL_FLOW
-		 * WMI_WRONG_MAP_ITERATOR
-		 */
-//		/*
-//		 * Quantities' distribution of all violation types.
-//		 */
-//		quantityOfEachViolationType();
-//		/*
-//		 * Widespread of each violation type.
-//		 */
-//		widespreadOfEachViolationType();
-//		/*
-//		 * Statistics of categories of all violation types.
-//		 */
-//		statisticWithCategories();
-//		
-//		/*
-//		 * Quantity of each violation type in each project.
-//		 */
-//		reloadData();
-//		
-//		/*
-//		 * Quantities' distribution of all fixed violation types.
-//		 * Widespread of each fixed violation type.
-//		 * Statistics of categories of all fixed violation types.
-//		 * Quantity of each fixed violation type in each project.
-//		 */
-//		statisticOfFixedViolations();
-//		fixedVSunfixed();
-		
-		/**
-		 * Do statistics from two files: 
-		 */
-		statistics("../FPM_Violations/RQ1/all-leafnodes-per-project-vtype.csv", "", map1, 16918530, 730);
-//		statistics("../FPM_Violations/RQ1/distinct-fixed-summary-per-project-vtype.csv", "Fixed");
-		statistics("../FPM_Violations/RQ1/fixedViolations-v-1.0.csv", "Fixed_1.0", map2, 88927, 548);
-//		fixedVSunfixed();
-		StringBuilder builder = new StringBuilder();
-		for (Map.Entry<String, Integer> entry : map1.entrySet()) {
-			String key = entry.getKey();
-			builder.append(key + "," + entry.getValue() + "," + (map2.containsKey(key) ? map2.get(key) : 0) + "\n");
-		}
-		FileHelper.outputToFile(Configuration.ROOT_PATH + "RQ2/quantity-ratios.csv", builder, false);
-		
-//		statisticsOfFixedViolations();
-		
-		//rsync -avP gaia-cluster:/work/users/kliu/FixPattern/FPM_Violations/UnfixedViolations/BC_UNCONFIRMED_CAST/Sizes.list Sizes/Sizes1.list
-//		String s = "rsync -avP gaia-cluster:/work/users/kliu/FixPattern/FPM_Violations/UnfixedViolations_RQ3/";
-//		File[] files = new File(Configuration.ROOT_PATH + "RQ3_1/UnfixedInstances/").listFiles();
-//		int i = 0;
-//		for (File file : files) {
-//			if (file.getName().endsWith(".list")) {
-//				i ++;
-//				System.out.println(s + FileHelper.getFileNameWithoutExtension(file) + "/Sizes.list Sizes/Sizes" + i + ".list");
-//			}
-//		}
-//		tokenSizes();
-	}
-	
-	public static void tokenSizes() {
-		List<Integer> sizes = new ArrayList<>();
-		List<File> files = FileHelper.getAllFilesInCurrentDiectory(Configuration.ROOT_PATH + "RQ3_1/Sizes/", ".list");
-		StringBuilder builder = new StringBuilder();
-		for (File file : files) {
-			try {
-				String content = FileHelper.readFile(file);
-				BufferedReader reader = new BufferedReader(new StringReader(content));
-				String line = null;
-				while ((line = reader.readLine()) != null) {
-					sizes.add(Integer.parseInt(line));
-					builder.append("1,").append(line).append("\n");
-				}
-				reader.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		System.out.println(sizes.size());
-		FileHelper.outputToFile(Configuration.ROOT_PATH + "RQ3_1/Sizes.csv", builder, false);
-	}
-
-	public static void statisticsOfFixedViolations() {
-		String statistic = "../FPM_Violations/OUTPUT3/";
-		List<File> files = FileHelper.getAllFiles(statistic, ".list");
-		
-		int positions = 0;
-		int numV = 0;
-		int testAlarms = 0;
-		int nullGumTreeResults = 0;
-		int nullMappingGumTreeResults = 0;
-		int pureDeletion = 0;
-		int timeout = 0;
-		int noSourceCodeChagnes = 0;
-		int largeHunk = 0;
-		int nullSourceCode = 0;
-		int noStatementChanges = 0;
-		int nullDiffentry = 0;
-		int TestingInfo = 0;
-		int i = 0;
-		Map<String, Integer> types1 = new HashMap<>();
-		for (File file : files) {
-			if (file.getName().startsWith("statistic")) {
-				String content = FileHelper.readFile(file);
-				BufferedReader reader = new BufferedReader(new StringReader(content));
-				String line = null;
-				i ++;
-				try {
-					while ((line = reader.readLine()) !=  null) {
-						if (line.startsWith("Positions")) {
-							positions += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						} else if (line.startsWith("NumViolations")) {
-							numV += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						} else
-						if (line.startsWith("TestViolations")) {
-							testAlarms += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						} else if (line.startsWith("NullGumTreeResults")) {
-							nullGumTreeResults += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						} else if (line.startsWith("NoSourceCodeChanges")) {
-							noSourceCodeChagnes += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						} else if (line.startsWith("NoStatementChanges")) {
-							noStatementChanges += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						} else if (line.startsWith("NullDiffEntry")) {
-							nullDiffentry += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						} else if (line.startsWith("NullMatchedGumTreeResults")) {
-							nullMappingGumTreeResults += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						} else if (line.startsWith("PureDeletion")) {
-							pureDeletion += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						} else if (line.startsWith("LargeHunk")) {
-							largeHunk += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						} else if (line.startsWith("NullSourceCode")) {
-							nullSourceCode += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						} else if (line.startsWith("Timeout")) {
-							timeout += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						} else if (line.startsWith("TestingInfo")) {
-							TestingInfo +=Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim());
-						}
-					}
-				} catch (IOException e) {
-					e.printStackTrace();
-				} finally {
-					try {
-						reader.close();
-					} catch (IOException e) {
-						e.printStackTrace();
-					}
-				}
-			}
-			
-			
-			if (file.getName().startsWith("UnfixedV")) {
-				String content = FileHelper.readFile(file);
-				BufferedReader reader = new BufferedReader(new StringReader(content));
-				String line = null;
-				try {
-					while ((line = reader.readLine()) !=  null) {
-//						types1
-						if (line.startsWith("## OAR [")) break;
-						String type = line.substring(0, line.indexOf(":"));
-						if (types1.containsKey(type)) {
-							types1.put(type, types1.get(type)  + 1);
-						} else {
-							types1.put(type, 1);
-						}
-						if (line.startsWith("#NullSourceCode:")) {
-							System.out.println(line);
-						}
-					}
-				} catch(IOException e) {
-					e.printStackTrace();
-				} finally {
-					try {
-						reader.close();
-					} catch (IOException e) {
-						e.printStackTrace();
-					}
-				}
-			}
-		}
-		
-		Map<String, Integer> types = new HashMap<>();
-//		FileInputStream fis = new FileInputStream("../FPM_Violations/OAR.FPM.4222208.stderr");
-//		Scanner scanner = new Scanner(fis);
-//		while (scanner.hasNextLine()) {
-//			String line = scanner.nextLine();
-//			if (line.startsWith("## OAR [")) break;
-//			String type = line.substring(0, line.indexOf(":"));
-//			if (types.containsKey(type)) {
-//				types.put(type, types.get(type)  + 1);
-//			} else {
-//				types.put(type, 1);
-//			}
-//		}
-//		scanner.close();
-//		fis.close();
-//		int sum = 0;
-//		int sum2 = 0;
-//		for (Map.Entry<String, Integer> entry : types.entrySet()) {
-//			System.out.println(entry.getKey() + ": " + entry.getValue());
-//			if (!entry.getKey().startsWith("#PureDeletion")) {
-//				if (!entry.getKey().startsWith("#Timeout") && !entry.getKey().startsWith("#TestViolation"))
-//					sum += entry.getValue();
-//				else sum2 += entry.getValue();
-//			}
-//		}
-		int sum3 = 0;
-		int sum4 = 0;
-		int sum5 = 0;
-		for (Map.Entry<String, Integer> entry : types1.entrySet()) {
-			System.out.println(entry.getKey() + ": " + entry.getValue());
-			if (!entry.getKey().startsWith("#PureDeletion")) {
-				if (!entry.getKey().startsWith("#Timeout") && !entry.getKey().startsWith("#TestViolation"))
-					sum3 += entry.getValue();
-				else sum4 += entry.getValue();
-				sum5+= entry.getValue();
-			}
-		}
-		System.out.println(sum5);
-		
-		System.out.println(i);
-		System.out.println("\n\nStatistics:\nPositions: " + positions);
-		System.out.println("NumViolations: " + numV);
-		System.out.println("\nTestViolation: " + testAlarms + " :: " + types.get("#TestViolation") + " :: " + types1.get("#TestViolation"));
-		System.out.println("NullGumTreeResults: " + nullGumTreeResults + " :: " + types.get("#NullGumTreeResults") + " :: " + types1.get("#NullGumTreeResults"));
-		System.out.println("NoSourceCodeChange: " + noSourceCodeChagnes + " :: " + types.get("#NoSourceCodeChange") + " :: " + types1.get("#NoSourceCodeChange"));
-		System.out.println("NoStatementChange: " + noStatementChanges + " :: " + types.get("#NoStatementChange") + " :: " + types1.get("#NoStatementChange"));
-		System.out.println("NullDiffEntry: " + nullDiffentry + " :: " + types.get("#NullDiffEntry") + " :: " + types1.get("#NullDiffEntry"));
-		System.out.println("NullMatchedGumTreeResult: " + nullMappingGumTreeResults + " :: " + types.get("#NullMatchedGumTreeResult") + " :: " + types1.get("#NullMatchedGumTreeResult"));
-		System.out.println("PureDeletion: " + pureDeletion + " :: " + types.get("#PureDeletion") + " :: " + types1.get("#PureDeletion"));
-		System.out.println("LargeHunk: " + largeHunk + " :: " + types.get("#LargeHunk") + " :: " + types1.get("#LargeHunk"));
-		System.out.println("NullSourceCode: " + nullSourceCode + " :: " + types.get("#NullSourceCode") + " :: " + types1.get("#NullSourceCode"));
-		System.out.println("Timeout: " + timeout + " :: " + types.get("#Timeout") + " :: " + types1.get("#Timeout"));
-		System.out.println("TestingInfo: " + TestingInfo + " :: " + types.get("#TestingInfo") + " :: " + types1.get("#TestingInfo"));
-//		System.out.println("A: " + (positions + testAlarms + timeout));
-//		System.out.println("B: " + (numV + testAlarms + timeout));
-		System.out.println(testAlarms + nullGumTreeResults + noSourceCodeChagnes + noStatementChanges +
-				nullDiffentry + nullMappingGumTreeResults + nullSourceCode + timeout + TestingInfo);
-//		System.out.println(nullGumTreeResults + noSourceCodeChagnes + noStatementChanges +
-//				nullDiffentry + nullMappingGumTreeResults + nullSourceCode + TestingInfo);
-//		System.out.println(testAlarms + timeout);
-//		System.out.println(sum);
-//		System.out.println(sum2);
-		System.out.println(sum3);
-		System.out.println(sum4);
-		System.out.println(types1);
-		/*32690 56237 ,, 88927  31782
-		 * Statistics:
-
-TestViolation: 4682 :: null :: null
-NullGumTreeResults: 0 :: null :: null
-NoSourceCodeChange: 7010 :: null :: 6984
-NoStatementChange: 163 :: null :: 163
-NullDiffEntry: 6943 :: null :: 6943
-NullMatchedGumTreeResult: 25747 :: null :: 25747
-PureDeletion: 10815 :: null :: 10815
-LargeHunk: 6318 :: null :: 6318
-NullSourceCode: 1025 :: null :: 1025
-Timeout: 0 :: null :: null
-TestingInfo: 0 :: null :: null
-A: 4682
-B: 4682
-51888
-47206
-4682
-47180
-0
-		 */
-	}
-
-	public static void statistics(String fileName, String type, Map<String, Integer> map, int totalQ, int totalS) throws IOException {
-		FileInputStream fis = new FileInputStream(fileName);
-		Scanner scanner = new Scanner(fis);
-		
-		Map<String, Integer> violationTypesMap = new HashMap<>();
-		Map<String, Integer> projectsMap = new HashMap<>();
-		Map<String, Integer> perVperProjMap = new HashMap<>();
-		Map<String, List<String>> perVProjs = new HashMap<>();
-		Map<String, List<String>> widespreadViolationsMap = new HashMap<>();
-		
-		while (scanner.hasNextLine()) {
-			String line = scanner.nextLine();
-			String[] elements = line.split(",");
-			String projectName = elements[0];
-			String violationType = elements[1];
-			int quantity = Integer.parseInt(elements[2]);
-			
-			addToMap(projectsMap, projectName, quantity);
-			addToMap(violationTypesMap, violationType, quantity);
-			addToMap(perVperProjMap, projectName + "," + violationType, quantity);
-			
-			if (widespreadViolationsMap.containsKey(violationType)) {
-				List<String> projectList = widespreadViolationsMap.get(violationType);
-				if (!projectList.contains(projectName)) {
-					projectList.add(projectName);
-				}
-			} else {
-				List<String> projectList = new ArrayList<>();
-				projectList.add(projectName);
-				widespreadViolationsMap.put(violationType, projectList);
-			}
-			
-			if (perVProjs.containsKey(violationType)) {
-				perVProjs.get(violationType).add(projectName);
-			} else {
-				List<String> projs = new ArrayList<>();
-				projs.add(projectName);
-				perVProjs.put(violationType, projs);
-			}
-		}
-		
-		scanner.close();
-		fis.close();
-		
-		
-		// Category
-		MapSorter<String, Integer> sorter = new MapSorter<String, Integer>();
-		violationTypesMap = sorter.sortByValueDescending(violationTypesMap);
-		projectsMap = sorter.sortByValueDescending(projectsMap);
-		
-		Map<String, String> categories = new HashMap<>();
-		Map<String, List<String>> categoryVList = new HashMap<>();
-		String content = FileHelper.readFile("../FPM_Violations/RQ1/ViolationCategory.list");
-		BufferedReader reader = new BufferedReader(new StringReader(content));
-		String line = null;
-		while ((line = reader.readLine()) != null) {
-			String[] elements = line.split("@@");
-			categories.put(elements[1], elements[0]); // Violation type, category
-		}
-		reader.close();
-		
-		// Sort Violation types by widespread.
-		Map<String, Integer> widespreadOfAllViolations = new HashMap<>();
-		for (Map.Entry<String, List<String>> entry : widespreadViolationsMap.entrySet()) {
-			widespreadOfAllViolations.put(entry.getKey(), entry.getValue().size());
-		}
-		widespreadOfAllViolations = sorter.sortByValueDescending(widespreadOfAllViolations);
-		StringBuilder wbuilder = new StringBuilder("Type,Identifier,Quantity,Category\n");
-		int identifier1 = 0;
-		for (Map.Entry<String, Integer> entry : widespreadOfAllViolations.entrySet()) {
-			identifier1 ++;
-			String violationType = entry.getKey();
-			String category = categories.get(violationType);
-			if (category == null || category.equals("null")) {
-				category = "Other";
-			}
-			wbuilder.append(violationType + "," + identifier1 + "," + entry.getValue() + "," + category + "\n"); 
-			
-			if (categoryVList.containsKey(category)) {
-				categoryVList.get(category).add(violationType);
-			} else {
-				List<String> list = new ArrayList<>();
-				list.add(violationType);
-				categoryVList.put(category, list);
-			}
-		}
-		
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Widespread-per-" + type + "V-Type.csv", wbuilder, false);
-		
-		// output statistics
-		List<String> sortedViolationTypes = new ArrayList<>();
-		
-		Map<String, Integer> quantityOfCategory = new HashMap<>();
-		Map<String, List<String>> violationTypesOfCategory = new HashMap<>();
-		Map<String, List<String>> projectsOfCategory = new HashMap<>();
-		StringBuilder violationsBuilder = new StringBuilder("Type,Identifier,Quantity,Ratio,Widespread,Ratio2, Categories\n");
-		int identifier = 0;
-		for (Map.Entry<String, Integer> entry : violationTypesMap.entrySet()) {
-			String violationType = entry.getKey();
-			int quantity = entry.getValue();
-			identifier ++;
-			String category = categories.get(violationType);
-			if (category == null || category.equals("null")) {
-				category = "Other";
-			}
-			int spread = widespreadViolationsMap.get(violationType).size();
-			violationsBuilder.append(violationType + "," + identifier + "," + quantity + "," + ((double) quantity / totalQ * 100) + "," 
-						+ spread + "," + ((double) spread / totalS * 100) + "," + category + "\n"); 
-			
-			if (quantityOfCategory.containsKey(category)) {
-				quantityOfCategory.put(category, quantityOfCategory.get(category) + quantity);
-			} else {
-				quantityOfCategory.put(category, quantity);
-			}
-			
-			if (violationTypesOfCategory.containsKey(category)) {
-				List<String> violationTypes = violationTypesOfCategory.get(category);
-				if (!violationTypes.contains(violationType)) {
-					violationTypes.add(violationType);
-				}
-			} else {
-				List<String> violationTypes = new ArrayList<>();
-				violationTypes.add(violationType);
-				violationTypesOfCategory.put(category, violationTypes);
-			}
-			
-			if (projectsOfCategory.containsKey(category)) {
-				List<String> projs = projectsOfCategory.get(category);
-				List<String> projs2 = perVProjs.get(violationType);
-				for (String proj : projs2) {
-					if (!projs.contains(proj)) {
-						projs.add(proj);
-					}
-				}
-			} else {
-				projectsOfCategory.put(category, perVProjs.get(violationType));
-			}
-			
-			sortedViolationTypes.add(violationType);
-			
-			map.put(violationType, quantity);
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-" + type + "V-Type.csv", violationsBuilder, false);
-		
-		StringBuilder pBuilder = new StringBuilder("Project,Quantity\n");
-		List<String> projectNames = new ArrayList<>();
-		for (Map.Entry<String, Integer> entry : projectsMap.entrySet()) {
-			String project = entry.getKey();
-			pBuilder.append(project + "," + entry.getValue() + "\n"); 
-			projectNames.add(project);
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-" + type + "Proj.csv", pBuilder, false);
-		
-		StringBuilder categoryBuilder = new StringBuilder("Category,Quantity,Types,Projects\n");
-		for (Map.Entry<String, Integer> entry : quantityOfCategory.entrySet()) {
-			String key = entry.getKey();
-			categoryBuilder.append(key + "," + entry.getValue() + "," + violationTypesOfCategory.get(key).size() + "," + projectsOfCategory.get(key).size() + "\n");
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-" + type + "Category.csv", categoryBuilder, false);
-		
-		StringBuilder builder = new StringBuilder("Projects");
-		String a = "";
-		String b = "";
-		for (int i = 0; i < sortedViolationTypes.size(); i ++) {
-			builder.append("," + sortedViolationTypes.get(i));
-			if (i < 50) {
-				a += "a$" + sortedViolationTypes.get(i) + ",";
-				b += "'" + (i + 1) + "',";
-			}
-		}
-		builder.append("\n");
-		System.out.println(a);
-		System.out.println(b);
-//		for (int i = 0; i < sortedViolationTypes.size(); i ++) {
-//			builder.append("," + i);
-//		}
-//		builder.append("\n");
-		StringBuilder bui = new StringBuilder();
-		for (int i = 0; i < projectNames.size(); i++) {
-			String projectName = projectNames.get(i);
-			builder.append(projectName);
-			
-			for (int j = 0; j < sortedViolationTypes.size(); j ++) {
-				String violationType = sortedViolationTypes.get(j);
-				String key = projectName + "," + violationType;
-				Integer value = perVperProjMap.get(key);
-				if (value == null) {
-					value = 0;
-				} else {
-					bui.append(projectName).append(",").append(violationType).append(",").append(value).append(",").append(categories.get(violationType) == null ? "Other" : categories.get(violationType)).append("\n");
-				}
-				builder.append("," + value);
-			}
-			builder.append("\n");
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-project-per-" + type + "type.csv", builder, false);
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-project-per-" + type + "type___.csv", bui, false);
-		
-		StringBuilder ssbuilder = new StringBuilder("Type, Identifier, Quantity, Category\n");
-		Map<String, Integer> perTypePerProj = new HashMap<>();
-		Map<String, List<String>> categoryProjects = new HashMap<>();
-		
-		List<String> others = new ArrayList<>();
-		for (int j = 0; j < sortedViolationTypes.size(); j ++) {
-			String violationType = sortedViolationTypes.get(j);
-			List<Integer> projs = new ArrayList<>();
-			
-			for (int i = 0; i < projectNames.size(); i++) {
-				String projectName = projectNames.get(i);
-				String key = projectName + "," + violationType;
-				Integer value = perVperProjMap.get(key);
-				
-				if (value != null) {
-					String category = categories.get(violationType);
-					if (category == null || category.equals("null")) {
-						category = "Other";
-						if (!others.contains(violationType)) {
-							others.add(violationType);
-						}
-					}
-					ssbuilder.append(violationType + "," + (j + 1) + "," + value + "," + category + "\n");
-					
-					projs.add(value);
-					
-					if (categoryProjects.containsKey(category)) {
-						List<String> projects = categoryProjects.get(category);
-						if (!projects.contains(projectName)) {
-							projects.add(projectName);
-						}
-					} else {
-						List<String> projects = new ArrayList<>();
-						projects.add(projectName);
-						categoryProjects.put(category, projects);
-					}
-				}
-			}
-			ListSorter<Integer> sorter2 = new ListSorter<Integer>(projs);
-			projs = sorter2.sortAscending();
-			int index = projs.size() % 2 == 0 ? projs.size() / 2 - 1 : projs.size() / 2;
-			perTypePerProj.put(violationType, projs.get(index));
-		}
-
-		System.out.println(others);
-		
-		for (Map.Entry<String, List<String>> entry : categoryVList.entrySet()) {
-			System.out.println(entry.getKey() + ":" + entry.getValue().size() + ":" + categoryProjects.get(entry.getKey()).size());
-		}
-		
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-project-per-" + type + "type2.csv", ssbuilder, false);
-		StringBuilder ssbuilder2 = new StringBuilder("Type, Identifier, Quantity, Category\n");
-		perTypePerProj = sorter.sortByValueDescending(perTypePerProj);
-		int j = 0;
-		for (Map.Entry<String, Integer> entry : perTypePerProj.entrySet()) {
-			String violationType = entry.getKey();
-//			System.out.println(entry.getValue());
-			j ++;
-			for (int i = 0; i < projectNames.size(); i++) {
-				String projectName = projectNames.get(i);
-				String key = projectName + "," + violationType;
-				Integer value = perVperProjMap.get(key);
-				
-				if (value != null) {
-					String category = categories.get(violationType);
-					if (category == null || category.equals("null")) {
-						category = "Other";
-					}
-					ssbuilder2.append(violationType + "," + j + "," + value + "," + category + "\n");
-				}
-			}
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-project-per-" + type + "type3.csv", ssbuilder2, false);
-//		StringBuilder pVpPBuilder = new StringBuilder();
-//		for (Map.Entry<String, Integer> entry : perVperProjMap.entrySet()) {
-//			pVpPBuilder.append(entry.getKey() + "," + entry.getValue() + "\n");
-//		}
-//		FileHelper.outputToFile("../FPM_Violations/RQ1/Per-project-per-" + type + "type.csv", pVpPBuilder, false);
-	}
-
-	private static void addToMap(Map<String, Integer> map, String key, int value) {
-		if (map.containsKey(key)) {
-			map.put(key, map.get(key) + value);
-		} else {
-			map.put(key, value);
-		}
-	}
-
-	public static void quantityOfEachViolationType() {
-		Map<String, Integer> violationQuantities = readTypeQuantityMap("../FPM_Violations/RQ1/distinct-per-vtype.csv");
-		
-		Map<String, Integer> violationWidespread = readWidespread("../FPM_Violations/RQ1/distinct-per-project-vtype.csv");
-		
-		StringBuilder buidler = new StringBuilder("Violation Type, Identifier, Quantity, Quantity of Projects, Ratio\n");
-		int identifier = 0;
-		double totality = 15961605d;
-		int sum = 0;
-		for (Map.Entry<String, Integer> entry : violationQuantities.entrySet()) {
-			String key = entry.getKey();
-			identifier ++;
-			int quantity = entry.getValue();
-			sum += quantity;
-			buidler.append(key + "," + identifier + "," + quantity + "," + violationWidespread.get(key) + "," + (sum / totality) + "\n");
-//			if (identifier >= 50) break;
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-V-type.csv", buidler, false);
-	}
-
-	public static void widespreadOfEachViolationType() {
-		Map<String, Integer> violationWidespread = readWidespread("../FPM_Violations/RQ1/distinct-per-project-vtype.csv");
-		System.out.println("Violation types: " + violationWidespread.size());
-		
-		StringBuilder buidler = new StringBuilder("Violation Type, Identifier, Quantity of Projects\n");
-		int identifier = 0;
-		for (Map.Entry<String, Integer> entry : violationWidespread.entrySet()) {
-			identifier ++;
-			buidler.append(entry.getKey() + "," + identifier + "," + entry.getValue() + "\n");
-//			if (identifier >= 50) break;
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Widespread-per-V-type.csv", buidler, false);
-	}
-
-	public static void statisticWithCategories() throws IOException {
-		Map<String, String> categories = new HashMap<>();
-		String content = FileHelper.readFile("../FPM_Violations/RQ1/ViolationCategory.list");
-		BufferedReader reader = new BufferedReader(new StringReader(content));
-		String line = null;
-		while ((line = reader.readLine()) != null) {
-			String[] elements = line.split("@@");
-			categories.put(elements[1], elements[0]); // Violation type, category
-		}
-		reader.close();
-		
-		Map<String, Integer> quantityOfCategory = new HashMap<>();
-		
-		String content2 = FileHelper.readFile("../FPM_Violations/RQ1/distinct-per-vtype.csv");
-		reader = new BufferedReader(new StringReader(content2));
-		line = reader.readLine();
-		while ((line = reader.readLine()) != null) {
-			String[] elements = line.split(",");
-			String violationType = elements[0];
-			int quantity = Integer.parseInt(elements[1]);
-			String category = categories.get(violationType);
-			if (quantityOfCategory.containsKey(category)) {
-				quantityOfCategory.put(category, quantityOfCategory.get(category) + quantity);
-			} else {
-				quantityOfCategory.put(category, quantity);
-			}
-		}
-		reader.close();
-		
-		String categoryQuantity = "Category Type, Quantity\n";
-		for (Map.Entry<String, Integer> entry : quantityOfCategory.entrySet()) {
-			categoryQuantity += entry.getKey() + "," + entry.getValue() + "\n";
-		}
-		
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-Category.csv", categoryQuantity, false);
-	}
-	
-	public static void reloadData() {
-		// ordered projects by quantity of violations
-		Map<String, Integer> projectQuantities = readTypeQuantityMap("../FPM_Violations/RQ1/distinct-per-project.csv");
-		List<String> projectNames = new ArrayList<>();
-		for (Map.Entry<String, Integer> entry : projectQuantities.entrySet()) {
-			projectNames.add(entry.getKey());
-		}
-		
-		// get ordered types by quantity of violations.
-		Map<String, Integer> violations = readTypeQuantityMap("../FPM_Violations/RQ1/distinct-per-vtype.csv");
-		List<String> violationTypes = new ArrayList<>();
-		for (Map.Entry<String, Integer> entry : violations.entrySet()) {
-			violationTypes.add(entry.getKey());
-		}
-		
-		Map<String, String> perVperProjs = readData("../FPM_Violations/RQ1/distinct-per-project-vtype.csv");
-		
-		StringBuilder builder = new StringBuilder("Projects");
-		for (int i = 0; i < violationTypes.size(); i ++) {
-			builder.append("," + violationTypes.get(i));
-		}
-		builder.append("\n");
-		for (int i = 0; i < projectNames.size(); i++) {
-			String projectName = projectNames.get(i);
-			builder.append(projectName);
-			for (int j = 0; j < violationTypes.size(); j ++) {
-				String violationType = violationTypes.get(j);
-				String key = projectName + "," + violationType;
-				String value = perVperProjs.get(key);
-				if (value == null) {
-					value = "0";
-				}
-				builder.append("," + value);
-				
-			}
-			builder.append("\n");
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-project-per-type.csv", builder, false);
-	}
-
-	public static void statisticOfFixedViolations() throws IOException {
-		String fileName = "../FPM_Violations/RQ1/fixed-alarms-v1.0.list";
-		FileInputStream fis = new FileInputStream(fileName);
-		Scanner scanner = new Scanner(fis);
-		
-		Map<String, Integer> violations = new HashMap<>();
-		Map<String, Integer> projects = new HashMap<>();
-		Map<String, Integer> perVperPro = new HashMap<>();
-		Map<String, List<String>> widespreadFixedV = new HashMap<>();
-		while (scanner.hasNextLine()) {
-			String line = scanner.nextLine();
-			String[] elements = line.split(":");
-			String violationType = elements[0];
-			String projectName = elements[1];
-			
-			if (violations.containsKey(violationType)) {
-				violations.put(violationType, violations.get(violationType) + 1);
-			} else {
-				violations.put(violationType, 1);
-			}
-			
-			if (projects.containsKey(projectName)) {
-				projects.put(projectName, projects.get(projectName) + 1);
-			} else {
-				projects.put(projectName, 1);
-			}
-			
-			String perVperProj = projectName + "," + violationType;
-			if (perVperPro.containsKey(perVperProj)) {
-				perVperPro.put(perVperProj, perVperPro.get(perVperProj) + 1);
-			} else {
-				perVperPro.put(perVperProj, 1);
-			}
-			
-			if (widespreadFixedV.containsKey(violationType)) {
-				List<String> projectList = widespreadFixedV.get(violationType);
-				if (!projectList.contains(projectName)) {
-					projectList.add(projectName);
-				}
-			} else {
-				List<String> projectList = new ArrayList<>();
-				projectList.add(projectName);
-				widespreadFixedV.put(violationType, projectList);
-			}
-		}
-		
-		scanner.close();
-		fis.close();
-		
-		MapSorter<String, Integer> sorter = new MapSorter<String, Integer>();
-		violations = sorter.sortByValueDescending(violations);
-		projects = sorter.sortByValueDescending(projects);
-		
-		Map<String, String> categories = new HashMap<>();
-		String content = FileHelper.readFile("../FPM_Violations/RQ1/ViolationCategory.list");
-		BufferedReader reader = new BufferedReader(new StringReader(content));
-		String line = null;
-		while ((line = reader.readLine()) != null) {
-			String[] elements = line.split("@@");
-			categories.put(elements[1], elements[0]); // Violation type, category
-		}
-		reader.close();
-		
-		List<String> violationTypes = new ArrayList<>();
-		
-		Map<String, Integer> quantityOfCategory = new HashMap<>();
-		StringBuilder violationsBuilder = new StringBuilder();
-		for (Map.Entry<String, Integer> entry : violations.entrySet()) {
-			String violationType = entry.getKey();
-			int quantity = entry.getValue();
-			
-			violationsBuilder.append(violationType + "," + quantity + "," + widespreadFixedV.get(violationType).size() + "\n"); 
-			
-			String category = categories.get(violationType);
-			if (quantityOfCategory.containsKey(category)) {
-				quantityOfCategory.put(category, quantityOfCategory.get(category) + quantity);
-			} else {
-				quantityOfCategory.put(category, quantity);
-			}
-			
-			violationTypes.add(violationType);
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-FixedV-Type.csv", violationsBuilder, false);
-		
-		StringBuilder pBuilder = new StringBuilder();
-		List<String> projectNames = new ArrayList<>();
-		for (Map.Entry<String, Integer> entry : projects.entrySet()) {
-			String project = entry.getKey();
-			pBuilder.append(project + "," + entry.getValue() + "\n"); 
-			projectNames.add(project);
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-FixedV-Proj.csv", pBuilder, false);
-		
-		StringBuilder categoryBuilder = new StringBuilder();
-		for (Map.Entry<String, Integer> entry : quantityOfCategory.entrySet()) {
-			categoryBuilder.append(entry.getKey() + "," + entry.getValue() + "\n");
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-Fixed-Category.csv", categoryBuilder, false);
-		
-		StringBuilder builder = new StringBuilder("Projects");
-		for (int i = 0; i < violationTypes.size(); i ++) {
-			builder.append("," + violationTypes.get(i));
-			if (i < 500) {
-			}
-		}
-		builder.append("\n");
-		for (int i = 0; i < projectNames.size(); i++) {
-			String projectName = projectNames.get(i);
-			builder.append(projectName);
-			for (int j = 0; j < violationTypes.size(); j ++) {
-				String violationType = violationTypes.get(j);
-				String key = projectName + "," + violationType;
-				Integer value = perVperPro.get(key);
-				if (value == null) {
-					value = 0;
-				}
-				builder.append("," + value);
-			}
-			builder.append("\n");
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-project-per-Fixed-type.csv", builder, false);
-		
-		StringBuilder pVpPBuilder = new StringBuilder();
-		for (Map.Entry<String, Integer> entry : perVperPro.entrySet()) {
-			pVpPBuilder.append(entry.getKey() + "," + entry.getValue() + "\n");
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Per-project-per-Fixed-type.csv", pVpPBuilder, false);
-	}
-	
-	public static void fixedVSunfixed() throws IOException {
-		String fileName = "../FPM_Violations/RQ1/Quantity-per-V-type.csv"; // all violations
-		Map<String, Integer> allViolations = readTypeQuantityMap(fileName);
-		String file = "../FPM_Violations/RQ1/Quantity-per-FixedV-Type.csv";  // fixed violations
-		Map<String, Integer> fixedViolations = readTypeQuantityMap(file);
-
-		MapSorter<String, Integer> sorter = new MapSorter<>();
-		allViolations = sorter.sortByValueDescending(allViolations);
-		StringBuilder builder = new StringBuilder("Type,fixed,unfixed,all,fixed Ratio,unfixed Ratio\n");
-		for (Map.Entry<String, Integer> entry : allViolations.entrySet()) {
-			String violationType = entry.getKey();
-			int quantity = entry.getValue();
-			Integer fixedQuantity = fixedViolations.get(violationType);
-			if (fixedQuantity == null) {
-				builder.append(violationType + "," + 0 + "," + quantity + "," + quantity  + ",0.0,1\n");
-			} else {
-				builder.append(violationType + "," + fixedQuantity + "," + (quantity)
-						+ "," + quantity + "," + ((double)fixedQuantity) / ((double) quantity)
-						+ "," + ((double)(quantity)) / ((double) quantity) + "\n");
-			}
-		}
-		FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-Fixed-type-VS-per-unFixed-type.csv", builder, false);
-	}
-
-	private static Map<String, String> readData(String fileName) {
-		Map<String, String> perVperPros = new HashMap<>();
-		FileInputStream fis = null;
-		Scanner scanner = null;
-		try {
-			fis = new FileInputStream(fileName);
-			scanner = new Scanner(fis);
-			while (scanner.hasNextLine()) {
-				String line = scanner.nextLine();
-				String[] elements = line.split(",");
-				String key = elements[0] + "," + elements[1];
-				String value = elements[2];
-				perVperPros.put(key, value);
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				scanner.close();
-				fis.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		
-		return perVperPros;
-	}
-
-	private static Map<String, Integer> readTypeQuantityMap(String fileName) {
-		Map<String, Integer> map = new HashMap<>();
-		String fileContent = FileHelper.readFile(fileName);
-		BufferedReader reader = new BufferedReader(new StringReader(fileContent));
-		
-		try {
-			String line= reader.readLine();
-			while ((line = reader.readLine()) != null) {
-				String[] elements = line.split(",");
-				map.put(elements[0], Integer.valueOf(elements[2]));
-			}
-		} catch (IOException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				reader.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		
-		MapSorter<String, Integer> sorter = new MapSorter<>();
-		map = sorter.sortByValueDescending(map);
-		return map;
-	}
-	
-	private static Map<String, Integer> readWidespread(String fileName) {
-		Map<String, Integer> violationWidespread = new HashMap<String, Integer>();
-		
-		String fileContent = FileHelper.readFile(fileName);
-		BufferedReader reader = new BufferedReader(new StringReader(fileContent));
-		
-		try {
-			String line = null;
-			while ((line = reader.readLine()) != null) {
-				String[] strArray = line.split(",");
-				String key = strArray[1];
-				if (violationWidespread.containsKey(key)) {
-					violationWidespread.put(key, violationWidespread.get(key) + 1);
-				} else {
-					violationWidespread.put(key, 1);
-				}
-				
-//				String[] elements = line.split(",");
-//				violationWidespread.put(elements[0], Integer.valueOf(elements[1]));
-			}
-		} catch (IOException e) {
-			e.printStackTrace();
-		} finally {
-			try {
-				reader.close();
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		}
-		
-		MapSorter<String, Integer> sorter = new MapSorter<>();
-		violationWidespread = sorter.sortByValueDescending(violationWidespread);
-		return violationWidespread;
-	}
-}