Program: 74843
Project: 74843
Buggy source:
protected void internalTransform(String phaseName,Map options){
  int localCount=0;
  System.out.println("String_Node_Str" + phaseName + "String_Node_Str"+ options+ "String_Node_Str");
  List modifiedConstructorClassList=new LinkedList();
  for (Iterator i=Scene.v().getApplicationClasses().iterator(); i.hasNext(); ) {
    SootClass theClass=(SootClass)i.next();
    if (SootUtilities.derivesFrom(theClass,PtolemyUtilities.actorClass) || SootUtilities.derivesFrom(theClass,PtolemyUtilities.compositeActorClass) || SootUtilities.derivesFrom(theClass,PtolemyUtilities.attributeClass)) {
      if (theClass.declaresFieldByName(ModelTransformer.getContainerFieldName())) {
        for (Iterator methods=theClass.getMethods().iterator(); methods.hasNext(); ) {
          SootMethod method=(SootMethod)methods.next();
          if (method.getName().equals("String_Node_Str") && (method.getParameterCount() == 2)) {
            SootField containerField=theClass.getFieldByName(ModelTransformer.getContainerFieldName());
            RefType containerType=(RefType)containerField.getType();
            List typeList=new LinkedList();
            typeList.add(containerType);
            typeList.add(RefType.v("String_Node_Str"));
            method.setParameterTypes(typeList);
            theClass.removeMethod(method);
            theClass.addMethod(method);
            JimpleBody body=(JimpleBody)method.retrieveActiveBody();
            for (Iterator units=body.getUnits().snapshotIterator(); units.hasNext(); ) {
              Stmt unit=(Stmt)units.next();
              if (unit instanceof IdentityStmt) {
                IdentityStmt identityStmt=(IdentityStmt)unit;
                Value value=identityStmt.getRightOp();
                if (value instanceof ParameterRef) {
                  ParameterRef parameterRef=(ParameterRef)value;
                  if (parameterRef.getIndex() == 0) {
                    ValueBox box=identityStmt.getRightOpBox();
                    box.setValue(Jimple.v().newParameterRef(method.getParameterType(0),0));
                  }
                }
              }
            }
          }
        }
        modifiedConstructorClassList.add(theClass);
        System.out.println("String_Node_Str" + theClass);
      }
    }
  }
  Scene.v().setActiveHierarchy(new Hierarchy());
  Scene.v().setFastHierarchy(new FastHierarchy());
  for (Iterator i=Scene.v().getApplicationClasses().iterator(); i.hasNext(); ) {
    SootClass theClass=(SootClass)i.next();
    for (Iterator methods=theClass.getMethods().iterator(); methods.hasNext(); ) {
      SootMethod method=(SootMethod)methods.next();
      JimpleBody body=(JimpleBody)method.retrieveActiveBody();
      for (Iterator units=body.getUnits().snapshotIterator(); units.hasNext(); ) {
        Stmt unit=(Stmt)units.next();
        if (unit.containsInvokeExpr()) {
          ValueBox box=unit.getInvokeExprBox();
          Value value=box.getValue();
          if (value instanceof SpecialInvokeExpr) {
            System.out.println("String_Node_Str" + unit);
            SpecialInvokeExpr expr=(SpecialInvokeExpr)value;
            SootClass declaringClass=expr.getMethodRef().declaringClass();
            System.out.println("String_Node_Str" + declaringClass);
            if (expr.getMethod().getName().equals("String_Node_Str") && modifiedConstructorClassList.contains(declaringClass)) {
              System.out.println("String_Node_Str" + unit + "String_Node_Str"+ method);
              SootMethod newConstructor=declaringClass.getMethodByName("String_Node_Str");
              if (newConstructor.getParameterCount() == 2) {
                SpecialInvokeExpr r=(SpecialInvokeExpr)value;
                r.setMethodRef(newConstructor.makeRef());
              }
            }
          }
        }
      }
    }
  }
}

Fixed version (ground truth):
protected void internalTransform(String phaseName,Map options){
  int localCount=0;
  System.out.println("String_Node_Str" + phaseName + "String_Node_Str"+ options+ "String_Node_Str");
  List modifiedConstructorClassList=new LinkedList();
  HashMap classToConstructorMap=new HashMap();
  for (Iterator i=Scene.v().getApplicationClasses().iterator(); i.hasNext(); ) {
    SootClass theClass=(SootClass)i.next();
    if (SootUtilities.derivesFrom(theClass,PtolemyUtilities.actorClass) || SootUtilities.derivesFrom(theClass,PtolemyUtilities.compositeActorClass) || SootUtilities.derivesFrom(theClass,PtolemyUtilities.attributeClass)) {
      if (theClass.declaresFieldByName(ModelTransformer.getContainerFieldName())) {
        for (Iterator methods=theClass.getMethods().iterator(); methods.hasNext(); ) {
          SootMethod method=(SootMethod)methods.next();
          if (method.getName().equals("String_Node_Str") && (method.getParameterCount() == 2)) {
            SootField containerField=theClass.getFieldByName(ModelTransformer.getContainerFieldName());
            RefType containerType=(RefType)containerField.getType();
            List typeList=new LinkedList();
            typeList.add(containerType);
            typeList.add(RefType.v("String_Node_Str"));
            method.setParameterTypes(typeList);
            theClass.removeMethod(method);
            theClass.addMethod(method);
            classToConstructorMap.put(theClass,method);
            JimpleBody body=(JimpleBody)method.retrieveActiveBody();
            for (Iterator units=body.getUnits().snapshotIterator(); units.hasNext(); ) {
              Stmt unit=(Stmt)units.next();
              if (unit instanceof IdentityStmt) {
                IdentityStmt identityStmt=(IdentityStmt)unit;
                Value value=identityStmt.getRightOp();
                if (value instanceof ParameterRef) {
                  ParameterRef parameterRef=(ParameterRef)value;
                  if (parameterRef.getIndex() == 0) {
                    ValueBox box=identityStmt.getRightOpBox();
                    box.setValue(Jimple.v().newParameterRef(method.getParameterType(0),0));
                  }
                }
              }
            }
          }
        }
        modifiedConstructorClassList.add(theClass);
        System.out.println("String_Node_Str" + theClass);
      }
    }
  }
  Scene.v().setActiveHierarchy(new Hierarchy());
  Scene.v().setFastHierarchy(new FastHierarchy());
  for (Iterator i=Scene.v().getApplicationClasses().iterator(); i.hasNext(); ) {
    SootClass theClass=(SootClass)i.next();
    for (Iterator methods=theClass.getMethods().iterator(); methods.hasNext(); ) {
      SootMethod method=(SootMethod)methods.next();
      JimpleBody body=(JimpleBody)method.retrieveActiveBody();
      for (Iterator units=body.getUnits().snapshotIterator(); units.hasNext(); ) {
        Stmt unit=(Stmt)units.next();
        if (unit.containsInvokeExpr()) {
          ValueBox box=unit.getInvokeExprBox();
          Value value=box.getValue();
          if (value instanceof SpecialInvokeExpr) {
            System.out.println("String_Node_Str" + unit);
            SpecialInvokeExpr expr=(SpecialInvokeExpr)value;
            SootClass declaringClass=expr.getMethodRef().declaringClass();
            System.out.println("String_Node_Str" + declaringClass);
            if (expr.getMethod().getName().equals("String_Node_Str") && modifiedConstructorClassList.contains(declaringClass)) {
              System.out.println("String_Node_Str" + unit + "String_Node_Str"+ method);
              SootMethod newConstructor=(SootMethod)classToConstructorMap.get(declaringClass);
              if (newConstructor.getParameterCount() == 2) {
                SpecialInvokeExpr r=(SpecialInvokeExpr)value;
                r.setMethodRef(newConstructor.makeRef());
              }
            }
          }
        }
      }
    }
  }
}