Program: 42191
Project: 42191
Buggy source:
private static void runEquivalent(ArrayList<SAFA<CharPred,Character>> safaRHS,ArrayList<SFA<CharPred,Character>> sfaLHS,ArrayList<SFA<CharPred,Character>> sfaRHS,long timeOut){
  try {
    Timers.setTimeout(Long.MAX_VALUE);
    Triple<SAFA<CharPred,Character>,PositiveBooleanExpression,PositiveBooleanExpression> tempTriple=IntersectedSAFA(safaRHS);
    long fullTimeSAFAIntersect=Timers.getFull();
    long solverTimeSAFAIntersect=Timers.getSolver();
    long subTimeSAFAIntersect=Timers.getSubsumption();
    Timers.setTimeout(Long.MAX_VALUE);
    SAFA<CharPred,Character> tempSAFA=tempTriple.getLeft();
    SAFA.checkEquivalenceOfTwoConfigurations(tempSAFA,tempTriple.getMiddle(),tempSAFA.getInitialState(),solver,SAFA.getBooleanExpressionFactory(),timeOut - fullTimeSAFAIntersect);
    fullTimeSAFA=Timers.getFull() + fullTimeSAFAIntersect;
    solverTimeSAFA=Timers.getSolver() + solverTimeSAFAIntersect;
    subTimeSAFA=Timers.getSubsumption() + subTimeSAFAIntersect;
  }
 catch (  Exception e) {
    fullTimeSAFA=timeOut;
    solverTimeSAFA=timeOut;
    subTimeSAFA=timeOut;
  }
  try {
    long startDate=System.currentTimeMillis();
    SFA<CharPred,Character> tempLeftSFA=IntersectedSFA(sfaLHS,timeOut);
    long endDate=System.currentTimeMillis();
    long totalTimeLeft=endDate - startDate;
    startDate=System.currentTimeMillis();
    SFA<CharPred,Character> tempRightSFA=IntersectedSFA(sfaRHS,timeOut - totalTimeLeft);
    endDate=System.currentTimeMillis();
    long totalTimeRight=endDate - startDate;
    long startDateEquiv=System.currentTimeMillis();
    SFA.areHopcroftKarpEquivalent(tempLeftSFA,tempRightSFA,solver);
    long endDateEquiv=System.currentTimeMillis();
    totalTimeSFA=endDateEquiv - startDateEquiv + totalTimeLeft + totalTimeRight;
  }
 catch (  Exception e) {
    totalTimeSFA=timeOut;
  }
}

Fixed version (ground truth):
private static void runEquivalent(ArrayList<SAFA<CharPred,Character>> safaRHS,ArrayList<SFA<CharPred,Character>> sfaLHS,ArrayList<SFA<CharPred,Character>> sfaRHS,long timeOut){
  try {
    long start=System.currentTimeMillis();
    Triple<SAFA<CharPred,Character>,PositiveBooleanExpression,PositiveBooleanExpression> tempTriple=IntersectedSAFA(safaRHS);
    long totalTime=System.currentTimeMillis() - start;
    long fullTimeSAFAIntersect=totalTime;
    long solverTimeSAFAIntersect=0;
    long subTimeSAFAIntersect=0;
    SAFA<CharPred,Character> tempSAFA=tempTriple.getLeft();
    Timers.setTimeout(Long.MAX_VALUE);
    BooleanExpressionFactory<BDDExpression> bef=new BDDExpressionFactory(tempSAFA.stateCount() + 1);
    SAFA.checkEquivalenceOfTwoConfigurations(tempSAFA,tempTriple.getMiddle(),tempSAFA.getInitialState(),solver,bef,timeOut - fullTimeSAFAIntersect);
    fullTimeSAFA=Timers.getFull() + fullTimeSAFAIntersect;
    solverTimeSAFA=Timers.getSolver() + solverTimeSAFAIntersect;
    subTimeSAFA=Timers.getSubsumption() + subTimeSAFAIntersect;
  }
 catch (  Exception e) {
    fullTimeSAFA=timeOut;
    solverTimeSAFA=timeOut;
    subTimeSAFA=timeOut;
  }
  try {
    long startDate=System.currentTimeMillis();
    SFA<CharPred,Character> tempLeftSFA=IntersectedSFA(sfaLHS,timeOut);
    long endDate=System.currentTimeMillis();
    long totalTimeLeft=endDate - startDate;
    startDate=System.currentTimeMillis();
    SFA<CharPred,Character> tempRightSFA=IntersectedSFA(sfaRHS,timeOut - totalTimeLeft);
    endDate=System.currentTimeMillis();
    long totalTimeRight=endDate - startDate;
    long startDateEquiv=System.currentTimeMillis();
    SFA.areHopcroftKarpEquivalent(tempLeftSFA,tempRightSFA,solver);
    long endDateEquiv=System.currentTimeMillis();
    totalTimeSFA=endDateEquiv - startDateEquiv + totalTimeLeft + totalTimeRight;
  }
 catch (  Exception e) {
    totalTimeSFA=timeOut;
  }
}