Program: 6622
Project: 6622
Buggy source:
@Override public List<List<Location>> applyChannel(List<ChannelConstraint> constraints,List<Compartment> compartments){
  List<List<Location>> result=new ArrayList<List<Location>>();
  if (isValidSourceLocations(templateConstraints,constraints,compartments)) {
    for (int templateIndex=0; templateIndex < templateConstraints.size(); templateIndex++) {
      Location templateSourceLocation=templateConstraints.get(templateIndex).sourceLocation;
      Location templateTargetLocation=templateConstraints.get(templateIndex).targetConstraint;
      ChannelConstraint constraint=constraints.get(templateIndex);
      Location sourceLocation=constraint.sourceLocation;
      Location targetConstraint=constraint.targetConstraint;
      Compartment sourceCompartment=getCompartment(compartments,templateSourceLocation.getName());
      Compartment targetCompartment=getCompartment(compartments,templateTargetLocation.getName());
      if (sourceLocation.getIndices().length != sourceCompartment.getDimensions().length || !sourceLocation.getName().equals(templateSourceLocation.getName())) {
        continue;
      }
      List<Location> newLocations=null;
      if (sourceCompartment.getDimensions().length == 2) {
        newLocations=getLateralLocations2D(sourceLocation,sourceCompartment);
      }
 else {
        newLocations=getLateralLocations3D(sourceLocation,sourceCompartment);
      }
      if (isNesting(sourceCompartment,targetCompartment)) {
        newLocations=applyNestingOffsets(sourceCompartment,targetCompartment,newLocations);
      }
      for (      Location location : newLocations) {
        if (targetCompartment.isValidVoxel(location)) {
          if (targetConstraint == null || targetConstraint.equals(location) || targetConstraint.isRefinement(location)) {
            result.add(getList(location));
          }
        }
      }
    }
  }
  return result;
}

Fixed version (ground truth):
@Override public List<List<Location>> applyChannel(List<ChannelConstraint> constraints,List<Compartment> compartments){
  List<List<Location>> result=new ArrayList<List<Location>>();
  if (isValidSourceLocations(templateConstraints,constraints,compartments)) {
    for (int templateIndex=0; templateIndex < templateConstraints.size(); templateIndex++) {
      Location templateSourceLocation=templateConstraints.get(templateIndex).sourceLocation;
      Location templateTargetLocation=templateConstraints.get(templateIndex).targetConstraint;
      ChannelConstraint constraint=constraints.get(templateIndex);
      Location sourceLocation=constraint.sourceLocation;
      Location targetConstraint=constraint.targetConstraint;
      Compartment sourceCompartment=getCompartment(compartments,templateSourceLocation.getName());
      Compartment targetCompartment=getCompartment(compartments,templateTargetLocation.getName());
      if (sourceLocation.getIndices().length != sourceCompartment.getDimensions().length || !sourceLocation.getName().equals(templateSourceLocation.getName())) {
        continue;
      }
      List<Location> newLocations=null;
      if (sourceCompartment.getDimensions().length == 2) {
        newLocations=getLateralLocations2D(sourceLocation,sourceCompartment);
      }
 else {
        newLocations=getLateralLocations3D(sourceLocation,sourceCompartment);
      }
      if (isNesting(sourceCompartment,targetCompartment)) {
        newLocations=applyNestingOffsets(sourceCompartment,targetCompartment,newLocations);
      }
      for (      Location location : newLocations) {
        if (targetCompartment.isValidVoxel(location)) {
          if (targetConstraint == null || targetConstraint.equals(location) || targetConstraint.isRefinement(location)) {
            result.add(getList(location));
          }
        }
      }
    }
  }
  removeMotionlessResults(constraints,result);
  return result;
}