Program: 190313
Project: 190313
Buggy source:
public void updateWorld(){
  cacheMarker++;
  GraphModel graphModel=controller.getModel();
  if (graphModel == null) {
    engine.worldUpdated(cacheMarker);
    return;
  }
  HierarchicalGraph graph;
  if (graphModel.isDirected()) {
    undirected=false;
    graph=graphModel.getHierarchicalDirectedGraphVisible();
  }
 else   if (graphModel.isUndirected()) {
    undirected=true;
    graph=graphModel.getHierarchicalUndirectedGraphVisible();
  }
 else   if (graphModel.isMixed()) {
    undirected=false;
    graph=graphModel.getHierarchicalMixedGraphVisible();
  }
 else {
    return;
  }
  ProjectController pc=Lookup.getDefault().lookup(ProjectController.class);
  graphView=graph.getView().getViewId();
  ModelClass[] object3dClasses=engine.getModelClasses();
  graph.readLock();
  ModelClass nodeClass=object3dClasses[AbstractEngine.CLASS_NODE];
  if (nodeClass.isEnabled() && (graph.getNodeVersion() > nodeVersion || modeManager.requireModeChange())) {
    updateNodes(graph);
    nodeClass.setCacheMarker(cacheMarker);
  }
  ModelClass edgeClass=object3dClasses[AbstractEngine.CLASS_EDGE];
  if (edgeClass.isEnabled() && (graph.getEdgeVersion() > edgeVersion || modeManager.requireModeChange())) {
    updateEdges(graph);
    updateMetaEdges(graph);
    edgeClass.setCacheMarker(cacheMarker);
    if (!undirected && vizConfig.isShowArrows()) {
      object3dClasses[AbstractEngine.CLASS_ARROW].setCacheMarker(cacheMarker);
    }
  }
  ModelClass potatoClass=object3dClasses[AbstractEngine.CLASS_POTATO];
  if (potatoClass.isEnabled() && (graph.getNodeVersion() > nodeVersion || modeManager.requireModeChange())) {
    updatePotatoes(graph);
    potatoClass.setCacheMarker(cacheMarker);
  }
  nodeVersion=graph.getNodeVersion();
  edgeVersion=graph.getEdgeVersion();
  graph.readUnlock();
  engine.worldUpdated(cacheMarker);
}

Fixed version (ground truth):
public void updateWorld(){
  cacheMarker++;
  GraphModel graphModel=controller.getModel();
  if (graphModel == null) {
    engine.worldUpdated(cacheMarker);
    return;
  }
  HierarchicalGraph graph;
  if (graphModel.isDirected()) {
    undirected=false;
    graph=graphModel.getHierarchicalDirectedGraphVisible();
  }
 else   if (graphModel.isUndirected()) {
    undirected=true;
    graph=graphModel.getHierarchicalUndirectedGraphVisible();
  }
 else   if (graphModel.isMixed()) {
    undirected=false;
    graph=graphModel.getHierarchicalMixedGraphVisible();
  }
 else {
    undirected=false;
    graph=graphModel.getHierarchicalDirectedGraphVisible();
  }
  ProjectController pc=Lookup.getDefault().lookup(ProjectController.class);
  graphView=graph.getView().getViewId();
  ModelClass[] object3dClasses=engine.getModelClasses();
  graph.readLock();
  ModelClass nodeClass=object3dClasses[AbstractEngine.CLASS_NODE];
  if (nodeClass.isEnabled() && (graph.getNodeVersion() > nodeVersion || modeManager.requireModeChange())) {
    updateNodes(graph);
    nodeClass.setCacheMarker(cacheMarker);
  }
  ModelClass edgeClass=object3dClasses[AbstractEngine.CLASS_EDGE];
  if (edgeClass.isEnabled() && (graph.getEdgeVersion() > edgeVersion || modeManager.requireModeChange())) {
    updateEdges(graph);
    updateMetaEdges(graph);
    edgeClass.setCacheMarker(cacheMarker);
    if (!undirected && vizConfig.isShowArrows()) {
      object3dClasses[AbstractEngine.CLASS_ARROW].setCacheMarker(cacheMarker);
    }
  }
  ModelClass potatoClass=object3dClasses[AbstractEngine.CLASS_POTATO];
  if (potatoClass.isEnabled() && (graph.getNodeVersion() > nodeVersion || modeManager.requireModeChange())) {
    updatePotatoes(graph);
    potatoClass.setCacheMarker(cacheMarker);
  }
  nodeVersion=graph.getNodeVersion();
  edgeVersion=graph.getEdgeVersion();
  graph.readUnlock();
  engine.worldUpdated(cacheMarker);
}