public void removeEntryPoint(RefElement anEntryPoint) {
    if (anEntryPoint instanceof RefClass) {
      RefClass refClass = (RefClass) anEntryPoint;
      if (!refClass.isInterface()) {
        anEntryPoint = refClass.getDefaultConstructor();
      }
    }

    if (anEntryPoint == null) return;

    myTemporaryEntryPoints.remove(anEntryPoint);

    Set<Map.Entry<String, SmartRefElementPointer>> set = myPersistentEntryPoints.entrySet();
    String key = null;
    for (Map.Entry<String, SmartRefElementPointer> entry : set) {
      SmartRefElementPointer value = entry.getValue();
      if (value.getRefElement() == anEntryPoint) {
        key = entry.getKey();
        break;
      }
    }

    if (key != null) {
      myPersistentEntryPoints.remove(key);
      ((RefElementImpl) anEntryPoint).setEntry(false);
    }

    if (anEntryPoint.isPermanentEntry() && anEntryPoint.isValid()) {
      final Project project = anEntryPoint.getElement().getProject();
      final EntryPointsManagerImpl entryPointsManager = getInstance(project);
      if (this != entryPointsManager) {
        entryPointsManager.removeEntryPoint(anEntryPoint);
      }
    }
  }
  @Override
  public void addEntryPoint(@NotNull RefElement newEntryPoint, boolean isPersistent) {
    if (!newEntryPoint.isValid()) return;
    if (isPersistent) {
      if (newEntryPoint instanceof RefMethod && ((RefMethod) newEntryPoint).isConstructor()
          || newEntryPoint instanceof RefClass) {
        final ClassPattern classPattern = new ClassPattern();
        classPattern.pattern = new SmartRefElementPointerImpl(newEntryPoint, true).getFQName();
        getPatterns().add(classPattern);

        final EntryPointsManager entryPointsManager =
            getInstance(newEntryPoint.getElement().getProject());
        if (this != entryPointsManager) {
          entryPointsManager.addEntryPoint(newEntryPoint, true);
        }

        return;
      }
    }

    if (newEntryPoint instanceof RefClass) {
      RefClass refClass = (RefClass) newEntryPoint;

      if (refClass.isAnonymous()) {
        // Anonymous class cannot be an entry point.
        return;
      }

      List<RefMethod> refConstructors = refClass.getConstructors();
      if (refConstructors.size() == 1) {
        addEntryPoint(refConstructors.get(0), isPersistent);
      } else if (refConstructors.size() > 1) {
        // Many constructors here. Need to ask user which ones are used
        for (RefMethod refConstructor : refConstructors) {
          addEntryPoint(refConstructor, isPersistent);
        }
      }
    }

    if (!isPersistent) {
      myTemporaryEntryPoints.add(newEntryPoint);
      ((RefElementImpl) newEntryPoint).setEntry(true);
    } else {
      if (myPersistentEntryPoints.get(newEntryPoint.getExternalName()) == null) {
        final SmartRefElementPointerImpl entry =
            new SmartRefElementPointerImpl(newEntryPoint, true);
        myPersistentEntryPoints.put(entry.getFQName(), entry);
        ((RefElementImpl) newEntryPoint).setEntry(true);
        ((RefElementImpl) newEntryPoint).setPermanentEntry(true);
        if (entry.isPersistent()) { // do save entry points
          final EntryPointsManager entryPointsManager =
              getInstance(newEntryPoint.getElement().getProject());
          if (this != entryPointsManager) {
            entryPointsManager.addEntryPoint(newEntryPoint, true);
          }
        }
      }
    }
  }
  @Override
  public Element export(
      @NotNull RefEntity refEntity, @NotNull final Element element, final int actualLine) {
    refEntity = getRefinedElement(refEntity);

    Element problem = new Element("problem");

    if (refEntity instanceof RefElement) {
      final RefElement refElement = (RefElement) refEntity;
      final SmartPsiElementPointer pointer = refElement.getPointer();
      PsiFile psiFile = pointer.getContainingFile();
      if (psiFile == null) return null;

      Element fileElement = new Element("file");
      Element lineElement = new Element("line");
      final VirtualFile virtualFile = psiFile.getVirtualFile();
      LOG.assertTrue(virtualFile != null);
      fileElement.addContent(virtualFile.getUrl());

      if (actualLine == -1) {
        final Document document =
            PsiDocumentManager.getInstance(pointer.getProject()).getDocument(psiFile);
        LOG.assertTrue(document != null);
        final Segment range = pointer.getRange();
        lineElement.addContent(
            String.valueOf(
                range != null ? document.getLineNumber(range.getStartOffset()) + 1 : -1));
      } else {
        lineElement.addContent(String.valueOf(actualLine));
      }

      problem.addContent(fileElement);
      problem.addContent(lineElement);

      appendModule(problem, refElement.getModule());
    } else if (refEntity instanceof RefModule) {
      final RefModule refModule = (RefModule) refEntity;
      final VirtualFile moduleFile = refModule.getModule().getModuleFile();
      final Element fileElement = new Element("file");
      fileElement.addContent(moduleFile != null ? moduleFile.getUrl() : refEntity.getName());
      problem.addContent(fileElement);
      appendModule(problem, refModule);
    }

    for (RefManagerExtension extension : myExtensions.values()) {
      extension.export(refEntity, problem);
    }

    new SmartRefElementPointerImpl(refEntity, true).writeExternal(problem);
    element.addContent(problem);
    return problem;
  }
 @Override
 public void iterate(@NotNull RefVisitor visitor) {
   for (RefElement refElement : getSortedElements()) {
     refElement.accept(visitor);
   }
   if (myModules != null) {
     for (RefModule refModule : myModules.values()) {
       refModule.accept(visitor);
     }
   }
   for (RefManagerExtension extension : myExtensions.values()) {
     extension.iterate(visitor);
   }
 }
  @Override
  public void removeRefElement(
      @NotNull RefElement refElement, @NotNull List<RefElement> deletedRefs) {
    List<RefEntity> children = refElement.getChildren();
    if (children != null) {
      RefElement[] refElements = children.toArray(new RefElement[children.size()]);
      for (RefElement refChild : refElements) {
        removeRefElement(refChild, deletedRefs);
      }
    }

    ((RefManagerImpl) refElement.getRefManager()).removeReference(refElement);
    ((RefElementImpl) refElement).referenceRemoved();
    if (!deletedRefs.contains(refElement)) deletedRefs.add(refElement);
  }
  protected HighlightSeverity getSeverity(@NotNull RefElement element) {
    final PsiElement psiElement = element.getPointer().getContainingFile();
    if (psiElement != null) {
      final GlobalInspectionContextImpl context = getContext();
      final String shortName = getSeverityDelegateName();
      final Tools tools = context.getTools().get(shortName);
      if (tools != null) {
        for (ScopeToolState state : tools.getTools()) {
          InspectionToolWrapper toolWrapper = state.getTool();
          if (toolWrapper == getToolWrapper()) {
            return context
                .getCurrentProfile()
                .getErrorLevel(HighlightDisplayKey.find(shortName), psiElement)
                .getSeverity();
          }
        }
      }

      final InspectionProfile profile =
          InspectionProjectProfileManager.getInstance(context.getProject()).getInspectionProfile();
      final HighlightDisplayLevel level =
          profile.getErrorLevel(HighlightDisplayKey.find(shortName), psiElement);
      return level.getSeverity();
    }
    return null;
  }
  @Override
  public void removeEntryPoint(@NotNull RefElement anEntryPoint) {
    myTemporaryEntryPoints.remove(anEntryPoint);

    Set<Map.Entry<String, SmartRefElementPointer>> set = myPersistentEntryPoints.entrySet();
    String key = null;
    for (Map.Entry<String, SmartRefElementPointer> entry : set) {
      SmartRefElementPointer value = entry.getValue();
      if (value.getRefElement() == anEntryPoint) {
        key = entry.getKey();
        break;
      }
    }

    if (key != null) {
      myPersistentEntryPoints.remove(key);
    }
    ((RefElementImpl) anEntryPoint).setEntry(false);

    if (anEntryPoint.isPermanentEntry() && anEntryPoint.isValid()) {
      final Project project = anEntryPoint.getElement().getProject();
      final EntryPointsManager entryPointsManager = getInstance(project);
      if (this != entryPointsManager) {
        entryPointsManager.removeEntryPoint(anEntryPoint);
      }
    }

    if (anEntryPoint instanceof RefMethod && ((RefMethod) anEntryPoint).isConstructor()
        || anEntryPoint instanceof RefClass) {
      final RefClass aClass =
          anEntryPoint instanceof RefClass
              ? (RefClass) anEntryPoint
              : ((RefMethod) anEntryPoint).getOwnerClass();
      final String qualifiedName = aClass.getQualifiedName();
      for (Iterator<ClassPattern> iterator = getPatterns().iterator(); iterator.hasNext(); ) {
        if (Comparing.equal(iterator.next().pattern, qualifiedName)) {
          // todo if inheritance or pattern?
          iterator.remove();
        }
      }
    }
  }
  private void validateEntryPoints() {
    long count = PsiManager.getInstance(myProject).getModificationTracker().getModificationCount();
    if (count != myLastModificationCount) {
      myLastModificationCount = count;
      Collection<SmartRefElementPointer> collection = myPersistentEntryPoints.values();
      SmartRefElementPointer[] entries =
          collection.toArray(new SmartRefElementPointer[collection.size()]);
      for (SmartRefElementPointer entry : entries) {
        RefElement refElement = (RefElement) entry.getRefElement();
        if (refElement != null && !refElement.isValid()) {
          myPersistentEntryPoints.remove(entry.getFQName());
        }
      }

      final Iterator<RefElement> it = myTemporaryEntryPoints.iterator();
      while (it.hasNext()) {
        RefElement refElement = it.next();
        if (!refElement.isValid()) {
          it.remove();
        }
      }
    }
  }
  @Override
  @Nullable
  public String getGroupName(final RefElement entity) {
    for (RefManagerExtension extension : myExtensions.values()) {
      final String groupName = extension.getGroupName(entity);
      if (groupName != null) return groupName;
    }

    final LinkedList<String> containingDirs = new LinkedList<>();
    RefEntity parent = entity.getOwner();
    while (parent != null && !(parent instanceof RefDirectory)) {
      parent = parent.getOwner();
    }
    while (parent instanceof RefDirectory) {
      containingDirs.addFirst(parent.getName());
      parent = parent.getOwner();
    }
    return containingDirs.isEmpty() ? null : StringUtil.join(containingDirs, File.separator);
  }
  void removeReference(@NotNull RefElement refElem) {
    final PsiElement element = refElem.getElement();
    final RefManagerExtension extension =
        element != null ? getExtension(element.getLanguage()) : null;
    if (extension != null) {
      extension.removeReference(refElem);
    }

    synchronized (myRefTable) {
      mySortedRefs = null;
      if (element != null && myRefTable.remove(createAnchor(element)) != null) return;

      // PsiElement may have been invalidated and new one returned by getElement() is different so
      // we need to do this stuff.
      for (Map.Entry<PsiAnchor, RefElement> entry : myRefTable.entrySet()) {
        RefElement value = entry.getValue();
        PsiAnchor anchor = entry.getKey();
        if (value == refElem) {
          myRefTable.remove(anchor);
          break;
        }
      }
    }
  }