public void reset(@NotNull Collection<X509Certificate> certificates) {
   myCertificates.clear();
   for (X509Certificate certificate : certificates) {
     addCertificate(certificate);
   }
   // expand organization nodes at the same time
   // initRootNode();
   queueUpdateFrom(RootDescriptor.ROOT, true)
       .doWhenDone(() -> CertificateTreeBuilder.this.expandAll(null));
 }
  public void search() {
    myFiles.clear();
    myJars.clear();

    PsiManager psiManager = PsiManager.getInstance(myProject);
    for (PsiFile file : search(myModule, myProject)) {
      VirtualFile jar = JarFileSystem.getInstance().getVirtualFileForJar(file.getVirtualFile());
      if (jar != null) {
        myJars.putValue(jar, file);
      } else {
        Module module = ModuleUtilCore.findModuleForPsiElement(file);
        if (module != null) {
          myFiles.putValue(module, file);
        } else {
          VirtualFile virtualFile = file.getVirtualFile();
          myVirtualFiles.putValue(virtualFile.getParent(), psiManager.findFile(virtualFile));
        }
      }
    }
  }
 public void doClearFoldRegions() {
   myGroups.clear();
   myFoldTree.clear();
 }
  public final RunnerResult analyzeMethod(
      @NotNull PsiElement psiBlock,
      InstructionVisitor visitor,
      boolean ignoreAssertions,
      @NotNull Collection<DfaMemoryState> initialStates) {
    try {
      prepareAnalysis(psiBlock, initialStates);

      final ControlFlow flow =
          createControlFlowAnalyzer().buildControlFlow(psiBlock, ignoreAssertions);
      if (flow == null) return RunnerResult.NOT_APPLICABLE;

      int endOffset = flow.getInstructionCount();
      myInstructions = flow.getInstructions();
      myFields = flow.getFields();
      myNestedClosures.clear();

      if (LOG.isDebugEnabled()) {
        LOG.debug("Analyzing code block: " + psiBlock.getText());
        for (int i = 0; i < myInstructions.length; i++) {
          Instruction instruction = myInstructions[i];
          LOG.debug(i + ": " + instruction.toString());
        }
      }

      Integer tooExpensiveHash = psiBlock.getUserData(TOO_EXPENSIVE_HASH);
      if (tooExpensiveHash != null && tooExpensiveHash == psiBlock.getText().hashCode()) {
        LOG.debug("Too complex because hasn't changed since being too complex already");
        return RunnerResult.TOO_COMPLEX;
      }

      final ArrayList<DfaInstructionState> queue = new ArrayList<DfaInstructionState>();
      for (final DfaMemoryState initialState : initialStates) {
        queue.add(new DfaInstructionState(myInstructions[0], initialState));
      }

      long timeLimit = ourTimeLimit;
      final boolean unitTestMode = ApplicationManager.getApplication().isUnitTestMode();
      WorkingTimeMeasurer measurer = new WorkingTimeMeasurer(timeLimit);
      int count = 0;
      while (!queue.isEmpty()) {
        if (count % 50 == 0 && !unitTestMode && measurer.isTimeOver()) {
          LOG.debug("Too complex because the analysis took too long");
          psiBlock.putUserData(TOO_EXPENSIVE_HASH, psiBlock.getText().hashCode());
          return RunnerResult.TOO_COMPLEX;
        }
        ProgressManager.checkCanceled();

        DfaInstructionState instructionState = queue.remove(0);
        if (LOG.isDebugEnabled()) {
          LOG.debug(instructionState.toString());
        }
        // System.out.println(instructionState.toString());

        Instruction instruction = instructionState.getInstruction();
        long distance = instructionState.getDistanceFromStart();

        if (instruction instanceof BranchingInstruction) {
          if (!instruction.setMemoryStateProcessed(
              instructionState.getMemoryState().createCopy())) {
            LOG.debug("Too complex because too many different possible states");
            return RunnerResult.TOO_COMPLEX; // Too complex :(
          }
        }

        DfaInstructionState[] after = acceptInstruction(visitor, instructionState);
        for (DfaInstructionState state : after) {
          Instruction nextInstruction = state.getInstruction();
          if ((!(nextInstruction instanceof BranchingInstruction)
                  || !nextInstruction.isMemoryStateProcessed(state.getMemoryState()))
              && instruction.getIndex() < endOffset) {
            state.setDistanceFromStart(distance + 1);
            queue.add(state);
          }
        }

        count++;
      }

      psiBlock.putUserData(TOO_EXPENSIVE_HASH, null);
      LOG.debug("Analysis ok");
      return RunnerResult.OK;
    } catch (ArrayIndexOutOfBoundsException e) {
      LOG.error(psiBlock.getText(), e); // TODO fix in better times
      return RunnerResult.ABORTED;
    } catch (EmptyStackException e) {
      if (LOG.isDebugEnabled()) {
        LOG.error(e); // TODO fix in better times
      }
      return RunnerResult.ABORTED;
    }
  }
 public void dispose() {
   myGroups.clear();
   myFoldTree.clear();
 }
  public boolean updateStep() {
    final MultiMap<VcsRoot, String> dirty = new MultiMap<VcsRoot, String>();
    final long oldPoint =
        System.currentTimeMillis()
            - (myVcsConfiguration.CHANGED_ON_SERVER_INTERVAL > 0
                ? myVcsConfiguration.CHANGED_ON_SERVER_INTERVAL * 60000
                : DISCRETE);

    synchronized (myLock) {
      // just copies myQueries MultiMap to dirty MultiMap
      for (VcsRoot root : myQueries.keySet()) {
        final Collection<String> collection = myQueries.get(root);
        for (String s : collection) {
          dirty.putValue(root, s);
        }
      }
      myQueries.clear();

      // collect roots for which cache update should be performed (by timestamp)
      final Set<VcsRoot> roots = new HashSet<VcsRoot>();
      for (Map.Entry<VcsRoot, Long> entry : myTs.entrySet()) {
        // ignore timestamp, as still remote changes checking is required
        // TODO: why not to add in roots anyway??? - as dirty is still checked when adding myChanged
        // files.
        if (!dirty.get(entry.getKey()).isEmpty()) continue;

        // update only if timeout expired
        final Long ts = entry.getValue();
        if ((ts == null) || (oldPoint > ts)) {
          roots.add(entry.getKey());
        }
      }

      // Add dirty files from those vcs roots, that
      // - needs to be update by timestamp criteria
      // - that already contain files for update through manually added requests
      for (Map.Entry<String, Pair<Boolean, VcsRoot>> entry : myChanged.entrySet()) {
        final VcsRoot vcsRoot = entry.getValue().getSecond();
        if ((!dirty.get(vcsRoot).isEmpty()) || roots.contains(vcsRoot)) {
          dirty.putValue(vcsRoot, entry.getKey());
        }
      }
    }

    if (dirty.isEmpty()) return false;

    final Map<String, Pair<Boolean, VcsRoot>> results =
        new HashMap<String, Pair<Boolean, VcsRoot>>();
    for (VcsRoot vcsRoot : dirty.keySet()) {
      // todo - actually it means nothing since the only known VCS to use this scheme is Git and now
      // it always allow
      // todo - background operations. when it changes, develop more flexible behavior here
      if (!vcsRoot.getVcs().isVcsBackgroundOperationsAllowed(vcsRoot.getPath())) continue;
      final TreeDiffProvider provider = vcsRoot.getVcs().getTreeDiffProvider();
      if (provider == null) continue;

      final Collection<String> paths = dirty.get(vcsRoot);
      final Collection<String> remotelyChanged =
          provider.getRemotelyChanged(vcsRoot.getPath(), paths);
      for (String path : paths) {
        // TODO: Contains invoked for each file - better to use Set (implementations just use List)
        // TODO: Why to store boolean for changed or not - why not just remove such values from
        // myChanged???
        results.put(path, new Pair<Boolean, VcsRoot>(remotelyChanged.contains(path), vcsRoot));
      }
    }

    final long curTime = System.currentTimeMillis();
    synchronized (myLock) {
      myChanged.putAll(results);
      for (VcsRoot vcsRoot : dirty.keySet()) {
        myTs.put(vcsRoot, curTime);
      }
    }

    return true;
  }
  public boolean updateStep(final AtomicSectionsAware atomicSectionsAware) {
    final MultiMap<VcsRoot, String> dirty = new MultiMap<VcsRoot, String>();
    final long oldPoint =
        System.currentTimeMillis()
            - (myVcsConfiguration.CHANGED_ON_SERVER_INTERVAL > 0
                ? myVcsConfiguration.CHANGED_ON_SERVER_INTERVAL * 60000
                : DISCRETE);

    synchronized (myLock) {
      for (VcsRoot root : myQueries.keySet()) {
        final Collection<String> collection = myQueries.get(root);
        for (String s : collection) {
          dirty.putValue(root, s);
        }
      }
      myQueries.clear();

      final Set<VcsRoot> roots = new HashSet<VcsRoot>();
      for (Map.Entry<VcsRoot, Long> entry : myTs.entrySet()) {
        if (!dirty.get(entry.getKey()).isEmpty()) continue;

        final Long ts = entry.getValue();
        if ((ts == null) || (oldPoint > ts)) {
          roots.add(entry.getKey());
        }
      }
      for (Map.Entry<String, Pair<Boolean, VcsRoot>> entry : myChanged.entrySet()) {
        final VcsRoot vcsRoot = entry.getValue().getSecond();
        if ((!dirty.get(vcsRoot).isEmpty()) || roots.contains(vcsRoot)) {
          dirty.putValue(vcsRoot, entry.getKey());
        }
      }
    }

    if (dirty.isEmpty()) return false;

    final Map<String, Pair<Boolean, VcsRoot>> results =
        new HashMap<String, Pair<Boolean, VcsRoot>>();
    for (VcsRoot vcsRoot : dirty.keySet()) {
      atomicSectionsAware.checkShouldExit();
      // todo - actually it means nothing since the only known VCS to use this scheme is Git and now
      // it always allow
      // todo - background operations. when it changes, develop more flexible behavior here
      if (!vcsRoot.vcs.isVcsBackgroundOperationsAllowed(vcsRoot.path)) continue;
      final TreeDiffProvider provider = vcsRoot.vcs.getTreeDiffProvider();
      if (provider == null) continue;

      final Collection<String> paths = dirty.get(vcsRoot);
      final Collection<String> remotelyChanged = provider.getRemotelyChanged(vcsRoot.path, paths);
      for (String path : paths) {
        results.put(path, new Pair<Boolean, VcsRoot>(remotelyChanged.contains(path), vcsRoot));
      }
    }

    final long curTime = System.currentTimeMillis();
    synchronized (myLock) {
      myChanged.putAll(results);
      for (VcsRoot vcsRoot : dirty.keySet()) {
        myTs.put(vcsRoot, curTime);
      }
    }

    return true;
  }
  @NotNull
  final RunnerResult analyzeMethod(
      @NotNull PsiElement psiBlock,
      @NotNull InstructionVisitor visitor,
      boolean ignoreAssertions,
      @NotNull Collection<DfaMemoryState> initialStates) {
    if (PsiTreeUtil.findChildOfType(psiBlock, OuterLanguageElement.class) != null)
      return RunnerResult.NOT_APPLICABLE;

    try {
      final ControlFlow flow =
          new ControlFlowAnalyzer(myValueFactory, psiBlock, ignoreAssertions).buildControlFlow();
      if (flow == null) return RunnerResult.NOT_APPLICABLE;
      int[] loopNumber = LoopAnalyzer.calcInLoop(flow);

      int endOffset = flow.getInstructionCount();
      myInstructions = flow.getInstructions();
      myNestedClosures.clear();

      Set<Instruction> joinInstructions = ContainerUtil.newHashSet();
      for (int index = 0; index < myInstructions.length; index++) {
        Instruction instruction = myInstructions[index];
        if (instruction instanceof GotoInstruction) {
          joinInstructions.add(myInstructions[((GotoInstruction) instruction).getOffset()]);
        } else if (instruction instanceof ConditionalGotoInstruction) {
          joinInstructions.add(
              myInstructions[((ConditionalGotoInstruction) instruction).getOffset()]);
        } else if (instruction instanceof MethodCallInstruction
            && !((MethodCallInstruction) instruction).getContracts().isEmpty()) {
          joinInstructions.add(myInstructions[index + 1]);
        }
      }

      if (LOG.isDebugEnabled()) {
        LOG.debug("Analyzing code block: " + psiBlock.getText());
        for (int i = 0; i < myInstructions.length; i++) {
          LOG.debug(i + ": " + myInstructions[i]);
        }
      }
      // for (int i = 0; i < myInstructions.length; i++) System.out.println(i + ": " +
      // myInstructions[i].toString());

      Integer tooExpensiveHash = psiBlock.getUserData(TOO_EXPENSIVE_HASH);
      if (tooExpensiveHash != null && tooExpensiveHash == psiBlock.getText().hashCode()) {
        LOG.debug("Too complex because hasn't changed since being too complex already");
        return RunnerResult.TOO_COMPLEX;
      }

      final StateQueue queue = new StateQueue();
      for (final DfaMemoryState initialState : initialStates) {
        queue.offer(new DfaInstructionState(myInstructions[0], initialState));
      }

      MultiMap<BranchingInstruction, DfaMemoryState> processedStates = MultiMap.createSet();
      MultiMap<BranchingInstruction, DfaMemoryState> incomingStates = MultiMap.createSet();

      long msLimit =
          shouldCheckTimeLimit()
              ? Registry.intValue("ide.dfa.time.limit.online")
              : Registry.intValue("ide.dfa.time.limit.offline");
      WorkingTimeMeasurer measurer = new WorkingTimeMeasurer(msLimit * 1000 * 1000);
      int count = 0;
      while (!queue.isEmpty()) {
        List<DfaInstructionState> states = queue.getNextInstructionStates(joinInstructions);
        for (DfaInstructionState instructionState : states) {
          if (count++ % 1024 == 0 && measurer.isTimeOver()) {
            LOG.debug("Too complex because the analysis took too long");
            psiBlock.putUserData(TOO_EXPENSIVE_HASH, psiBlock.getText().hashCode());
            return RunnerResult.TOO_COMPLEX;
          }
          ProgressManager.checkCanceled();

          if (LOG.isDebugEnabled()) {
            LOG.debug(instructionState.toString());
          }
          // System.out.println(instructionState.toString());

          Instruction instruction = instructionState.getInstruction();

          if (instruction instanceof BranchingInstruction) {
            BranchingInstruction branching = (BranchingInstruction) instruction;
            Collection<DfaMemoryState> processed = processedStates.get(branching);
            if (processed.contains(instructionState.getMemoryState())) {
              continue;
            }
            if (processed.size() > MAX_STATES_PER_BRANCH) {
              LOG.debug("Too complex because too many different possible states");
              return RunnerResult.TOO_COMPLEX; // Too complex :(
            }
            if (loopNumber[branching.getIndex()] != 0) {
              processedStates.putValue(branching, instructionState.getMemoryState().createCopy());
            }
          }

          DfaInstructionState[] after = acceptInstruction(visitor, instructionState);
          for (DfaInstructionState state : after) {
            Instruction nextInstruction = state.getInstruction();
            if (nextInstruction.getIndex() >= endOffset) {
              continue;
            }
            handleStepOutOfLoop(
                instruction,
                nextInstruction,
                loopNumber,
                processedStates,
                incomingStates,
                states,
                after,
                queue);
            if (nextInstruction instanceof BranchingInstruction) {
              BranchingInstruction branching = (BranchingInstruction) nextInstruction;
              if (processedStates.get(branching).contains(state.getMemoryState())
                  || incomingStates.get(branching).contains(state.getMemoryState())) {
                continue;
              }
              if (loopNumber[branching.getIndex()] != 0) {
                incomingStates.putValue(branching, state.getMemoryState().createCopy());
              }
            }
            queue.offer(state);
          }
        }
      }

      psiBlock.putUserData(TOO_EXPENSIVE_HASH, null);
      LOG.debug("Analysis ok");
      return RunnerResult.OK;
    } catch (ArrayIndexOutOfBoundsException e) {
      LOG.error(psiBlock.getText(), e);
      return RunnerResult.ABORTED;
    } catch (EmptyStackException e) {
      LOG.error(psiBlock.getText(), e);
      return RunnerResult.ABORTED;
    }
  }