private void updateRightTreeModel() {
   Set<PsiFile> deps = new HashSet<PsiFile>();
   Set<PsiFile> scope = getSelectedScope(myLeftTree);
   myIllegalsInRightTree = new HashSet<PsiFile>();
   for (PsiFile psiFile : scope) {
     Map<DependencyRule, Set<PsiFile>> illegalDeps = myIllegalDependencies.get(psiFile);
     if (illegalDeps != null) {
       for (final DependencyRule rule : illegalDeps.keySet()) {
         myIllegalsInRightTree.addAll(illegalDeps.get(rule));
       }
     }
     final Set<PsiFile> psiFiles = myDependencies.get(psiFile);
     if (psiFiles != null) {
       for (PsiFile file : psiFiles) {
         if (file != null && file.isValid()) {
           deps.add(file);
         }
       }
     }
   }
   deps.removeAll(scope);
   myRightTreeExpansionMonitor.freeze();
   myRightTree.setModel(buildTreeModel(deps, myRightTreeMarker));
   myRightTreeExpansionMonitor.restore();
   expandFirstLevel(myRightTree);
 }
 @Override
 public void addRow() {
   final Set<Module> projectModules =
       new HashSet<Module>(Arrays.asList(ModuleManager.getInstance(myProject).getModules()));
   projectModules.removeAll(getAllModules());
   final ChooseModulesDialog chooser =
       new ChooseModulesDialog(
           ProcessedModulesTable.this, new ArrayList<Module>(projectModules), "ChooseModule");
   if (chooser.showAndGet()) {
     final List<Module> chosen = chooser.getChosenElements();
     for (Module module : chosen) {
       addElement(module, null);
     }
   }
 }
 @Nullable
 private AnalysisScope getScope() {
   final Set<PsiFile> selectedScope = getSelectedScope(myRightTree);
   Set<PsiFile> result = new HashSet<PsiFile>();
   ((PackageDependenciesNode) myLeftTree.getModel().getRoot())
       .fillFiles(result, !mySettings.UI_FLATTEN_PACKAGES);
   selectedScope.removeAll(result);
   if (selectedScope.isEmpty()) return null;
   List<VirtualFile> files = new ArrayList<VirtualFile>();
   final ProjectFileIndex fileIndex = ProjectRootManager.getInstance(myProject).getFileIndex();
   for (PsiFile psiFile : selectedScope) {
     final VirtualFile file = psiFile.getVirtualFile();
     LOG.assertTrue(file != null);
     if (fileIndex.isInContent(file)) {
       files.add(file);
     }
   }
   if (!files.isEmpty()) {
     return new AnalysisScope(myProject, files);
   }
   return null;
 }
예제 #4
0
  @NotNull
  @Override
  public List<SearchScope> getPredefinedScopes(
      @NotNull final Project project,
      @Nullable final DataContext dataContext,
      boolean suggestSearchInLibs,
      boolean prevSearchFiles,
      boolean currentSelection,
      boolean usageView,
      boolean showEmptyScopes) {
    Collection<SearchScope> result = ContainerUtil.newLinkedHashSet();
    result.add(GlobalSearchScope.projectScope(project));
    if (suggestSearchInLibs) {
      result.add(GlobalSearchScope.allScope(project));
    }

    if (ModuleUtil.isSupportedRootType(project, JavaSourceRootType.TEST_SOURCE)) {
      result.add(GlobalSearchScopesCore.projectProductionScope(project));
      result.add(GlobalSearchScopesCore.projectTestScope(project));
    }

    final GlobalSearchScope openFilesScope = GlobalSearchScopes.openFilesScope(project);
    if (openFilesScope != GlobalSearchScope.EMPTY_SCOPE) {
      result.add(openFilesScope);
    } else if (showEmptyScopes) {
      result.add(
          new LocalSearchScope(PsiElement.EMPTY_ARRAY, IdeBundle.message("scope.open.files")));
    }

    final Editor selectedTextEditor =
        ApplicationManager.getApplication().isDispatchThread()
            ? FileEditorManager.getInstance(project).getSelectedTextEditor()
            : null;
    final PsiFile psiFile =
        (selectedTextEditor != null)
            ? PsiDocumentManager.getInstance(project).getPsiFile(selectedTextEditor.getDocument())
            : null;
    PsiFile currentFile = psiFile;

    if (dataContext != null) {
      PsiElement dataContextElement = CommonDataKeys.PSI_FILE.getData(dataContext);
      if (dataContextElement == null) {
        dataContextElement = CommonDataKeys.PSI_ELEMENT.getData(dataContext);
      }

      if (dataContextElement == null && psiFile != null) {
        dataContextElement = psiFile;
      }

      if (dataContextElement != null) {
        if (!PlatformUtils.isCidr()) { // TODO: have an API to disable module scopes.
          Module module = ModuleUtilCore.findModuleForPsiElement(dataContextElement);
          if (module == null) {
            module = LangDataKeys.MODULE.getData(dataContext);
          }
          if (module != null && !(ModuleType.get(module) instanceof InternalModuleType)) {
            result.add(module.getModuleScope());
          }
        }
        if (currentFile == null) {
          currentFile = dataContextElement.getContainingFile();
        }
      }
    }

    if (currentFile != null || showEmptyScopes) {
      PsiElement[] scope =
          currentFile != null ? new PsiElement[] {currentFile} : PsiElement.EMPTY_ARRAY;
      result.add(new LocalSearchScope(scope, IdeBundle.message("scope.current.file")));
    }

    if (currentSelection && selectedTextEditor != null && psiFile != null) {
      SelectionModel selectionModel = selectedTextEditor.getSelectionModel();
      if (selectionModel.hasSelection()) {
        int start = selectionModel.getSelectionStart();
        final PsiElement startElement = psiFile.findElementAt(start);
        if (startElement != null) {
          int end = selectionModel.getSelectionEnd();
          final PsiElement endElement = psiFile.findElementAt(end);
          if (endElement != null) {
            final PsiElement parent = PsiTreeUtil.findCommonParent(startElement, endElement);
            if (parent != null) {
              final List<PsiElement> elements = new ArrayList<PsiElement>();
              final PsiElement[] children = parent.getChildren();
              TextRange selection = new TextRange(start, end);
              for (PsiElement child : children) {
                if (!(child instanceof PsiWhiteSpace)
                    && child.getContainingFile() != null
                    && selection.contains(child.getTextOffset())) {
                  elements.add(child);
                }
              }
              if (!elements.isEmpty()) {
                SearchScope local =
                    new LocalSearchScope(
                        PsiUtilCore.toPsiElementArray(elements),
                        IdeBundle.message("scope.selection"));
                result.add(local);
              }
            }
          }
        }
      }
    }

    if (usageView) {
      addHierarchyScope(project, result);
      UsageView selectedUsageView = UsageViewManager.getInstance(project).getSelectedUsageView();
      if (selectedUsageView != null && !selectedUsageView.isSearchInProgress()) {
        final Set<Usage> usages = ContainerUtil.newTroveSet(selectedUsageView.getUsages());
        usages.removeAll(selectedUsageView.getExcludedUsages());
        final List<PsiElement> results = new ArrayList<PsiElement>(usages.size());

        if (prevSearchFiles) {
          final Set<VirtualFile> files = collectFiles(usages, true);
          if (!files.isEmpty()) {
            GlobalSearchScope prev =
                new GlobalSearchScope(project) {
                  private Set<VirtualFile> myFiles = null;

                  @NotNull
                  @Override
                  public String getDisplayName() {
                    return IdeBundle.message("scope.files.in.previous.search.result");
                  }

                  @Override
                  public synchronized boolean contains(@NotNull VirtualFile file) {
                    if (myFiles == null) {
                      myFiles = collectFiles(usages, false);
                    }
                    return myFiles.contains(file);
                  }

                  @Override
                  public int compare(@NotNull VirtualFile file1, @NotNull VirtualFile file2) {
                    return 0;
                  }

                  @Override
                  public boolean isSearchInModuleContent(@NotNull Module aModule) {
                    return true;
                  }

                  @Override
                  public boolean isSearchInLibraries() {
                    return true;
                  }
                };
            result.add(prev);
          }
        } else {
          for (Usage usage : usages) {
            if (usage instanceof PsiElementUsage) {
              final PsiElement element = ((PsiElementUsage) usage).getElement();
              if (element != null && element.isValid() && element.getContainingFile() != null) {
                results.add(element);
              }
            }
          }

          if (!results.isEmpty()) {
            result.add(
                new LocalSearchScope(
                    PsiUtilCore.toPsiElementArray(results),
                    IdeBundle.message("scope.previous.search.results")));
          }
        }
      }
    }

    final FavoritesManager favoritesManager = FavoritesManager.getInstance(project);
    if (favoritesManager != null) {
      for (final String favorite : favoritesManager.getAvailableFavoritesListNames()) {
        final Collection<TreeItem<Pair<AbstractUrl, String>>> rootUrls =
            favoritesManager.getFavoritesListRootUrls(favorite);
        if (rootUrls.isEmpty()) continue; // ignore unused root
        result.add(
            new GlobalSearchScope(project) {
              @NotNull
              @Override
              public String getDisplayName() {
                return "Favorite \'" + favorite + "\'";
              }

              @Override
              public boolean contains(@NotNull final VirtualFile file) {
                return ApplicationManager.getApplication()
                    .runReadAction(
                        (Computable<Boolean>) () -> favoritesManager.contains(favorite, file));
              }

              @Override
              public int compare(
                  @NotNull final VirtualFile file1, @NotNull final VirtualFile file2) {
                return 0;
              }

              @Override
              public boolean isSearchInModuleContent(@NotNull final Module aModule) {
                return true;
              }

              @Override
              public boolean isSearchInLibraries() {
                return true;
              }
            });
      }
    }

    ContainerUtil.addIfNotNull(result, getSelectedFilesScope(project, dataContext));

    return ContainerUtil.newArrayList(result);
  }
  public void install(@Nullable final Runnable onSuccess, boolean confirmed) {
    IdeaPluginDescriptor[] selection = getPluginTable().getSelectedObjects();

    if (confirmed || userConfirm(selection)) {
      final List<PluginNode> list = new ArrayList<PluginNode>();
      for (IdeaPluginDescriptor descr : selection) {
        PluginNode pluginNode = null;
        if (descr instanceof PluginNode) {
          pluginNode = (PluginNode) descr;
        } else if (descr instanceof IdeaPluginDescriptorImpl) {
          PluginId pluginId = descr.getPluginId();
          pluginNode = new PluginNode(pluginId);
          pluginNode.setName(descr.getName());
          pluginNode.setDepends(
              Arrays.asList(descr.getDependentPluginIds()), descr.getOptionalDependentPluginIds());
          pluginNode.setSize("-1");
          pluginNode.setRepositoryName(PluginInstaller.UNKNOWN_HOST_MARKER);
        }

        if (pluginNode != null) {
          list.add(pluginNode);
          ourInstallingNodes.add(pluginNode);
        }
      }

      final InstalledPluginsTableModel installedModel =
          (InstalledPluginsTableModel) myInstalled.getPluginsModel();
      final Set<IdeaPluginDescriptor> disabled = new HashSet<IdeaPluginDescriptor>();
      final Set<IdeaPluginDescriptor> disabledDependants = new HashSet<IdeaPluginDescriptor>();
      for (PluginNode node : list) {
        final PluginId pluginId = node.getPluginId();
        if (installedModel.isDisabled(pluginId)) {
          disabled.add(node);
        }
        final List<PluginId> depends = node.getDepends();
        if (depends != null) {
          final Set<PluginId> optionalDeps =
              new HashSet<PluginId>(Arrays.asList(node.getOptionalDependentPluginIds()));
          for (PluginId dependantId : depends) {
            if (optionalDeps.contains(dependantId)) continue;
            final IdeaPluginDescriptor pluginDescriptor = PluginManager.getPlugin(dependantId);
            if (pluginDescriptor != null && installedModel.isDisabled(dependantId)) {
              disabledDependants.add(pluginDescriptor);
            }
          }
        }
      }

      if (suggestToEnableInstalledPlugins(installedModel, disabled, disabledDependants, list)) {
        myInstalled.setRequireShutdown(true);
      }

      try {
        Runnable onInstallRunnable =
            new Runnable() {
              @Override
              public void run() {
                for (PluginNode node : list) {
                  installedModel.appendOrUpdateDescriptor(node);
                }
                if (!myInstalled.isDisposed()) {
                  getPluginTable().updateUI();
                  myInstalled.setRequireShutdown(true);
                } else {
                  boolean needToRestart = false;
                  for (PluginNode node : list) {
                    final IdeaPluginDescriptor pluginDescriptor =
                        PluginManager.getPlugin(node.getPluginId());
                    if (pluginDescriptor == null || pluginDescriptor.isEnabled()) {
                      needToRestart = true;
                      break;
                    }
                  }

                  if (needToRestart) {
                    PluginManagerMain.notifyPluginsUpdated(null);
                  }
                }
                if (onSuccess != null) {
                  onSuccess.run();
                }
              }
            };
        Runnable cleanupRunnable =
            new Runnable() {
              @Override
              public void run() {
                ourInstallingNodes.removeAll(list);
              }
            };
        PluginManagerMain.downloadPlugins(
            list, myHost.getPluginsModel().getAllPlugins(), onInstallRunnable, cleanupRunnable);
      } catch (final IOException e1) {
        ourInstallingNodes.removeAll(list);
        PluginManagerMain.LOG.error(e1);
        //noinspection SSBasedInspection
        SwingUtilities.invokeLater(
            new Runnable() {
              @Override
              public void run() {
                IOExceptionDialog.showErrorDialog(
                    IdeBundle.message("action.download.and.install.plugin"),
                    IdeBundle.message("error.plugin.download.failed"));
              }
            });
      }
    }
  }
예제 #6
0
  @Override
  @SuppressWarnings("HardCodedStringLiteral")
  public void setupSdkPaths(@NotNull Sdk sdk) {
    String homePath = sdk.getHomePath();
    assert homePath != null : sdk;

    File jdkHome = new File(homePath);
    List<VirtualFile> classes = findClasses(jdkHome, false);
    VirtualFile sources = findSources(jdkHome);
    VirtualFile docs = findDocs(jdkHome, "docs/api");
    SdkModificator sdkModificator = sdk.getSdkModificator();

    Set<VirtualFile> previousRoots =
        new LinkedHashSet<>(Arrays.asList(sdkModificator.getRoots(OrderRootType.CLASSES)));
    sdkModificator.removeRoots(OrderRootType.CLASSES);
    previousRoots.removeAll(new HashSet<>(classes));
    for (VirtualFile aClass : classes) {
      sdkModificator.addRoot(aClass, OrderRootType.CLASSES);
    }
    for (VirtualFile root : previousRoots) {
      sdkModificator.addRoot(root, OrderRootType.CLASSES);
    }

    if (sources != null) {
      sdkModificator.addRoot(sources, OrderRootType.SOURCES);
    }
    VirtualFile javaFxSources = findSources(jdkHome, "javafx-src");
    if (javaFxSources != null) {
      sdkModificator.addRoot(javaFxSources, OrderRootType.SOURCES);
    }

    if (docs != null) {
      sdkModificator.addRoot(docs, JavadocOrderRootType.getInstance());
    } else if (SystemInfo.isMac) {
      VirtualFile commonDocs = findDocs(jdkHome, "docs");
      if (commonDocs == null) {
        commonDocs = findInJar(new File(jdkHome, "docs.jar"), "doc/api");
        if (commonDocs == null) {
          commonDocs = findInJar(new File(jdkHome, "docs.jar"), "docs/api");
        }
      }
      if (commonDocs != null) {
        sdkModificator.addRoot(commonDocs, JavadocOrderRootType.getInstance());
      }

      VirtualFile appleDocs = findDocs(jdkHome, "appledocs");
      if (appleDocs == null) {
        appleDocs = findInJar(new File(jdkHome, "appledocs.jar"), "appledoc/api");
      }
      if (appleDocs != null) {
        sdkModificator.addRoot(appleDocs, JavadocOrderRootType.getInstance());
      }

      if (commonDocs == null && appleDocs == null && sources == null) {
        String url = getDefaultDocumentationUrl(sdk);
        if (url != null) {
          sdkModificator.addRoot(
              VirtualFileManager.getInstance().findFileByUrl(url),
              JavadocOrderRootType.getInstance());
        }
      }
    } else if (getVersion(sdk) == JavaSdkVersion.JDK_1_7) {
      VirtualFile url =
          VirtualFileManager.getInstance().findFileByUrl("http://docs.oracle.com/javafx/2/api/");
      sdkModificator.addRoot(url, JavadocOrderRootType.getInstance());
    }

    attachJdkAnnotations(sdkModificator);

    sdkModificator.commitChanges();
  }
예제 #7
0
  /**
   * Goal-driven recursive (depth-first, exhaustive) search with backtracking
   *
   * @param problem
   * @param algorithm
   * @param subtaskRelsInPath
   * @param depth
   */
  private boolean subtaskPlanningImpl(
      PlanningContext context,
      Set<Rel> relsWithSubtasks,
      EvaluationAlgorithm algorithm,
      LinkedList<Rel> subtaskRelsInPath,
      int depth) {

    Set<Rel> relsWithSubtasksCopy = new LinkedHashSet<Rel>(relsWithSubtasks);

    Set<Rel> relsWithSubtasksToRemove = new LinkedHashSet<Rel>();

    boolean firstMLB = true;

    // start building Maximal Linear Branch (MLB)
    MLB:
    while (!relsWithSubtasksCopy.isEmpty()) {

      if (isSubtaskLoggingOn()) {
        String print = p(depth) + "Starting new MLB with: ";
        for (Rel rel : relsWithSubtasksCopy) {
          print +=
              "\n" + p(depth) + "  " + rel.getParent().getFullName() + " : " + rel.getDeclaration();
        }
        /*
        print += "\n" + p( depth ) + " All remaining rels in problem:";
        for ( Rel rel : problem.getAllRels() ) {
            print += "\n" + p( depth ) + " " + rel.getParentObjectName() + " : " + rel.getDeclaration();
        }
        print += "\n" + p( depth ) + "All found variables: ";
        for ( Var var : problem.getFoundVars() ) {
            print += "\n" + p( depth ) + " " + var.toString();
        }
        */
        logger.debug(print);
      }

      // if this is a first attempt to construct an MLB to solve a subtask(i.e. depth>0),
      // do not invoke linear planning because it has already been done
      if ((depth == 0) || !firstMLB) {

        boolean solvedIntermediately = linearForwardSearch(context, algorithm, true);

        // Having constructed some MLBs the (sub)problem may be solved
        // and there is no need in wasting precious time planning unnecessary branches
        if (solvedIntermediately
            && ( // on the top level optimize only if computing goals
            (depth == 0 && !computeAll)
                // otherwise (inside subtasks) always optimize
                || (depth != 0))) {
          // If the problem is solved, optimize and return
          if (!isOptDisabled) Optimizer.optimize(context, algorithm);
          return true;
        }
      } else {
        firstMLB = false;
      }

      // or children
      OR:
      for (Iterator<Rel> subtaskRelIterator = relsWithSubtasksCopy.iterator();
          subtaskRelIterator.hasNext(); ) {

        Rel subtaskRel = subtaskRelIterator.next();

        if (isSubtaskLoggingOn())
          logger.debug(
              p(depth)
                  + "OR: depth: "
                  + (depth + 1)
                  + " rel - "
                  + subtaskRel.getParent().getFullName()
                  + " : "
                  + subtaskRel.getDeclaration());

        if (subtaskRel.equals(subtaskRelsInPath.peekLast())
            || (!context.isRelReadyToUse(subtaskRel))
            || context.getFoundVars().containsAll(subtaskRel.getOutputs())
            || (!isSubtaskRepetitionAllowed && subtaskRelsInPath.contains(subtaskRel))) {

          if (isSubtaskLoggingOn()) {
            logger.debug(p(depth) + "skipped");
            if (!context.isRelReadyToUse(subtaskRel)) {
              logger.debug(p(depth) + "because it has unknown inputs"); // TODO print unknown
            } else if (context.getFoundVars().containsAll(subtaskRel.getOutputs())) {
              logger.debug(p(depth) + "because all outputs in FoundVars");
            } else if (subtaskRel.equals(subtaskRelsInPath.peekLast())) {
              logger.debug(p(depth) + "because it is nested in itself");
            } else if (!isSubtaskRepetitionAllowed && subtaskRelsInPath.contains(subtaskRel)) {
              logger.debug(
                  p(depth)
                      + "This rel with subtasks is already in use, path: "
                      + subtaskRelsInPath);
            }
          }
          continue OR;
        }

        LinkedList<Rel> newPath = new LinkedList<Rel>(subtaskRelsInPath);
        newPath.add(subtaskRel);

        PlanningResult result = new PlanningResult(subtaskRel, true);

        // this is true if all subtasks are solvable
        boolean allSolved = true;
        // and children
        AND:
        for (SubtaskRel subtask : subtaskRel.getSubtasks()) {
          if (isSubtaskLoggingOn()) logger.debug(p(depth) + "AND: subtask - " + subtask);

          EvaluationAlgorithm sbtAlgorithm = null;

          ////////////////////// INDEPENDENT SUBTASK////////////////////////////////////////
          if (subtask.isIndependent()) {
            if (isSubtaskLoggingOn()) logger.debug("Independent!!!");

            if (subtask.isSolvable() == null) {
              if (isSubtaskLoggingOn())
                logger.debug("Start solving independent subtask " + subtask.getDeclaration());
              // independent subtask is solved only once
              Problem problemContext = subtask.getContext();
              DepthFirstPlanner planner = new DepthFirstPlanner();
              planner.indSubtasks = indSubtasks;
              planner.nested = true;
              sbtAlgorithm = planner.invokePlaning(problemContext, isOptDisabled);
              PlanningContext indCntx = problemContext.getCurrentContext();
              boolean solved = indCntx.getFoundVars().containsAll(indCntx.getAllGoals());
              if (solved) {
                subtask.setSolvable(Boolean.TRUE);
                indSubtasks.put(subtask, sbtAlgorithm);
                if (isSubtaskLoggingOn()) logger.debug("Solved " + subtask.getDeclaration());
              } else {
                subtask.setSolvable(Boolean.FALSE);
                if (RuntimeProperties.isLogInfoEnabled()) {
                  logger.debug("Unable to solve " + subtask.getDeclaration());
                }
              }
              allSolved &= solved;
            } else if (subtask.isSolvable() == Boolean.TRUE) {
              if (isSubtaskLoggingOn()) logger.debug("Already solved");
              allSolved &= true;
              sbtAlgorithm = indSubtasks.get(subtask);
            } else {
              if (isSubtaskLoggingOn()) logger.debug("Not solvable");
              allSolved &= false;
            }
            if (isSubtaskLoggingOn()) logger.debug("End of independent subtask " + subtask);

            if (!allSolved) {
              continue OR;
            }

            assert sbtAlgorithm != null;

            result.addSubtaskAlgorithm(subtask, sbtAlgorithm);
          }
          ////////////////////// DEPENDENT SUBTASK//////////////////////////////////////
          else {
            // lets clone the environment
            PlanningContext newContext = prepareNewContext(context, subtask);

            sbtAlgorithm = new EvaluationAlgorithm();

            // during linear planning, if some goals are found, they are removed from the set
            // "goals"
            boolean solved =
                linearForwardSearch(
                    newContext,
                    sbtAlgorithm,
                    // do not optimize here, because the solution may require additional rels with
                    // subtasks
                    true);

            if (solved) {
              if (isSubtaskLoggingOn()) logger.debug(p(depth) + "SOLVED subtask: " + subtask);

              if (!isOptDisabled) {
                // if a subtask has been solved, optimize its algorithm
                Optimizer.optimize(newContext, sbtAlgorithm);
              }

              result.addSubtaskAlgorithm(subtask, sbtAlgorithm);
              allSolved &= solved;
              continue AND;
            } else if (!solved && (depth == maxDepth)) {
              if (isSubtaskLoggingOn())
                logger.debug(p(depth) + "NOT SOLVED and cannot go any deeper, subtask: " + subtask);
              continue OR;
            }

            if (isSubtaskLoggingOn()) logger.debug(p(depth) + "Recursing deeper");

            solved =
                subtaskPlanningImpl(newContext, relsWithSubtasks, sbtAlgorithm, newPath, depth + 1);

            if (isSubtaskLoggingOn()) logger.debug(p(depth) + "Back to depth " + (depth + 1));

            // the linear planning has been performed at the end of MLB on the depth+1,
            // if the problem was solved, there is no need to run linear planning again
            if ((solved || (solved = linearForwardSearch(newContext, sbtAlgorithm, true)))
                && !isOptDisabled) {
              // if solved, optimize here with full list of goals in order to get rid of
              // unnecessary subtask instances and other relations
              Optimizer.optimize(newContext, sbtAlgorithm);
            }

            if (isSubtaskLoggingOn())
              logger.debug(p(depth) + (solved ? "" : "NOT") + " SOLVED subtask: " + subtask);

            allSolved &= solved;

            // if at least one subtask is not solvable, try another
            // branch
            if (!allSolved) {
              continue OR;
            }

            result.addSubtaskAlgorithm(subtask, sbtAlgorithm);
          }
        } // AND

        if (allSolved) {
          algorithm.add(result);

          Set<Var> newVars = new LinkedHashSet<Var>();

          unfoldVarsToSet(subtaskRel.getOutputs(), newVars);

          context.getKnownVars().addAll(newVars);
          context.getFoundVars().addAll(newVars);

          subtaskRelIterator.remove();

          if (isSubtaskLoggingOn()) {
            logger.debug(
                p(depth)
                    + "SOLVED ALL SUBTASKS for "
                    + subtaskRel.getParent().getFullName()
                    + " : "
                    + subtaskRel.getDeclaration());
            logger.debug(p(depth) + "Updating the problem graph and continuing building new MLB");
          }

          // this is used for incremental dfs
          if (depth == 0) {
            relsWithSubtasksToRemove.add(subtaskRel);
          }

          continue MLB;
        }
        if (isSubtaskLoggingOn())
          logger.debug(
              p(depth)
                  + "NOT SOLVED ALL subtasks, removing from path "
                  + subtaskRel.getParent().getFullName()
                  + " : "
                  + subtaskRel.getDeclaration());
        newPath.remove(subtaskRel);
      } // end OR

      // exit loop because there are no more rels with subtasks to be
      // applied
      // (i.e. no more rels can introduce new variables into the
      // algorithm)
      if (isSubtaskLoggingOn()) logger.debug(p(depth) + "No more MLB can be constructed");
      break MLB;
    }

    // incremental dfs, remove solved subtasks
    if (depth == 0) {
      relsWithSubtasks.removeAll(relsWithSubtasksToRemove);
    }

    return false;
  }
  public boolean execute() {
    if (CDState.getCycle() % period != 0) return false;

    MycoCast mycocast = (MycoCast) Network.get(0).getProtocol(mycocastPid);

    int bio = mycocast.countBiomass();
    int ext = mycocast.countExtending();
    int bra = mycocast.countBranching();
    int imm = mycocast.countImmobile();

    // Update vertices
    Set<MycoNode> activeNodes = new HashSet<MycoNode>();
    for (int i = 0; i < Network.size(); i++) {
      MycoNode n = (MycoNode) Network.get(i);
      activeNodes.add(n);
      HyphaData data = n.getHyphaData();
      // if (data.isBiomass()) { continue; }
      if (graph.containsVertex(n)) {
        graph.removeVertex(n);
      }
      if (!graph.containsVertex(n)) {
        graph.addVertex(n);
      }
    }
    Set<MycoNode> jungNodes = new HashSet<MycoNode>(graph.getVertices());
    jungNodes.removeAll(activeNodes);

    for (MycoNode n : jungNodes) {
      graph.removeVertex(n);
    }

    // Update edges
    for (int i = 0; i < Network.size(); i++) {
      MycoNode n = (MycoNode) Network.get(i);
      HyphaData data = n.getHyphaData();
      HyphaLink link = n.getHyphaLink();

      synchronized (graph) {

        // We now add in all links and tune out display in Visualizer
        java.util.List<MycoNode> neighbors = (java.util.List<MycoNode>) link.getNeighbors();

        //// Adding only links to hypha thins out links to biomass
        //    (java.util.List<MycoNode>) link.getHyphae();

        Collection<MycoNode> jungNeighbors = graph.getNeighbors(n);

        // Remove edges from Jung graph that are not in peersim graph
        for (MycoNode o : jungNeighbors) {
          if (!neighbors.contains(o)) {
            MycoEdge edge = graph.findEdge(n, o);
            while (edge != null) {
              graph.removeEdge(edge);
              edge = graph.findEdge(n, o);
            }
          }
        }

        // Add missing edges to Jung graph that are in peersim graph
        for (MycoNode o : neighbors) {
          if (graph.findEdge(n, o) == null) {
            MycoEdge edge = new MycoEdge();
            graph.addEdge(edge, n, o, EdgeType.DIRECTED);
          }
        }
      }

      // log.finest("VERTICES: " + graph.getVertices());
      // log.finest("EDGES: " + graph.getEdges());
    }

    for (ChangeListener cl : changeListeners) {
      cl.stateChanged(new ChangeEvent(graph));
    }
    if (walking) {
      try {
        Thread.sleep(walkDelay);
      } catch (InterruptedException e) {
      }
      stepBlocked = false;
    }

    try {
      while (stepBlocked && !noBlock) {
        synchronized (JungGraphObserver.class) {
          JungGraphObserver.class.wait();
        }
      }
    } catch (InterruptedException e) {
      stepBlocked = true;
    }
    stepBlocked = true;
    // System.out.println(graph.toString());
    return false;
  }