Beispiel #1
0
  @Override
  @NotNull
  public SuggestedNameInfo suggestUniqueVariableName(
      @NotNull final SuggestedNameInfo baseNameInfo,
      PsiElement place,
      boolean ignorePlaceName,
      boolean lookForward) {
    final String[] names = baseNameInfo.names;
    final LinkedHashSet<String> uniqueNames = new LinkedHashSet<String>(names.length);
    for (String name : names) {
      if (ignorePlaceName && place instanceof PsiNamedElement) {
        final String placeName = ((PsiNamedElement) place).getName();
        if (Comparing.strEqual(placeName, name)) {
          uniqueNames.add(name);
          continue;
        }
      }
      uniqueNames.add(suggestUniqueVariableName(name, place, lookForward));
    }

    return new SuggestedNameInfo(ArrayUtil.toStringArray(uniqueNames)) {
      @Override
      public void nameChosen(String name) {
        baseNameInfo.nameChosen(name);
      }
    };
  }
  /**
   * Test importing of Clinical Data File.
   *
   * @throws DaoException Database Access Error.
   * @throws IOException IO Error.
   */
  @Test
  @Ignore("To be fixed")
  public void testImportClinicalDataSurvival() throws Exception {

    // TBD: change this to use getResourceAsStream()
    File clinicalFile = new File("target/test-classes/clinical_data.txt");
    ImportClinicalData importClinicalData = new ImportClinicalData(study, clinicalFile);
    importClinicalData.importData();

    LinkedHashSet<String> caseSet = new LinkedHashSet<String>();
    caseSet.add("TCGA-A1-A0SB");
    caseSet.add("TCGA-A1-A0SI");
    caseSet.add("TCGA-A1-A0SE");

    List<Patient> clinicalCaseList =
        DaoClinicalData.getSurvivalData(study.getInternalId(), caseSet);
    assertEquals(3, clinicalCaseList.size());

    Patient clinical0 = clinicalCaseList.get(0);
    assertEquals(new Double(79.04), clinical0.getAgeAtDiagnosis());
    assertEquals("DECEASED", clinical0.getOverallSurvivalStatus());
    assertEquals("Recurred/Progressed", clinical0.getDiseaseFreeSurvivalStatus());
    assertEquals(new Double(43.8), clinical0.getOverallSurvivalMonths());
    assertEquals(new Double(15.05), clinical0.getDiseaseFreeSurvivalMonths());

    Patient clinical1 = clinicalCaseList.get(1);
    assertEquals(new Double(55.53), clinical1.getAgeAtDiagnosis());
    assertEquals("LIVING", clinical1.getOverallSurvivalStatus());
    assertEquals("DiseaseFree", clinical1.getDiseaseFreeSurvivalStatus());
    assertEquals(new Double(49.02), clinical1.getOverallSurvivalMonths());
    assertEquals(new Double(49.02), clinical1.getDiseaseFreeSurvivalMonths());

    Patient clinical2 = clinicalCaseList.get(2);
    assertEquals(null, clinical2.getDiseaseFreeSurvivalMonths());
  }
Beispiel #3
0
  /**
   * Insert the method's description here. Creation date: (21.12.2000 22:24:23)
   *
   * @return boolean
   * @param object com.cosylab.vdct.graphics.objects.VisibleObject
   * @param zoomOnHilited sets the option whether the hilited object should be zoomed in
   */
  public boolean setAsHilited(VisibleObject object, boolean zoomOnHilited) {
    this.zoomOnHilited = zoomOnHilited;

    if (zoomOnHilited) {
      DrawingSurface.getInstance().repaint();
      hilitedObjects.clear();
      if (hilitedObject != null) {
        hilitedObjects.add(hilitedObject);
      }
    }

    if (object == null) {
      hilitedObjects.clear();
      hilitedObject = null;
      return false;
    }

    if (object != hilitedObject || hilitedObjects.size() == 1) {

      hilitedObject = object;

      // initialization
      hilitedObjects.clear();
      hilitedObjects.add(hilitedObject);
      Object obj = hilitedObject;

      // inlinks
      Vector outlinks = null;
      if (obj instanceof MultiInLink) {
        outlinks = ((MultiInLink) obj).getOutlinks();
      } else if (obj instanceof InLink) {
        outlinks = new Vector();
        outlinks.add(((InLink) obj).getOutput());
      }

      if (!zoomOnHilited) {
        if (outlinks != null)
          for (int i = 0; i < outlinks.size(); i++) {
            obj = outlinks.elementAt(i);
            hilitedObjects.add(obj);
            while (obj instanceof InLink) {
              obj = ((InLink) obj).getOutput();
              hilitedObjects.add(obj);
            }
          }

        // outLinks
        obj = hilitedObject;
        while (obj instanceof OutLink) {
          obj = ((OutLink) obj).getInput();
          hilitedObjects.add(obj);
        }
      }
      return true;
    } else return false;
  }
    public LinkedHashSet<Path> scan(FileSystem fs, Path filePath, Set<String> consumedFiles) {
      LinkedHashSet<Path> pathSet = Sets.newLinkedHashSet();
      try {
        LOG.debug("Scanning {} with pattern {}", filePath, this.filePatternRegexp);
        FileStatus[] files = fs.listStatus(filePath);
        for (FileStatus status : files) {
          Path path = status.getPath();
          String filePathStr = path.toString();

          if (consumedFiles.contains(filePathStr)) {
            continue;
          }

          if (ignoredFiles.contains(filePathStr)) {
            continue;
          }

          if (acceptFile(filePathStr)) {
            LOG.debug("Found {}", filePathStr);
            pathSet.add(path);
          } else {
            // don't look at it again
            ignoredFiles.add(filePathStr);
          }
        }
      } catch (FileNotFoundException e) {
        LOG.warn("Failed to list directory {}", filePath, e);
      } catch (IOException e) {
        throw new RuntimeException(e);
      }
      return pathSet;
    }
  @Override
  public void loadState(Element state) {
    final List<Element> abbreviations = state.getChildren("abbreviations");
    if (abbreviations != null && abbreviations.size() == 1) {
      final List<Element> actions = abbreviations.get(0).getChildren("action");
      if (actions != null && actions.size() > 0) {
        for (Element action : actions) {
          final String actionId = action.getAttributeValue("id");
          LinkedHashSet<String> values = myActionId2Abbreviations.get(actionId);
          if (values == null) {
            values = new LinkedHashSet<String>(1);
            myActionId2Abbreviations.put(actionId, values);
          }

          final List<Element> abbreviation = action.getChildren("abbreviation");
          if (abbreviation != null) {
            for (Element abbr : abbreviation) {
              final String abbrValue = abbr.getAttributeValue("name");
              if (abbrValue != null) {
                values.add(abbrValue);
              }
            }
          }
        }
      }
    }
  }
 public String[] getGroupNames() {
   LinkedHashSet<String> groups = new LinkedHashSet<String>();
   for (ApiDoc apiDoc : docs) {
     groups.add(apiDoc.group);
   }
   return groups.toArray(new String[groups.size()]);
 }
Beispiel #7
0
  public static LinkedHashSet<String> findJars(LogicalPlan dag, Class<?>[] defaultClasses) {
    List<Class<?>> jarClasses = new ArrayList<Class<?>>();

    for (String className : dag.getClassNames()) {
      try {
        Class<?> clazz = Thread.currentThread().getContextClassLoader().loadClass(className);
        jarClasses.add(clazz);
      } catch (ClassNotFoundException e) {
        throw new IllegalArgumentException("Failed to load class " + className, e);
      }
    }

    for (Class<?> clazz : Lists.newArrayList(jarClasses)) {
      // process class and super classes (super does not require deploy annotation)
      for (Class<?> c = clazz; c != Object.class && c != null; c = c.getSuperclass()) {
        // LOG.debug("checking " + c);
        jarClasses.add(c);
        jarClasses.addAll(Arrays.asList(c.getInterfaces()));
      }
    }

    jarClasses.addAll(Arrays.asList(defaultClasses));

    if (dag.isDebug()) {
      LOG.debug("Deploy dependencies: {}", jarClasses);
    }

    LinkedHashSet<String> localJarFiles = new LinkedHashSet<String>(); // avoid duplicates
    HashMap<String, String> sourceToJar = new HashMap<String, String>();

    for (Class<?> jarClass : jarClasses) {
      if (jarClass.getProtectionDomain().getCodeSource() == null) {
        // system class
        continue;
      }
      String sourceLocation =
          jarClass.getProtectionDomain().getCodeSource().getLocation().toString();
      String jar = sourceToJar.get(sourceLocation);
      if (jar == null) {
        // don't create jar file from folders multiple times
        jar = JarFinder.getJar(jarClass);
        sourceToJar.put(sourceLocation, jar);
        LOG.debug("added sourceLocation {} as {}", sourceLocation, jar);
      }
      if (jar == null) {
        throw new AssertionError("Cannot resolve jar file for " + jarClass);
      }
      localJarFiles.add(jar);
    }

    String libJarsPath = dag.getValue(LogicalPlan.LIBRARY_JARS);
    if (!StringUtils.isEmpty(libJarsPath)) {
      String[] libJars = StringUtils.splitByWholeSeparator(libJarsPath, LIB_JARS_SEP);
      localJarFiles.addAll(Arrays.asList(libJars));
    }

    LOG.info("Local jar file dependencies: " + localJarFiles);

    return localJarFiles;
  }
  public static LinkedHashSet<String> sortMatching(
      final PrefixMatcher matcher, Collection<String> _names) {
    ProgressManager.checkCanceled();

    List<String> sorted = new ArrayList<String>();
    for (String name : _names) {
      if (matcher.prefixMatches(name)) {
        sorted.add(name);
      }
    }

    ProgressManager.checkCanceled();
    Collections.sort(sorted, String.CASE_INSENSITIVE_ORDER);
    ProgressManager.checkCanceled();

    LinkedHashSet<String> result = new LinkedHashSet<String>();
    for (String name : sorted) {
      if (matcher.isStartMatch(name)) {
        result.add(name);
      }
    }

    ProgressManager.checkCanceled();

    result.addAll(sorted);
    return result;
  }
Beispiel #9
0
 public static void main(String[] args) throws Exception {
   ObjectOutputStream output = new ObjectOutputStream(new FileOutputStream("c:\\test.dat"));
   LinkedHashSet<String> set1 = new LinkedHashSet<String>();
   set1.add("New York");
   LinkedHashSet<String> set2 = (LinkedHashSet<String>) set1.clone();
   set1.add("Atlanta");
   output.writeObject(set1);
   output.writeObject(set2);
   output.close();
   ObjectInputStream input = new ObjectInputStream(new FileInputStream("c:\\test.dat"));
   set1 = (LinkedHashSet) input.readObject();
   set2 = (LinkedHashSet) input.readObject();
   System.out.println(set1);
   System.out.println(set2);
   output.close();
 }
 public static Set<PsiType> getDefaultExpectedTypes(@NotNull GrExpression element) {
   final LinkedHashSet<PsiType> result = new LinkedHashSet<PsiType>();
   for (TypeConstraint constraint : calculateTypeConstraints(element)) {
     result.add(constraint.getDefaultType());
   }
   return result;
 }
 public void bePatternConfiguration(List<PsiClass> classes, PsiMethod method) {
   data.TEST_OBJECT = TestType.PATTERN.getType();
   final String suffix;
   if (method != null) {
     data.METHOD_NAME = method.getName();
     suffix = "," + data.METHOD_NAME;
   } else {
     suffix = "";
   }
   LinkedHashSet<String> patterns = new LinkedHashSet<String>();
   for (PsiClass pattern : classes) {
     patterns.add(JavaExecutionUtil.getRuntimeQualifiedName(pattern) + suffix);
   }
   data.setPatterns(patterns);
   final Module module =
       RunConfigurationProducer.getInstance(TestNGPatternConfigurationProducer.class)
           .findModule(this, getConfigurationModule().getModule(), patterns);
   if (module == null) {
     data.setScope(TestSearchScope.WHOLE_PROJECT);
     setModule(null);
   } else {
     setModule(module);
   }
   setGeneratedName();
 }
  /**
   * Begins the in-place refactoring operation.
   *
   * @return true if the in-place refactoring was successfully started, false if it failed to start
   *     and a dialog should be shown instead.
   */
  public boolean startInplaceIntroduceTemplate() {
    final boolean replaceAllOccurrences = isReplaceAllOccurrences();
    final Ref<Boolean> result = new Ref<>();
    CommandProcessor.getInstance()
        .executeCommand(
            myProject,
            () -> {
              final String[] names = suggestNames(replaceAllOccurrences, getLocalVariable());
              final V variable = createFieldToStartTemplateOn(replaceAllOccurrences, names);
              boolean started = false;
              if (variable != null) {
                int caretOffset = getCaretOffset();
                myEditor.getCaretModel().moveToOffset(caretOffset);
                myEditor.getScrollingModel().scrollToCaret(ScrollType.MAKE_VISIBLE);

                final LinkedHashSet<String> nameSuggestions = new LinkedHashSet<>();
                nameSuggestions.add(variable.getName());
                nameSuggestions.addAll(Arrays.asList(names));
                initOccurrencesMarkers();
                setElementToRename(variable);
                updateTitle(getVariable());
                started = super.performInplaceRefactoring(nameSuggestions);
                if (started) {
                  onRenameTemplateStarted();
                  myDocumentAdapter =
                      new DocumentAdapter() {
                        @Override
                        public void documentChanged(DocumentEvent e) {
                          if (myPreview == null) return;
                          final TemplateState templateState =
                              TemplateManagerImpl.getTemplateState(myEditor);
                          if (templateState != null) {
                            final TextResult value =
                                templateState.getVariableValue(
                                    InplaceRefactoring.PRIMARY_VARIABLE_NAME);
                            if (value != null) {
                              updateTitle(getVariable(), value.getText());
                            }
                          }
                        }
                      };
                  myEditor.getDocument().addDocumentListener(myDocumentAdapter);
                  updateTitle(getVariable());
                  if (TemplateManagerImpl.getTemplateState(myEditor) != null) {
                    myEditor.putUserData(ACTIVE_INTRODUCE, this);
                  }
                }
              }
              result.set(started);
              if (!started) {
                finish(true);
              }
            },
            getCommandName(),
            getCommandName());
    return result.get();
  }
 private static void traverseDescriptors(
     InspectionTreeNode node, LinkedHashSet<CommonProblemDescriptor> descriptors) {
   if (node instanceof ProblemDescriptionNode) {
     descriptors.add(((ProblemDescriptionNode) node).getDescriptor());
   }
   for (int i = node.getChildCount() - 1; i >= 0; i--) {
     traverseDescriptors((InspectionTreeNode) node.getChildAt(i), descriptors);
   }
 }
 public void register(
     String abbreviation, String actionId, Map<String, LinkedHashSet<String>> storage) {
   LinkedHashSet<String> abbreviations = storage.get(actionId);
   if (abbreviations == null) {
     abbreviations = new LinkedHashSet<String>(1);
     storage.put(actionId, abbreviations);
   }
   abbreviations.add(abbreviation);
 }
 private static void addCurrentlySelectedItemToTop(
     Lookup lookup, List<LookupElement> items, LinkedHashSet<LookupElement> model) {
   if (!lookup.isSelectionTouched()) {
     LookupElement lastSelection = lookup.getCurrentItem();
     if (ContainerUtil.indexOfIdentity(items, lastSelection) >= 0) {
       model.add(lastSelection);
     }
   }
 }
Beispiel #16
0
 private void registerStaticColumns() {
   for (Tuple<String, DataType> column : staticColumns) {
     ReferenceInfo info =
         new ReferenceInfo(
             new ReferenceIdent(ident(), column.v1(), null), RowGranularity.DOC, column.v2());
     if (info.ident().isColumn()) {
       columns.add(info);
     }
     INFOS.put(info.ident().columnIdent(), info);
   }
 }
Beispiel #17
0
  LinkedHashSet<EqClass> getNonTrivialEqClasses() {
    if (myCachedNonTrivialEqClasses != null) return myCachedNonTrivialEqClasses;

    LinkedHashSet<EqClass> result = ContainerUtil.newLinkedHashSet();
    for (EqClass eqClass : myEqClasses) {
      if (eqClass != null && eqClass.size() > 1) {
        result.add(eqClass);
      }
    }
    return myCachedNonTrivialEqClasses = result;
  }
 private static void addSomeItems(
     LinkedHashSet<LookupElement> model,
     Iterator<LookupElement> iterator,
     Condition<LookupElement> stopWhen) {
   while (iterator.hasNext()) {
     LookupElement item = iterator.next();
     model.add(item);
     if (stopWhen.value(item)) {
       break;
     }
   }
 }
 public final void a(ajy paramajy, boolean paramBoolean)
 {
   if (paramBoolean) {
     K.add(paramajy);
   }
   for (;;)
   {
     A();
     return;
     K.remove(paramajy);
   }
 }
 private String constructAmendedMessage() {
   Set<VirtualFile> selectedRoots = getVcsRoots(getSelectedFilePaths()); // get only selected files
   LinkedHashSet<String> messages = ContainerUtil.newLinkedHashSet();
   if (myMessagesForRoots != null) {
     for (VirtualFile root : selectedRoots) {
       String message = myMessagesForRoots.get(root);
       if (message != null) {
         messages.add(message);
       }
     }
   }
   return DvcsUtil.joinMessagesOrNull(messages);
 }
  private static void findSourceFiles(LinkedHashSet<String> files, String file) {
    File f = new File(file);
    if (f.isFile()) {
      String ext = FilenameUtils.getExtension(f.getName());
      if ("java".equalsIgnoreCase(ext)) files.add(file);
    } else if (f.isDirectory()) {
      for (String sub : f.list()) {
        if (sub.equals(".") || sub.equals("..")) continue;

        findSourceFiles(files, FilenameUtils.concat(f.getAbsolutePath(), sub));
      }
    }
  }
 private static LinkedHashSet getProvidersNotUsingCache(
     String serviceName,
     String algName,
     String attrName,
     String filterValue,
     Provider[] allProviders) {
   LinkedHashSet candidates = new LinkedHashSet(5);
   for (int i = 0; i < allProviders.length; i++) {
     if (isCriterionSatisfied(allProviders[i], serviceName, algName, attrName, filterValue)) {
       candidates.add(allProviders[i]);
     }
   }
   return candidates;
 }
  public static LinkedHashSet<String> getLangs(HttpExchange t) {
    String hdr = t.getRequestHeaders().getFirst("Accept-language");
    LinkedHashSet<String> result = new LinkedHashSet<>();
    if (StringUtils.isEmpty(hdr)) {
      return result;
    }

    String[] tmp = hdr.split(",");
    for (String language : tmp) {
      String[] l1 = language.split(";");
      result.add(l1[0]);
    }
    return result;
  }
Beispiel #24
0
    public synchronized void addTaskAttempt(int volumeId, TaskAttempt attemptId) {
      synchronized (unassignedTaskForEachVolume) {
        LinkedHashSet<TaskAttempt> list = unassignedTaskForEachVolume.get(volumeId);
        if (list == null) {
          list = new LinkedHashSet<>();
          unassignedTaskForEachVolume.put(volumeId, list);
        }
        list.add(attemptId);
      }

      remainTasksNum.incrementAndGet();

      if (!diskVolumeLoads.containsKey(volumeId)) diskVolumeLoads.put(volumeId, 0);
    }
Beispiel #25
0
 // recursively initialize nodeDests from start node
 private void initNodeDests(SeqPhase phase, SeqNode n) throws Xcept {
   if (nodeDests.get(n) != null) return;
   if (stopAtFFTs && n.fft() != null) return;
   LinkedHashSet<SeqNode> dests = new LinkedHashSet<SeqNode>();
   nodeDests.put(n, dests);
   Iterator<SeqEdge> es = graph.getEdgesFrom(n);
   while (es.hasNext()) {
     SeqEdge e = es.next();
     SeqNode n1 = e.dest();
     dests.add(n1);
     if (phase != graph.getPhase(n1)) continue;
     if (stopAtFFTs && n1.fft() != null) continue;
     initNodeDests(phase, n1);
   }
 }
 @Nullable
 public String getDefaultMessageFor(FilePath[] filesToCheckin) {
   LinkedHashSet<String> messages = ContainerUtil.newLinkedHashSet();
   for (VirtualFile root : GitUtil.gitRoots(Arrays.asList(filesToCheckin))) {
     VirtualFile mergeMsg = root.findFileByRelativePath(GitRepositoryFiles.GIT_MERGE_MSG);
     VirtualFile squashMsg = root.findFileByRelativePath(GitRepositoryFiles.GIT_SQUASH_MSG);
     try {
       if (mergeMsg == null && squashMsg == null) {
         continue;
       }
       String encoding = GitConfigUtil.getCommitEncoding(myProject, root);
       if (mergeMsg != null) {
         messages.add(loadMessage(mergeMsg, encoding));
       } else {
         messages.add(loadMessage(squashMsg, encoding));
       }
     } catch (IOException e) {
       if (log.isDebugEnabled()) {
         log.debug("Unable to load merge message", e);
       }
     }
   }
   return DvcsUtil.joinMessagesOrNull(messages);
 }
  /** {@inheritDoc} */
  @Override
  public ConfigChangeResult applyConfigurationChange(BackupBackendCfg cfg) {
    ResultCode resultCode = ResultCode.SUCCESS;
    boolean adminActionRequired = false;
    ArrayList<Message> messages = new ArrayList<Message>();

    Set<String> values = cfg.getBackupDirectory();
    backupDirectories = new LinkedHashSet<File>(values.size());
    for (String s : values) {
      backupDirectories.add(getFileForPath(s));
    }

    currentConfig = cfg;
    return new ConfigChangeResult(resultCode, adminActionRequired, messages);
  }
  public void moveFieldInitializations() throws IncorrectOperationException {
    LOG.assertTrue(myMembersAfterMove != null);

    final LinkedHashSet<PsiField> movedFields = new LinkedHashSet<>();
    for (PsiMember member : myMembersAfterMove) {
      if (member instanceof PsiField) {
        movedFields.add((PsiField) member);
      }
    }

    if (movedFields.isEmpty()) return;

    PullUpHelper<MemberInfo> processor = getProcessor(myTargetSuperClass);
    LOG.assertTrue(processor != null, myTargetSuperClass);
    processor.moveFieldInitializations(movedFields);
  }
  public static BridgeInvocation_c[] getManyACT_BRGsOnR628(
      ActualParameter_c[] targets, ClassQueryInterface_c test, boolean loadComponent) {
    if (targets == null || targets.length == 0 || targets[0] == null)
      return new BridgeInvocation_c[0];

    LinkedHashSet<BridgeInvocation_c> elementsSet = new LinkedHashSet<BridgeInvocation_c>();
    for (int i = 0; i < targets.length; i++) {
      BridgeInvocation_c associate = targets[i].BridgeInvocation;
      if (targets[i] != null && associate != null && (test == null || test.evaluate(associate))) {
        if (elementsSet.add(associate)) {}
      }
    }

    BridgeInvocation_c[] result = new BridgeInvocation_c[elementsSet.size()];
    elementsSet.toArray(result);
    return result;
  }
  public static ComponentResultSet_c[] getManyPE_CRSsOnR8008(
      ComponentVisibility_c[] targets, ClassQueryInterface_c test, boolean loadComponent) {
    if (targets == null || targets.length == 0 || targets[0] == null)
      return new ComponentResultSet_c[0];

    LinkedHashSet<ComponentResultSet_c> elementsSet = new LinkedHashSet<ComponentResultSet_c>();
    for (int i = 0; i < targets.length; i++) {
      ComponentResultSet_c associate = targets[i].MakesUpAComponentResultSet;
      if (targets[i] != null && associate != null && (test == null || test.evaluate(associate))) {
        if (elementsSet.add(associate)) {}
      }
    }

    ComponentResultSet_c[] result = new ComponentResultSet_c[elementsSet.size()];
    elementsSet.toArray(result);
    return result;
  }