protected void stitchNeighbors(Set<Sector> neighbors, GeoPoint center) {
assert gatedAssertion(
neighbors.size() == 6
|| neighbors.size() == 5 && countDistinctGlobalSectors(neighbors) == 5);
if (!sector.equals(neighbors.iterator().next())) {
return;
}
Map<GeoPoint, GeoPoint> nextPoints = new HashMap<GeoPoint, GeoPoint>();
Sector second = null;
for (Sector s : neighbors) {
char vertex = s.getVertex(center);
Sector.Triangle cornerTriangle = s.getCornerTriangle(vertex);
GeoPoint[] geoPoints = cornerTriangle.getPoints(vertex);
nextPoints.put(geoPoints[1], geoPoints[2]);
if (second == null && countShared(s.points, sector.points) == 1) {
second = s;
}
}
assert gatedAssertion(second != null);
if (second != null) {
GeoPoint[] acre = new GeoPoint[nextPoints.size()];
GeoPoint point = nextPoints.values().iterator().next();
for (int idx = 0; idx < nextPoints.size(); idx++) {
assert !Arrays.asList(acre).contains(point);
acre[idx] = point;
point = nextPoints.get(point);
assert gatedAssertion(point != null);
if (point == null) {
return;
}
}
Sector[] others = new Sector[neighbors.size() - 2];
int idx = 0;
for (Sector s : neighbors) {
if (s != sector && s != second) {
others[idx++] = s;
}
}
Acre newAcre = new Acre(1, sector, second, Arrays.asList(others), center, acre);
CartographicElementView cartographicElementView = getFor(subdivisions);
for (Sector s : neighbors) {
char vertex = s.getVertex(center);
assert vertex == 'A' || vertex == 'B' || vertex == 'C';
Edge e = Edge.values()[vertex - 'A'];
List<Acre> vertexAcre =
cartographicElementView.get(
s.getSharedAcres(), CartographicElementView.Position.Vertex, e, false);
assert vertexAcre.size() == 1;
assert vertexAcre.get(0) == null;
vertexAcre.set(0, newAcre);
}
consume(newAcre);
}
}
private Color getThreadBlockColor(BumpThread bt) {
if (bt == null) return Color.BLACK;
synchronized (thread_colors) {
Color c = thread_colors.get(bt);
if (c == null) {
double v;
int ct = thread_colors.size();
if (ct == 0) v = 0;
else if (ct == 1) v = 1;
else {
v = 0.5;
int p0 = ct - 1;
int p1 = 1;
for (int p = p0; p > 1; p /= 2) {
v /= 2.0;
p0 -= p1;
p1 *= 2;
}
if ((p0 & 1) == 0) p0 = 2 * p1 - p0 + 1;
v = v * p0;
}
float h = (float) (v * 0.8);
float s = 0.7f;
float b = 1.0f;
int rgb = Color.HSBtoRGB(h, s, b);
rgb |= 0xc0000000;
c = new Color(rgb, true);
thread_colors.put(bt, c);
}
return c;
}
}
public List<String> find() throws IOException {
// Set<String> g1 = new HashSet<String>(Arrays.asList("HRAS", "NRAS", "KRAS"));
// Set<String> g2 = new HashSet<String>(Arrays.asList("BRAF"));
Set<String> g1 = new HashSet<String>(Arrays.asList("HRAS"));
Set<String> g2 = new HashSet<String>(Arrays.asList("NRAS", "KRAS"));
Map<String, Double> pvals = calcDifferencePvals(g1, g2);
System.out.println("pvals.size() = " + pvals.size());
List<String> list = FDR.select(pvals, null, fdrThr);
System.out.println("result size = " + list.size());
Map<String, Boolean> dirs = getChangeDirections(list, g1, g2);
int up = 0;
int dw = 0;
for (String gene : dirs.keySet()) {
Boolean d = dirs.get(gene);
if (d) up++;
else dw++;
}
System.out.println("up = " + up);
System.out.println("dw = " + dw);
return list;
}
private synchronized void startAnimation(
JComponent component, Part part, State startState, State endState, long millis) {
boolean isForwardAndReverse = false;
if (endState == State.DEFAULTED) {
isForwardAndReverse = true;
}
Map<Part, AnimationState> map = animationStateMap.get(component);
if (millis <= 0) {
if (map != null) {
map.remove(part);
if (map.size() == 0) {
animationStateMap.remove(component);
}
}
return;
}
if (map == null) {
map = new EnumMap<Part, AnimationState>(Part.class);
animationStateMap.put(component, map);
}
map.put(part, new AnimationState(startState, millis, isForwardAndReverse));
if (!timer.isRunning()) {
timer.start();
}
}
public UpdateOrStatusOptionsDialog(Project project, Map<Configurable, AbstractVcs> confs) {
super(project);
setTitle(getRealTitle());
myProject = project;
if (confs.size() == 1) {
myMainPanel = new JPanel(new BorderLayout());
final Configurable configurable = confs.keySet().iterator().next();
addComponent(confs.get(configurable), configurable, BorderLayout.CENTER);
myMainPanel.add(Box.createVerticalStrut(10), BorderLayout.SOUTH);
} else {
myMainPanel = new JBTabbedPane();
final ArrayList<AbstractVcs> vcses = new ArrayList<>(confs.values());
Collections.sort(
vcses,
new Comparator<AbstractVcs>() {
public int compare(final AbstractVcs o1, final AbstractVcs o2) {
return o1.getDisplayName().compareTo(o2.getDisplayName());
}
});
Map<AbstractVcs, Configurable> vcsToConfigurable = revertMap(confs);
for (AbstractVcs vcs : vcses) {
addComponent(vcs, vcsToConfigurable.get(vcs), vcs.getDisplayName());
}
}
init();
}
public synchronized void actionPerformed(ActionEvent e) {
java.util.List<JComponent> componentsToRemove = null;
java.util.List<Part> partsToRemove = null;
for (JComponent component : animationStateMap.keySet()) {
component.repaint();
if (partsToRemove != null) {
partsToRemove.clear();
}
Map<Part, AnimationState> map = animationStateMap.get(component);
if (!component.isShowing() || map == null || map.size() == 0) {
if (componentsToRemove == null) {
componentsToRemove = new ArrayList<JComponent>();
}
componentsToRemove.add(component);
continue;
}
for (Part part : map.keySet()) {
if (map.get(part).isDone()) {
if (partsToRemove == null) {
partsToRemove = new ArrayList<Part>();
}
partsToRemove.add(part);
}
}
if (partsToRemove != null) {
if (partsToRemove.size() == map.size()) {
// animation is done for the component
if (componentsToRemove == null) {
componentsToRemove = new ArrayList<JComponent>();
}
componentsToRemove.add(component);
} else {
for (Part part : partsToRemove) {
map.remove(part);
}
}
}
}
if (componentsToRemove != null) {
for (JComponent component : componentsToRemove) {
animationStateMap.remove(component);
}
}
if (animationStateMap.size() == 0) {
timer.stop();
}
}
/**
* \ Draw saved State (color dots on panel) on WhiteBoard
*
* @param outstream
* @throws IOException
*/
public void writeState(OutputStream outstream) throws IOException {
if (state == null) return;
synchronized (state) {
DataOutputStream dos = new DataOutputStream(new BufferedOutputStream(outstream));
// DataOutputStream dos=new DataOutputStream(outstream);
dos.writeInt(state.size());
for (Map.Entry<Point, Color> entry : state.entrySet()) {
Point point = entry.getKey();
Color col = entry.getValue();
dos.writeInt(point.x);
dos.writeInt(point.x);
dos.writeInt(col.getRGB());
}
dos.flush();
System.out.println("wrote " + state.size() + " elements");
}
}
private double[] toDoubleArray(Map<String, Double> map) {
double[] d = new double[map.size()];
int i = 0;
for (String key : map.keySet()) {
d[i++] = map.get(key);
}
return d;
}
/** Добавляет новую покупку. Обновляет данные о частоте использования типов. */
public void addPayObject(PayObject payObject) {
if (payObjects.size() != 0 && frequencyUsePayType.size() == 0) updateAllFrequencyUse();
payObjects.add(payObject);
updateFrequencyUse(payObject);
ApplicationService.writeData();
MonitoringMoney.mainFrame.updateData();
}
public Animation() {
String[] keys = {"no Animator found"};
if (tryDir(".")) // || tryDir("BLM305") || tryDir("CSE470"))
keys = map.keySet().toArray(keys);
System.out.println(map.size() + " classes loaded");
menu = new JComboBox(keys);
pan.setLayout(new BorderLayout(GAP, GAP - 4));
pan.setBorder(new javax.swing.border.EmptyBorder(GAP, GAP, GAP, GAP));
pan.setBackground(COLOR);
last = new JPanel();
last.setPreferredSize(DIM);
pan.add(last, "Center");
ref.setFont(NORM);
ref.setEditable(false);
ref.setColumns(35);
ref.setDragEnabled(true);
pan.add(ref, "North");
pan.add(bottomPanel(), "South");
pan.setToolTipText("A collective project for BLM320");
menu.setToolTipText("Animator classes");
who.setToolTipText("author()");
ref.setToolTipText("description()");
Closer ear = new Closer();
menu.addActionListener(ear);
stop.addActionListener(ear);
frm.addWindowListener(ear);
if (map.size() > 0) setItem(0);
frm.setContentPane(pan);
frm.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
frm.setLocation(scaled(120), scaled(90));
frm.pack(); // setSize() is called here
frm.setVisible(true);
start();
}
@NotNull
private List<HighlightSeverity> getDefaultOrder() {
Collection<SeverityBasedTextAttributes> values = myMap.values();
List<HighlightSeverity> order =
new ArrayList<HighlightSeverity>(STANDARD_SEVERITIES.size() + values.size());
for (HighlightInfoType type : STANDARD_SEVERITIES.values()) {
order.add(type.getSeverity(null));
}
for (SeverityBasedTextAttributes attributes : values) {
order.add(attributes.getSeverity());
}
ContainerUtil.sort(order);
return order;
}
/**
* Read State (color dots) from input stream
*
* @param instream
* @throws IOException
*/
public void readState(InputStream instream) throws IOException {
DataInputStream in = new DataInputStream(new BufferedInputStream(instream));
Map<Point, Color> new_state = new LinkedHashMap<Point, Color>();
int num = in.readInt();
for (int i = 0; i < num; i++) {
Point point = new Point(in.readInt(), in.readInt());
Color col = new Color(in.readInt());
new_state.put(point, col);
}
synchronized (state) {
state.clear();
state.putAll(new_state);
System.out.println("read " + state.size() + " elements");
createOffscreenImage(true);
}
}
boolean tryDir(String d) {
ClassLoader L = getClass().getClassLoader();
File p = new File(d, PACKAGE);
System.out.println("Try " + p);
if (!p.exists() || !p.isDirectory()) return false;
for (File f : p.listFiles()) {
String s = f.getName();
if (!s.endsWith(".class")) continue;
String name = s.substring(0, s.length() - 6);
try {
Class<?> c = L.loadClass(PACKAGE + "." + name);
if (!Animator.class.isAssignableFrom(c)) continue;
Animator a = (Animator) c.newInstance();
a.container().setPreferredSize(DIM);
map.put(name, a);
System.out.println(" " + name);
// ClassNotFoundException InstantiationException IllegalAccessException
} catch (Exception e) {
continue;
}
}
return map.size() > 0;
}
private boolean doRemoveModule(@NotNull ModuleEditor selectedEditor) {
String question;
if (myModuleEditors.size() == 1) {
question = ProjectBundle.message("module.remove.last.confirmation");
} else {
question =
ProjectBundle.message("module.remove.confirmation", selectedEditor.getModule().getName());
}
int result =
Messages.showYesNoDialog(
myProject,
question,
ProjectBundle.message("module.remove.confirmation.title"),
Messages.getQuestionIcon());
if (result != Messages.YES) {
return false;
}
// do remove
myModuleEditors.remove(selectedEditor.getModule());
// destroyProcess removed module
final Module moduleToRemove = selectedEditor.getModule();
// remove all dependencies on the module that is about to be removed
List<ModifiableRootModel> modifiableRootModels = new ArrayList<ModifiableRootModel>();
for (final ModuleEditor moduleEditor : myModuleEditors.values()) {
final ModifiableRootModel modifiableRootModel = moduleEditor.getModifiableRootModelProxy();
modifiableRootModels.add(modifiableRootModel);
}
// destroyProcess editor
ModuleDeleteProvider.removeModule(moduleToRemove, null, modifiableRootModels, myModuleModel);
processModuleCountChanged();
Disposer.dispose(selectedEditor);
return true;
}
public VisualizationPanel(List<String> metricNames, final Map<Project, Double[]> results) {
Map<String, IVisualization> vis = VisualizationsRegistry.visualizations;
int numVis = vis.size();
setLayout(new GridLayout(2 + numVis, 1));
this.metricNames = metricNames;
this.results = results;
metricNameComboBox = new JComboBox();
for (String name : metricNames) {
metricNameComboBox.addItem(name);
}
add(metricNameComboBox);
for (final String visName : vis.keySet()) {
JButton btn = new JButton(visName);
btn.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent actionEvent) {
showVis(visName);
}
});
add(btn);
}
JButton boxPlotCombined = new JButton("box and whisker combined");
boxPlotCombined.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent actionEvent) {
showCombined("box and whisker");
}
});
add(boxPlotCombined);
}
public HectorComponent(@NotNull PsiFile file) {
super(new GridBagLayout());
setBorder(BorderFactory.createEmptyBorder(0, 0, 7, 0));
myFile = file;
mySliders = new HashMap<Language, JSlider>();
final Project project = myFile.getProject();
final ProjectFileIndex fileIndex = ProjectRootManager.getInstance(project).getFileIndex();
final VirtualFile virtualFile = myFile.getContainingFile().getVirtualFile();
LOG.assertTrue(virtualFile != null);
final boolean notInLibrary =
!fileIndex.isInLibrarySource(virtualFile) && !fileIndex.isInLibraryClasses(virtualFile)
|| fileIndex.isInContent(virtualFile);
final FileViewProvider viewProvider = myFile.getViewProvider();
List<Language> languages = new ArrayList<Language>(viewProvider.getLanguages());
Collections.sort(languages, PsiUtilBase.LANGUAGE_COMPARATOR);
for (Language language : languages) {
@SuppressWarnings("UseOfObsoleteCollectionType")
final Hashtable<Integer, JLabel> sliderLabels = new Hashtable<Integer, JLabel>();
sliderLabels.put(1, new JLabel(EditorBundle.message("hector.none.slider.label")));
sliderLabels.put(2, new JLabel(EditorBundle.message("hector.syntax.slider.label")));
if (notInLibrary) {
sliderLabels.put(3, new JLabel(EditorBundle.message("hector.inspections.slider.label")));
}
final JSlider slider = new JSlider(SwingConstants.VERTICAL, 1, notInLibrary ? 3 : 2, 1);
if (UIUtil.isUnderGTKLookAndFeel()) {
// default GTK+ slider UI is way too ugly
slider.putClientProperty("Slider.paintThumbArrowShape", true);
slider.setUI(new BasicSliderUI(slider));
}
slider.setLabelTable(sliderLabels);
UIUtil.setSliderIsFilled(slider, true);
slider.setPaintLabels(true);
slider.setSnapToTicks(true);
slider.addChangeListener(
new ChangeListener() {
@Override
public void stateChanged(ChangeEvent e) {
int value = slider.getValue();
for (Enumeration<Integer> enumeration = sliderLabels.keys();
enumeration.hasMoreElements(); ) {
Integer key = enumeration.nextElement();
sliderLabels
.get(key)
.setForeground(
key.intValue() <= value
? UIUtil.getLabelForeground()
: UIUtil.getLabelDisabledForeground());
}
}
});
final PsiFile psiRoot = viewProvider.getPsi(language);
assert psiRoot != null : "No root in " + viewProvider + " for " + language;
slider.setValue(
getValue(
HighlightLevelUtil.shouldHighlight(psiRoot),
HighlightLevelUtil.shouldInspect(psiRoot)));
mySliders.put(language, slider);
}
GridBagConstraints gc =
new GridBagConstraints(
0,
GridBagConstraints.RELATIVE,
1,
1,
0,
0,
GridBagConstraints.NORTHWEST,
GridBagConstraints.NONE,
new Insets(0, 5, 0, 0),
0,
0);
JPanel panel = new JPanel(new GridBagLayout());
panel.setBorder(IdeBorderFactory.createTitledBorder(myTitle, false));
final boolean addLabel = mySliders.size() > 1;
if (addLabel) {
layoutVertical(panel);
} else {
layoutHorizontal(panel);
}
gc.gridx = 0;
gc.gridy = 0;
gc.weighty = 1.0;
gc.fill = GridBagConstraints.BOTH;
add(panel, gc);
gc.gridy = GridBagConstraints.RELATIVE;
gc.weighty = 0;
final HyperlinkLabel configurator = new HyperlinkLabel("Configure inspections");
gc.insets.right = 5;
gc.insets.bottom = 10;
gc.weightx = 0;
gc.fill = GridBagConstraints.NONE;
gc.anchor = GridBagConstraints.EAST;
add(configurator, gc);
configurator.addHyperlinkListener(
new HyperlinkListener() {
@Override
public void hyperlinkUpdate(HyperlinkEvent e) {
final JBPopup hector = getOldHector();
if (hector != null) {
hector.cancel();
}
if (!DaemonCodeAnalyzer.getInstance(myFile.getProject())
.isHighlightingAvailable(myFile)) return;
final Project project = myFile.getProject();
final ErrorsConfigurable errorsConfigurable =
ErrorsConfigurable.SERVICE.createConfigurable(project);
assert errorsConfigurable != null;
ShowSettingsUtil.getInstance().editConfigurable(project, errorsConfigurable);
}
});
gc.anchor = GridBagConstraints.WEST;
gc.weightx = 1.0;
gc.insets.right = 0;
gc.fill = GridBagConstraints.HORIZONTAL;
myAdditionalPanels = new ArrayList<HectorComponentPanel>();
for (HectorComponentPanelsProvider provider :
Extensions.getExtensions(HectorComponentPanelsProvider.EP_NAME, project)) {
final HectorComponentPanel componentPanel = provider.createConfigurable(file);
if (componentPanel != null) {
myAdditionalPanels.add(componentPanel);
add(componentPanel.createComponent(), gc);
componentPanel.reset();
}
}
}
@Override
public int getUsagesCount() {
return myUsageNodes.size();
}
public void apply() throws ConfigurationException {
// validate content and source roots
final Map<VirtualFile, String> contentRootToModuleNameMap = new HashMap<VirtualFile, String>();
final Map<VirtualFile, VirtualFile> srcRootsToContentRootMap =
new HashMap<VirtualFile, VirtualFile>();
for (final ModuleEditor moduleEditor : myModuleEditors.values()) {
final ModifiableRootModel rootModel = moduleEditor.getModifiableRootModel();
final ContentEntry[] contents = rootModel.getContentEntries();
for (ContentEntry contentEntry : contents) {
final VirtualFile contentRoot = contentEntry.getFile();
if (contentRoot == null) {
continue;
}
final String moduleName = moduleEditor.getName();
final String previousName = contentRootToModuleNameMap.put(contentRoot, moduleName);
if (previousName != null && !previousName.equals(moduleName)) {
throw new ConfigurationException(
ProjectBundle.message(
"module.paths.validation.duplicate.content.error",
contentRoot.getPresentableUrl(),
previousName,
moduleName));
}
for (VirtualFile srcRoot : contentEntry.getSourceFolderFiles()) {
final VirtualFile anotherContentRoot = srcRootsToContentRootMap.put(srcRoot, contentRoot);
if (anotherContentRoot != null) {
final String problematicModule;
final String correctModule;
if (VfsUtilCore.isAncestor(anotherContentRoot, contentRoot, true)) {
problematicModule = contentRootToModuleNameMap.get(anotherContentRoot);
correctModule = contentRootToModuleNameMap.get(contentRoot);
} else {
problematicModule = contentRootToModuleNameMap.get(contentRoot);
correctModule = contentRootToModuleNameMap.get(anotherContentRoot);
}
throw new ConfigurationException(
ProjectBundle.message(
"module.paths.validation.duplicate.source.root.error",
problematicModule,
srcRoot.getPresentableUrl(),
correctModule));
}
}
}
}
// additional validation: directories marked as src roots must belong to the same module as
// their corresponding content root
for (Map.Entry<VirtualFile, VirtualFile> entry : srcRootsToContentRootMap.entrySet()) {
final VirtualFile srcRoot = entry.getKey();
final VirtualFile correspondingContent = entry.getValue();
final String expectedModuleName = contentRootToModuleNameMap.get(correspondingContent);
for (VirtualFile candidateContent = srcRoot;
candidateContent != null && !candidateContent.equals(correspondingContent);
candidateContent = candidateContent.getParent()) {
final String moduleName = contentRootToModuleNameMap.get(candidateContent);
if (moduleName != null && !moduleName.equals(expectedModuleName)) {
throw new ConfigurationException(
ProjectBundle.message(
"module.paths.validation.source.root.belongs.to.another.module.error",
srcRoot.getPresentableUrl(),
expectedModuleName,
moduleName));
}
}
}
final List<ModifiableRootModel> models =
new ArrayList<ModifiableRootModel>(myModuleEditors.size());
for (ModuleEditor moduleEditor : myModuleEditors.values()) {
moduleEditor.canApply();
}
final Map<Sdk, Sdk> modifiedToOriginalMap = new HashMap<Sdk, Sdk>();
final ProjectSdksModel projectJdksModel =
ProjectStructureConfigurable.getInstance(myProject).getProjectJdksModel();
for (Map.Entry<Sdk, Sdk> entry : projectJdksModel.getProjectSdks().entrySet()) {
modifiedToOriginalMap.put(entry.getValue(), entry.getKey());
}
final Ref<ConfigurationException> exceptionRef = Ref.create();
DumbService.getInstance(myProject)
.allowStartingDumbModeInside(
DumbModePermission.MAY_START_BACKGROUND,
new Runnable() {
public void run() {
ApplicationManager.getApplication()
.runWriteAction(
new Runnable() {
@Override
public void run() {
try {
for (final ModuleEditor moduleEditor : myModuleEditors.values()) {
final ModifiableRootModel model = moduleEditor.apply();
if (model != null) {
if (!model.isSdkInherited()) {
// make sure the sdk is set to original SDK stored in the JDK
// Table
final Sdk modelSdk = model.getSdk();
if (modelSdk != null) {
final Sdk original = modifiedToOriginalMap.get(modelSdk);
if (original != null) {
model.setSdk(original);
}
}
}
models.add(model);
}
}
myFacetsConfigurator.applyEditors();
} catch (ConfigurationException e) {
exceptionRef.set(e);
return;
}
try {
final ModifiableRootModel[] rootModels =
models.toArray(new ModifiableRootModel[models.size()]);
ModifiableModelCommitter.multiCommit(rootModels, myModuleModel);
myModuleModelCommitted = true;
myFacetsConfigurator.commitFacets();
} finally {
ModuleStructureConfigurable.getInstance(myProject)
.getFacetEditorFacade()
.clearMaps(false);
myFacetsConfigurator = createFacetsConfigurator();
myModuleModel =
ModuleManager.getInstance(myProject).getModifiableModel();
myModuleModelCommitted = false;
}
}
});
}
});
if (!exceptionRef.isNull()) {
throw exceptionRef.get();
}
myModified = false;
}