private T processActiveRegion(
final ActiveRegion activeRegion,
final LinkedHashSet<GATKSAMRecord> reads,
final Queue<ActiveRegion> workQueue,
final T sum,
final ActiveRegionWalker<M, T> walker) {
final ArrayList<GATKSAMRecord> placedReads = new ArrayList<GATKSAMRecord>();
for (final GATKSAMRecord read : reads) {
final GenomeLoc readLoc = this.engine.getGenomeLocParser().createGenomeLoc(read);
if (activeRegion.getLocation().overlapsP(readLoc)) {
// The region which the highest amount of overlap is chosen as the primary region for the
// read (tie breaking is done as right most region)
long maxOverlap = activeRegion.getLocation().sizeOfOverlap(readLoc);
ActiveRegion bestRegion = activeRegion;
for (final ActiveRegion otherRegionToTest : workQueue) {
if (otherRegionToTest.getLocation().sizeOfOverlap(readLoc) >= maxOverlap) {
maxOverlap = otherRegionToTest.getLocation().sizeOfOverlap(readLoc);
bestRegion = otherRegionToTest;
}
}
bestRegion.add(read);
// The read is also added to all other regions in which it overlaps but marked as
// non-primary
if (walker.wantsNonPrimaryReads()) {
if (!bestRegion.equals(activeRegion)) {
activeRegion.add(read);
}
for (final ActiveRegion otherRegionToTest : workQueue) {
if (!bestRegion.equals(otherRegionToTest)
&& otherRegionToTest.getExtendedLoc().overlapsP(readLoc)) {
otherRegionToTest.add(read);
}
}
}
placedReads.add(read);
} else if (activeRegion.getExtendedLoc().overlapsP(readLoc)
&& walker.wantsNonPrimaryReads()) {
activeRegion.add(read);
}
}
reads.removeAll(
placedReads); // remove all the reads which have been placed into their active region
// WARNING: This hashset relies on reads being exactly equal when they are placed in the list as
// when they are removed. So the ActiveRegionWalker can't modify the reads in any way.
logger.debug(
">> Map call with "
+ activeRegion.getReads().size()
+ " "
+ (activeRegion.isActive ? "active" : "inactive")
+ " reads @ "
+ activeRegion.getLocation()
+ " with full extent: "
+ activeRegion.getReferenceLoc());
final M x = walker.map(activeRegion, null);
return walker.reduce(x, sum);
}
@Override
public void flushVariable(@NotNull final DfaVariableValue variable) {
List<DfaValue> updatedStack = ContainerUtil.map(myStack, value -> handleFlush(variable, value));
myStack.clear();
for (DfaValue value : updatedStack) {
myStack.push(value);
}
doFlush(variable, false);
flushDependencies(variable);
myUnknownVariables.remove(variable);
myUnknownVariables.removeAll(myFactory.getVarFactory().getAllQualifiedBy(variable));
myCachedHash = null;
}
private static Set<TemplateContextType> getDirectlyApplicableContextTypes(
@NotNull PsiFile file, int offset) {
LinkedHashSet<TemplateContextType> set = new LinkedHashSet<TemplateContextType>();
LinkedList<TemplateContextType> contexts = buildOrderedContextTypes();
for (TemplateContextType contextType : contexts) {
if (contextType.isInContext(file, offset)) {
set.add(contextType);
}
}
removeBases:
while (true) {
for (TemplateContextType type : set) {
if (set.removeAll(getBases(type))) {
continue removeBases;
}
}
return set;
}
}
/**
* @param addClearListItem - used for detecting whether the "Clear List" action should be added to
* the end of the returned list of actions
* @return
*/
public AnAction[] getRecentProjectsActions(boolean addClearListItem) {
validateRecentProjects();
final Set<String> openedPaths = ContainerUtil.newHashSet();
for (Project openProject : ProjectManager.getInstance().getOpenProjects()) {
ContainerUtil.addIfNotNull(openedPaths, getProjectPath(openProject));
}
final LinkedHashSet<String> paths;
synchronized (myStateLock) {
paths = ContainerUtil.newLinkedHashSet(myState.recentPaths);
}
paths.remove(null);
paths.removeAll(openedPaths);
ArrayList<AnAction> actions = new ArrayList<AnAction>();
Set<String> duplicates = getDuplicateProjectNames(openedPaths, paths);
for (final String path : paths) {
final String projectName = getProjectName(path);
String displayName;
synchronized (myStateLock) {
displayName = myState.names.get(path);
}
if (StringUtil.isEmptyOrSpaces(displayName)) {
displayName = duplicates.contains(path) ? path : projectName;
}
// It's better don't to remove non-existent projects. Sometimes projects stored
// on USB-sticks or flash-cards, and it will be nice to have them in the list
// when USB device or SD-card is mounted
if (new File(path).exists()) {
actions.add(new ReopenProjectAction(path, projectName, displayName));
}
}
if (actions.isEmpty()) {
return AnAction.EMPTY_ARRAY;
}
ArrayList<AnAction> list = new ArrayList<AnAction>();
for (AnAction action : actions) {
list.add(action);
}
if (addClearListItem) {
AnAction clearListAction =
new AnAction(IdeBundle.message("action.clear.list")) {
public void actionPerformed(AnActionEvent e) {
final int rc =
Messages.showOkCancelDialog(
e.getData(PlatformDataKeys.PROJECT),
"Would you like to clear the list of recent projects?",
"Clear Recent Projects List",
Messages.getQuestionIcon());
if (rc == 0) {
synchronized (myStateLock) {
myState.recentPaths.clear();
}
WelcomeFrame.clearRecents();
}
}
};
list.add(Separator.getInstance());
list.add(clearListAction);
}
return list.toArray(new AnAction[list.size()]);
}
private void setComboboxModel(
final JComboBox comboBox,
final VirtualFile initialTargetDirectorySourceRoot,
final VirtualFile oldSelection,
final ProjectFileIndex fileIndex,
final VirtualFile[] sourceRoots,
final Project project,
final boolean forceIncludeAll,
final Pass<String> updateErrorMessage) {
final LinkedHashSet<PsiDirectory> targetDirectories = new LinkedHashSet<PsiDirectory>();
final HashMap<PsiDirectory, String> pathsToCreate = new HashMap<PsiDirectory, String>();
MoveClassesOrPackagesUtil.buildDirectoryList(
new PackageWrapper(PsiManager.getInstance(project), getTargetPackage()),
sourceRoots,
targetDirectories,
pathsToCreate);
if (!forceIncludeAll && targetDirectories.size() > pathsToCreate.size()) {
targetDirectories.removeAll(pathsToCreate.keySet());
}
final ArrayList<DirectoryChooser.ItemWrapper> items =
new ArrayList<DirectoryChooser.ItemWrapper>();
DirectoryChooser.ItemWrapper initial = null;
DirectoryChooser.ItemWrapper oldOne = null;
for (PsiDirectory targetDirectory : targetDirectories) {
DirectoryChooser.ItemWrapper itemWrapper =
new DirectoryChooser.ItemWrapper(targetDirectory, pathsToCreate.get(targetDirectory));
items.add(itemWrapper);
final VirtualFile sourceRootForFile =
fileIndex.getSourceRootForFile(targetDirectory.getVirtualFile());
if (sourceRootForFile == initialTargetDirectorySourceRoot) {
initial = itemWrapper;
} else if (sourceRootForFile == oldSelection) {
oldOne = itemWrapper;
}
}
items.add(NULL_WRAPPER);
final DirectoryChooser.ItemWrapper selection =
chooseSelection(initialTargetDirectorySourceRoot, fileIndex, items, initial, oldOne);
final ComboBoxModel model = comboBox.getModel();
if (model instanceof CollectionComboBoxModel) {
boolean sameModel = model.getSize() == items.size();
if (sameModel) {
for (int i = 0; i < items.size(); i++) {
final DirectoryChooser.ItemWrapper oldItem =
(DirectoryChooser.ItemWrapper) model.getElementAt(i);
final DirectoryChooser.ItemWrapper itemWrapper = items.get(i);
if (!areItemsEquivalent(oldItem, itemWrapper)) {
sameModel = false;
break;
}
}
}
if (sameModel) {
if (areItemsEquivalent(
(DirectoryChooser.ItemWrapper) comboBox.getSelectedItem(), selection)) {
return;
}
}
}
updateErrorMessage(updateErrorMessage, fileIndex, selection);
Collections.sort(
items,
new Comparator<DirectoryChooser.ItemWrapper>() {
@Override
public int compare(DirectoryChooser.ItemWrapper o1, DirectoryChooser.ItemWrapper o2) {
if (o1 == NULL_WRAPPER) return -1;
if (o2 == NULL_WRAPPER) return 1;
return o1.getRelativeToProjectPath().compareToIgnoreCase(o2.getRelativeToProjectPath());
}
});
comboBox.setModel(new CollectionComboBoxModel(items, selection));
}
