@Override
public boolean isEmpty() {
for (Segment<K, V> segment : segments) {
if (segment.size() > 0) return false;
}
return true;
}
public Segment getSegmentDefinition(String segmentId) {
Segment definition = persistenceService.load(segmentId, Segment.class);
if (definition != null) {
ParserHelper.resolveConditionType(definitionsService, definition.getCondition());
}
return definition;
}
/**
* Method description
*
* @param heading
* @return
*/
public List<LocusScore> getWholeGenomeScores(String heading) {
List<LocusScore> wholeGenomeScores = wholeGenomeScoresCache.get(heading);
if ((wholeGenomeScores == null) || wholeGenomeScores.isEmpty()) {
int locationUnit = 1000;
// Compute the smallest concievable feature that could be viewed on the
// largest screen. Be conservative. The smallest feature is one at
// the screen resolution scale in <chr units> / <pixel>
int maxScreenSize = 4000;
double minFeatureSize = 0; // ((double) genome.getLength()) / (maxScreenSize * locationUnit);
long offset = 0;
wholeGenomeScores = new ArrayList(1000);
for (String chr : genome.getChromosomeNames()) {
List<LocusScore> chrSegments = getSegments(heading, chr);
if (chrSegments != null) {
int lastgEnd = -1;
for (LocusScore score : chrSegments) {
Segment seg = (Segment) score;
int gStart = (int) ((offset + score.getStart()) / locationUnit);
int gEnd = (int) ((offset + score.getEnd()) / locationUnit);
if ((gEnd - gStart) > minFeatureSize) {
wholeGenomeScores.add(
new Segment(gStart, gStart, gEnd, gEnd, seg.getScore(), seg.getDescription()));
}
}
}
offset += genome.getChromosome(chr).getLength();
}
wholeGenomeScoresCache.put(heading, wholeGenomeScores);
}
return wholeGenomeScores;
}
private List<Segment> getAllSegmentDefinitions() {
List<Segment> allItems = persistenceService.getAllItems(Segment.class);
for (Segment segment : allItems) {
ParserHelper.resolveConditionType(definitionsService, segment.getCondition());
}
return allItems;
}
public static Segment shallowCopy(Segment segment, Factory factory) {
Segment clone = factory.newSegment();
for (String key : segment.keys()) {
clone.setAttribute(key, segment.getAttribute(key));
}
return clone;
}
@Override
public int size() {
long total = 0;
for (Segment<K, V> segment : segments) {
total += segment.size();
}
return (int) Math.min(Integer.MAX_VALUE, total);
}
@Override
public long offHeapUsed() {
long total = 0;
for (Segment<K, V> segment : segments) {
total += segment.offHeapUsed();
}
return total;
}
public void addVariable(DapVariable var, List<Slice> slices) throws DapException {
if (findVariableIndex(var) < 0) {
Segment segment = new Segment(var);
segment.setSlices(slices);
this.segments.add(segment);
this.variables.add(var);
}
}
private Set<Segment> getScoringDependentSegments(String scoringId) {
Set<Segment> impactedSegments = new HashSet<>(this.allSegments.size());
for (Segment segment : this.allSegments) {
if (checkScoringDeletionImpact(segment.getCondition(), scoringId)) {
impactedSegments.add(segment);
}
}
return impactedSegments;
}
public void setSegmentDefinition(Segment segment) {
ParserHelper.resolveConditionType(definitionsService, segment.getCondition());
if (segment.getMetadata().isEnabled() && !segment.getMetadata().isMissingPlugins()) {
updateAutoGeneratedRules(segment.getMetadata(), segment.getCondition());
}
// make sure we update the name and description metadata that might not match, so first we
// remove the entry from the map
persistenceService.save(segment);
updateExistingProfilesForSegment(segment);
}
public PartialList<Metadata> getSegmentMetadatas(
String scope, int offset, int size, String sortBy) {
PartialList<Segment> segments =
persistenceService.query("metadata.scope", scope, sortBy, Segment.class, offset, size);
List<Metadata> details = new LinkedList<>();
for (Segment definition : segments.getList()) {
details.add(definition.getMetadata());
}
return new PartialList<>(
details, segments.getOffset(), segments.getPageSize(), segments.getTotalSize());
}
public DependentMetadata getScoringDependentMetadata(String scoringId) {
List<Metadata> segments = new LinkedList<>();
List<Metadata> scorings = new LinkedList<>();
for (Segment definition : getScoringDependentSegments(scoringId)) {
segments.add(definition.getMetadata());
}
for (Scoring definition : getScoringDependentScorings(scoringId)) {
scorings.add(definition.getMetadata());
}
return new DependentMetadata(segments, scorings);
}
public List<Metadata> getSegmentMetadatasForProfile(Profile profile) {
List<Metadata> metadatas = new ArrayList<>();
List<Segment> allSegments = this.allSegments;
for (Segment segment : allSegments) {
if (persistenceService.testMatch(segment.getCondition(), profile)) {
metadatas.add(segment.getMetadata());
}
}
return metadatas;
}
private Segment addRelativeDendrite(Segment parent, Point3f relPosition) {
Point3f newPosition = (new Point3f(parent.getEndPointPosition()));
newPosition.add(relPosition);
float newRadius = parent.getRadius() * .6f;
String newName = "Dend_" + getOnlyDendriticSegments().size();
Segment tempDend =
addDendriticSegment(newRadius, newName, newPosition, parent, 1, newName + "_Sec", true);
return tempDend;
}
@Override
@SuppressWarnings("SleepWhileHoldingLock")
public void run() {
try {
// initialize the statusbar
status.removeAll();
JProgressBar progress = new JProgressBar();
progress.setMinimum(0);
progress.setMaximum(doc.getLength());
status.add(progress);
status.revalidate();
// start writing
Writer out = new FileWriter(f);
Segment text = new Segment();
text.setPartialReturn(true);
int charsLeft = doc.getLength();
int offset = 0;
while (charsLeft > 0) {
doc.getText(offset, Math.min(4096, charsLeft), text);
out.write(text.array, text.offset, text.count);
charsLeft -= text.count;
offset += text.count;
progress.setValue(offset);
try {
Thread.sleep(10);
} catch (InterruptedException e) {
Logger.getLogger(FileSaver.class.getName()).log(Level.SEVERE, null, e);
}
}
out.flush();
out.close();
} catch (IOException e) {
final String msg = e.getMessage();
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
JOptionPane.showMessageDialog(
getFrame(),
"Could not save file: " + msg,
"Error saving file",
JOptionPane.ERROR_MESSAGE);
}
});
} catch (BadLocationException e) {
System.err.println(e.getMessage());
}
// we are done... get rid of progressbar
status.removeAll();
status.revalidate();
}
/**
* Compute dimension related information using slicing and redef info. In effect, this is where
* projection constraints are applied
*
* <p>Assume that the constraint compiler has given us the following info:
*
* <ol>
* <li>A list of the variables to include.
* <li>A pair (DapDimension,Slice) for each redef
* <li>For each variable in #1, a list of slices taken from the constraint expression
* </ol>
*
* <p>Two products will be produced.
*
* <ol>
* <li>The variables map will be modified so that the slices properly reflect any original or
* redef dimensions.
* <li>A set, dimrefs, of all referenced original dimensions.
* </ol>
*
* <p>The processing is as follows
*
* <ol>
* <li>For each redef create a new redef dimension
* <li>For each variable:
* <ol>
* <li>if the variable is scalar, do nothing.
* <li>if the variable has no associated slices, then make its new dimensions be the
* original dimensions.
* <li>otherwise, walk the slices and create new dimensions from them; use redefs where
* indicated
* <li>
* </ol>
* </ol>
*/
protected void computedimensions() throws DapException {
// Build the redefmap
for (DapDimension key : redefslice.keySet()) {
Slice slice = redefslice.get(key);
DapDimension newdim = (DapDimension) key.clone();
newdim.setSize(slice.getCount());
redef.put(key, newdim);
}
// Process each variable
for (int i = 0; i < segments.size(); i++) {
Segment seg = segments.get(i);
if (seg.var.getRank() == 0) continue;
List<Slice> slices = seg.slices;
List<DapDimension> orig = seg.var.getDimensions();
List<DapDimension> newdims = new ArrayList<>();
// If the slice list is short then pad it with
// default slices
if (slices == null) slices = new ArrayList<Slice>();
while (slices.size() < orig.size()) // pad
{
slices.add(new Slice().setConstrained(false));
}
assert (slices != null && slices.size() == orig.size());
for (int j = 0; j < slices.size(); j++) {
Slice slice = slices.get(j);
DapDimension dim0 = orig.get(j);
DapDimension newdim = redef.get(dim0);
if (newdim == null) newdim = dim0;
// fill in the undefined last value
slice.setMaxSize(newdim.getSize());
slice.finish();
Slice newslice = null;
if (slice.isConstrained()) {
// Construct an anonymous dimension for this slice
newdim = new DapDimension(slice.getCount());
} else { // replace with a new slice from the dim
newslice = new Slice(newdim);
if (newslice != null) {
// track set of referenced non-anonymous dimensions
if (!dimrefs.contains(dim0)) dimrefs.add(dim0);
slices.set(j, newslice);
}
}
// record the dimension per variable
newdims.add(newdim);
}
seg.setDimset(newdims);
}
}
@Override
public void startTag(String name, Attributes atts, Stack<String> context) {
if (name.equalsIgnoreCase(Constants.PERSONS_TAG)) {
persons = new HashSet<>();
} else if (name.equalsIgnoreCase(Constants.PERSON_TAG)) {
person = factory.newPerson(getAttribute(Constants.ID_KEY, atts));
for (int i = 0; i < atts.getLength(); i++) {
String type = atts.getLocalName(i);
if (!type.equalsIgnoreCase(Constants.ID_KEY)) {
if (!blacklist.contains(type)) {
person.setAttribute(type, getAttribute(type, atts));
}
}
}
} else if (name.equalsIgnoreCase(Constants.PLAN_TAG)) {
plan = factory.newEpisode();
for (int i = 0; i < atts.getLength(); i++) {
String type = atts.getLocalName(i);
if (!blacklist.contains(type)) {
plan.setAttribute(type, getAttribute(type, atts));
}
}
} else if (name.equalsIgnoreCase(Constants.ACTIVITY_TAG)) {
Segment act = factory.newSegment();
for (int i = 0; i < atts.getLength(); i++) {
String type = atts.getLocalName(i);
if (!blacklist.contains(type)) {
act.setAttribute(type, getAttribute(type, atts));
}
}
plan.addActivity(act);
} else if (name.equalsIgnoreCase(Constants.LEG_TAG)) {
Segment leg = factory.newSegment();
for (int i = 0; i < atts.getLength(); i++) {
String type = atts.getLocalName(i);
if (!blacklist.contains(type)) {
leg.setAttribute(type, getAttribute(type, atts));
}
}
plan.addLeg(leg);
}
}
private K nextSegmentKey() {
while (segmentIndex >= 0) {
Segment<K, V> segment = segments[segmentIndex];
K key = segment.getNextKey(lastSegmentKey);
if (key == null) {
segmentIndex--;
lastSegmentKey = null;
} else {
lastSegmentKey = key;
return key;
}
}
return null;
}
public static void main(String[] args) throws Exception {
String sourceUrlString = "data/test.html";
if (args.length == 0)
System.err.println("Using default argument of \"" + sourceUrlString + '"');
else sourceUrlString = args[0];
if (sourceUrlString.indexOf(':') == -1) sourceUrlString = "file:" + sourceUrlString;
StreamedSource streamedSource = new StreamedSource(new URL(sourceUrlString));
// streamedSource.setBuffer(new char[65000]); // uncomment this to use a fixed buffer size
Writer writer = null;
try {
writer =
new OutputStreamWriter(
new FileOutputStream("StreamedSourceCopyOutput.html"), streamedSource.getEncoding());
System.out.println("Processing segments:");
int lastSegmentEnd = 0;
for (Segment segment : streamedSource) {
System.out.println(segment.getDebugInfo());
if (segment.getEnd() <= lastSegmentEnd)
continue; // if this tag is inside the previous tag (e.g. a server tag) then ignore it as
// it was already output along with the previous tag.
lastSegmentEnd = segment.getEnd();
if (segment instanceof Tag) {
Tag tag = (Tag) segment;
// HANDLE TAG
// Uncomment the following line to ensure each tag is valid XML:
// writer.write(tag.tidy()); continue;
} else if (segment instanceof CharacterReference) {
CharacterReference characterReference = (CharacterReference) segment;
// HANDLE CHARACTER REFERENCE
// Uncomment the following line to decode all character references instead of copying them
// verbatim:
// characterReference.appendCharTo(writer); continue;
} else {
// HANDLE PLAIN TEXT
}
// unless specific handling has prevented getting to here, simply output the segment as is:
writer.write(segment.toString());
}
writer.close();
System.err.println(
"\nA copy of the source document has been output to StreamedSourceCopyOuput.html");
} catch (Exception ex) {
if (writer != null)
try {
writer.close();
} catch (IOException ex2) {
}
throw ex;
}
}
private Entry<K, V> nextSegmentEntry() {
while (segmentIndex >= 0) {
Segment<K, V> segment = segments[segmentIndex];
Entry<K, V> entry = segment.getNextEntry(lastSegmentKey);
if (entry == null) {
segmentIndex--;
lastSegmentKey = null;
} else {
lastSegmentKey = entry.getKey();
return entry;
}
}
return null;
}
public DependentMetadata removeScoringDefinition(String scoringId, boolean validate) {
Set<Segment> impactedSegments = getScoringDependentSegments(scoringId);
Set<Scoring> impactedScorings = getScoringDependentScorings(scoringId);
if (!validate || (impactedSegments.isEmpty() && impactedScorings.isEmpty())) {
// update profiles
updateExistingProfilesForRemovedScoring(scoringId);
// update impacted segments
for (Segment segment : impactedSegments) {
Condition updatedCondition =
updateScoringDependentCondition(segment.getCondition(), scoringId);
segment.setCondition(updatedCondition);
if (updatedCondition == null) {
clearAutoGeneratedRules(
persistenceService.query(
"linkedItems", segment.getMetadata().getId(), null, Rule.class),
segment.getMetadata().getId());
segment.getMetadata().setEnabled(false);
}
setSegmentDefinition(segment);
}
// update impacted scorings
for (Scoring scoring : impactedScorings) {
List<ScoringElement> updatedScoringElements = new ArrayList<>();
for (ScoringElement scoringElement : scoring.getElements()) {
Condition updatedCondition =
updateScoringDependentCondition(scoringElement.getCondition(), scoringId);
if (updatedCondition != null) {
scoringElement.setCondition(updatedCondition);
updatedScoringElements.add(scoringElement);
}
}
scoring.setElements(updatedScoringElements);
if (updatedScoringElements.isEmpty()) {
clearAutoGeneratedRules(
persistenceService.query(
"linkedItems", scoring.getMetadata().getId(), null, Rule.class),
scoring.getMetadata().getId());
scoring.getMetadata().setEnabled(false);
}
setScoringDefinition(scoring);
}
persistenceService.remove(scoringId, Scoring.class);
List<Rule> previousRules =
persistenceService.query("linkedItems", scoringId, null, Rule.class);
clearAutoGeneratedRules(previousRules, scoringId);
}
List<Metadata> segments = new LinkedList<>();
List<Metadata> scorings = new LinkedList<>();
for (Segment definition : impactedSegments) {
segments.add(definition.getMetadata());
}
for (Scoring definition : impactedScorings) {
scorings.add(definition.getMetadata());
}
return new DependentMetadata(segments, scorings);
}
@Override
public boolean replace(@NotNull K key, @NotNull V oldValue, @NotNull V newValue) {
long h = hasher.hash(key);
int segment = hasher.getSegment();
Segment<K, V> segment2 = segments[segment];
//noinspection SynchronizationOnLocalVariableOrMethodParameter
synchronized (segment2) {
V value2 = get(key);
if (value2 != null && oldValue.equals(value2)) {
segment2.put(h, key, newValue, true, true);
return true;
}
return false;
}
}
@Override
public boolean remove(@NotNull Object key, Object value) {
long h = hasher.hash(key);
int segment = hasher.getSegment();
Segment<K, V> segment2 = segments[segment];
//noinspection SynchronizationOnLocalVariableOrMethodParameter
synchronized (segment2) {
V value2 = get(key);
if (value2 != null && value.equals(value2)) {
segment2.remove(h, (K) key);
return true;
}
return false;
}
}
protected String getField(
Segment pSegment, int pFieldNum, boolean pMandatoryFl, String pErrorMessage) {
DataElement de = null;
String val = null;
String err = null;
try {
de = pSegment.getDataElement(pFieldNum);
} catch (Exception exc) {
if (pMandatoryFl) {
err = pErrorMessage + " (1)";
}
}
if (err == null && de == null && pMandatoryFl) {
err = pErrorMessage + " (2)";
}
if (err == null && de != null) {
try {
val = de.get();
} catch (Exception exc) {
}
if (!Utility.isSet(val) && pMandatoryFl) {
err = pErrorMessage + " (3)";
}
}
if (err != null) {
errorMsgs.add(err);
}
return val;
}
private void writeTextCollapseWhiteSpace(final int end, final int depth) throws IOException {
// sets index to end
// assert index < end
boolean lastWasWhiteSpace = false;
updateNextTag();
while (index < end) {
while (nextTag != null && index == nextTag.begin) {
if (lastWasWhiteSpace) {
writer.write(' ');
lastWasWhiteSpace = false;
}
writeTag(nextTag, depth, end);
if (index == end) return;
}
final char ch = sourceText.charAt(index++);
if (Segment.isWhiteSpace(ch)) {
lastWasWhiteSpace = true;
} else {
if (lastWasWhiteSpace) {
writer.write(' ');
lastWasWhiteSpace = false;
}
writer.write(ch);
}
}
if (lastWasWhiteSpace) writer.write(' ');
}
private V nextSegmentValue() {
while (segmentIndex >= 0) {
Segment<K, V> segment = segments[segmentIndex];
Map.Entry<K, V> entry =
segment.getNextEntry(
lastSegmentKey); // todo: not the most efficient to work through Entries...
if (entry == null) {
segmentIndex--;
lastSegmentKey = null;
} else {
lastSegmentKey = entry.getKey();
return entry.getValue();
}
}
return null;
}
public void writeTo(final Writer writer) throws IOException {
this.writer = writer;
if (segment instanceof Source) ((Source) segment).fullSequentialParse();
nextTag = segment.source.findNextTag(segment.begin);
index = segment.begin;
writeContent(segment.end, segment.getChildElements(), 0);
writer.flush();
}
private void validateRegions() {
if (region_map == null) return;
synchronized (region_map) {
if (regions_valid) return;
Segment s = new Segment();
region_map.clear();
for (BaleRegion br : fragment_regions) {
RegionData rd = new RegionData(indent_size);
region_map.put(br, rd);
int soff = br.getStart();
int eoff = br.getEnd();
if (eoff < soff) continue;
try {
base_document.getText(soff, eoff - soff, s);
} catch (BadLocationException e) {
BoardLog.logE("BALE", "Problem getting region indentation", e);
continue;
}
int ln = s.length();
LineData ld;
boolean sol = true;
for (int i = 0; i < ln; ++i) {
char c = s.charAt(i);
if (sol) {
ld = computeLineData(i, s);
rd.add(ld);
sol = false;
}
if (c == '\n') sol = true;
}
if (!sol) {
ld = computeLineData(ln, s);
rd.add(ld);
++ln;
}
}
regions_valid = true;
}
}
public static void renameNonCodeUsages(
@NotNull Project project, @NotNull NonCodeUsageInfo[] usages) {
PsiDocumentManager.getInstance(project).commitAllDocuments();
Map<Document, List<UsageOffset>> docsToOffsetsMap = new HashMap<Document, List<UsageOffset>>();
final PsiDocumentManager psiDocumentManager = PsiDocumentManager.getInstance(project);
for (NonCodeUsageInfo usage : usages) {
PsiElement element = usage.getElement();
if (element == null) continue;
element = CodeInsightUtilBase.forcePsiPostprocessAndRestoreElement(element, true);
if (element == null) continue;
final ProperTextRange rangeInElement = usage.getRangeInElement();
if (rangeInElement == null) continue;
final PsiFile containingFile = element.getContainingFile();
final Document document = psiDocumentManager.getDocument(containingFile);
final Segment segment = usage.getSegment();
LOG.assertTrue(segment != null);
int fileOffset = segment.getStartOffset();
List<UsageOffset> list = docsToOffsetsMap.get(document);
if (list == null) {
list = new ArrayList<UsageOffset>();
docsToOffsetsMap.put(document, list);
}
list.add(new UsageOffset(fileOffset, fileOffset + rangeInElement.getLength(), usage.newText));
}
for (Document document : docsToOffsetsMap.keySet()) {
List<UsageOffset> list = docsToOffsetsMap.get(document);
LOG.assertTrue(list != null, document);
UsageOffset[] offsets = list.toArray(new UsageOffset[list.size()]);
Arrays.sort(offsets);
for (int i = offsets.length - 1; i >= 0; i--) {
UsageOffset usageOffset = offsets[i];
document.replaceString(usageOffset.startOffset, usageOffset.endOffset, usageOffset.newText);
}
PsiDocumentManager.getInstance(project).commitDocument(document);
}
PsiDocumentManager.getInstance(project).commitAllDocuments();
}
private Segment addRelativeAxon(Segment parent, Point3f relPosition, float radius) {
Point3f newPosition = (new Point3f(parent.getEndPointPosition()));
newPosition.add(relPosition);
String newName = "Axon_" + getOnlyAxonalSegments().size();
Segment tempAxon = addAxonalSegment(radius, newName, newPosition, parent, 1, newName + "_Sec");
return tempAxon;
}
