/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.track;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.tools.FeatureSearcher;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.util.CancellableProgressDialog;
import org.broad.igv.ui.util.IndefiniteProgressMonitor;
import org.broad.igv.ui.util.ProgressMonitor;
import org.broad.igv.util.LongRunningTask;
import htsjdk.tribble.Feature;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.IOException;
import java.util.Iterator;
/**
*
*/
class FeatureTrackUtils {
private static volatile boolean isSearching;
/**
* Find the next/previous feature which lies outside chr:initStart-initEnd
* @param source
* @param chr
* @param initStart
* @param initEnd
* @param forward
* @return
* @throws IOException
*/
public static Feature nextFeature(FeatureSource source, String chr, int initStart, int initEnd, boolean forward) throws IOException {
Feature f = null;
int binSize = source.getFeatureWindowSize();
final Genome genome = GenomeManager.getInstance().getCurrentGenome();
if (forward) {
// Forward
int nextStart = initEnd;
String nextChr = chr;
while (nextChr != null) {
int chrLength = genome.getChromosome(nextChr).getLength();
while (nextStart < chrLength) {
int nextEnd = binSize > 0 ? nextStart + source.getFeatureWindowSize() : chrLength;
Iterator<Feature> iter = source.getFeatures(nextChr, nextStart, nextEnd);
if (iter != null) {
// The check on position should not be necessary, but not all implementations of getFeatures
// obey the contract to return features only in the interval.
while (iter.hasNext()) {
Feature feat = iter.next();
if (feat.getStart() > nextStart) {
return feat;
}
}
}
nextStart = nextEnd;
}
nextChr = genome.getNextChrName(nextChr);
nextStart = 0;
}
} else {
// Reverse
int nextEnd = initStart;
String nextChr = chr;
while (nextChr != null) {
while (nextEnd > 0) {
int nextStart = binSize > 0 ? Math.max(0, nextEnd - source.getFeatureWindowSize()) : 0;
Iterator<Feature> iter = source.getFeatures(nextChr, nextStart, nextEnd);
if (iter != null && iter.hasNext()) {
// The check on position should not be necessary, but not all implementations of getFeatures
// obey the contract to return features only in the interval.
Feature prevFeature = null;
while (iter.hasNext()) {
Feature feat = iter.next();
if (feat.getStart() < nextEnd) {
prevFeature = feat;
}
}
if (prevFeature != null) {
return prevFeature;
}
}
nextEnd = nextStart;
}
nextChr = genome.getPrevChrName(nextChr);
if (nextChr != null) {
nextEnd = genome.getChromosome(nextChr).getLength();
}
}
}
return f;
}
/**
* Find the next/previous feature, using FeatureSearcher. A cancellable dialog will be displayed so the user can cancel the
* search, null will be returned in that case.
* @param source
* @param chr
* @param initStart
* @param initEnd
* @param forward
* @param foundHandler Callback to invoke when searching is complete. Does not get called if search returns no result
* @return
* @throws IOException
*/
public static void nextFeatureSearch(FeatureSource source, String chr, int initStart, int initEnd, boolean forward,
final FeatureSearcher.IFeatureFound foundHandler) throws IOException{
//Only allow one to be shown at a time
if(isSearching()){
return;
}
Genome genome = GenomeManager.getInstance().getCurrentGenome();
//We search backwards by setting a negative searchIncrement
int searchIncrement = (initEnd - initStart) * (forward ? +1 : -1);
int start = initStart + searchIncrement;
IndefiniteProgressMonitor monitor = new IndefiniteProgressMonitor();
final FeatureSearcher searcher = new FeatureSearcher(source, genome, chr, start, monitor);
searcher.setSearchIncrement(searchIncrement);
final ActionListener cancelListener = new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
FeatureTrackUtils.isSearching = false;
searcher.cancel();
}
};
final CancellableProgressDialog dialog = CancellableProgressDialog.showCancellableProgressDialog(IGV.getMainFrame(), "Searching...", cancelListener, true, monitor);
dialog.getProgressBar().setIndeterminate(true);
monitor.addPropertyChangeListener(new PropertyChangeListener() {
@Override
public void propertyChange(PropertyChangeEvent evt) {
if(evt.getPropertyName().equals(ProgressMonitor.PROGRESS_PROPERTY) && (Integer) evt.getNewValue() >= 100){
FeatureTrackUtils.isSearching = false;
Iterator<? extends Feature> result = searcher.getResult();
if(result != null) foundHandler.processResult(result);
}
}
});
FeatureTrackUtils.isSearching = true;
LongRunningTask.submit(searcher);
}
private static boolean isSearching() {
return isSearching;
}
}