/*
* 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.data.seg;
import org.broad.igv.Globals;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.track.TrackType;
import org.broad.igv.util.ResourceLocator;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* @author jrobinso
*/
public class SegmentedBinaryDataSet implements SegmentedDataSet {
SegmentedBinaryReader reader;
private long lastRefreshTime = 0;
/**
* Assume data is non-log value until suggested otherwise by the precense
* of negative numbers. TODO This is a fragile assumption, the user should
* input this information directly.
*/
Boolean logNormalized = null;
private List<String> sampleNames = null;
/**
* Map of [heading -> [chr -> [list of segmentsCache]]]
*/
Map<String, Map<String, List<LocusScore>>> segmentsCache = new HashMap();
Map<String, SegmentedChromosomeData> chrData = new HashMap();
TrackType type = TrackType.COPY_NUMBER;
public SegmentedBinaryDataSet(ResourceLocator locator) {
reader = new SegmentedBinaryLocalReader(locator.getPath());
try {
type = TrackType.valueOf(reader.getStringAttribute("type"));
}
catch (Exception e) {
//ignore;
}
try {
String logNormalizedString = reader.getStringAttribute("logNormalized");
if (logNormalizedString != null) {
logNormalized = logNormalizedString.equals("true");
}
} catch (Exception exception) {
// ignore
}
}
// TODO -- the synchronized keyword can be removed with the async whole genome load
public List<LocusScore> getSegments(String heading, String chr) {
Map<String, List<LocusScore>> chrSegments = segmentsCache.get(heading);
if (chrSegments == null) {
chrSegments = new HashMap();
segmentsCache.put(heading, chrSegments);
}
List<LocusScore> segments = chrSegments.get(chr);
if (segments == null) {
SegmentedChromosomeData cd = chrData.get(chr);
if (cd == null) {
cd = reader.getChromosomeData(chr);
chrData.put(chr, cd);
}
int[] startLocations = cd.getStartLocations(heading);
int[] endLocations = cd.getEndLocations(heading);
float[] values = cd.getValues(heading);
if (startLocations == null || startLocations.length == 0) {
return null;
}
if (logNormalized == null) {
logNormalized = false;
for (int i = 0; i <
values.length; i++) {
if (values[i] < 0) {
logNormalized = true;
break;
}
}
}
assert (startLocations.length == endLocations.length);
assert (endLocations.length == values.length);
segments = new ArrayList(startLocations.length);
for (int i = 0; i <
startLocations.length; i++) {
segments.add(new Segment(startLocations[i], endLocations[i], values[i]));
chrSegments.put(chr, segments);
}
}
return segments;
}
public List<String> getSampleNames() {
if (sampleNames == null) {
sampleNames = reader.getSampleNames();
}
return sampleNames;
}
public TrackType getType() {
return type;
}
// TODO -- check for negative numbers
public boolean isLogNormalized() {
return logNormalized == null ? true : logNormalized;
}
public double getDataMax(String chr) {
return 3;
}
public double getDataMin(String chr) {
return -3;
}
public synchronized List<LocusScore> getWholeGenomeScores(String heading) {
return getSegments(heading, Globals.CHR_ALL);
}
public static class ChromosomeChunk {
}
}