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*
* Copyright (c) 2007-2015 Broad Institute
*
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*
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package org.broad.igv.data.cufflinks;
import org.apache.commons.math.stat.StatUtils;
import org.broad.igv.Globals;
import org.broad.igv.data.BasicScore;
import org.broad.igv.data.DataSource;
import org.broad.igv.data.GenomeSummaryData;
import org.broad.igv.feature.FeatureUtils;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.track.TrackType;
import org.broad.igv.track.WindowFunction;
import org.broad.igv.util.collections.DownsampledDoubleArrayList;
import java.util.*;
/**
* @author jrobinso
* Date: 3/8/13
* Time: 2:52 PM
*/
public class CufflinksDataSource implements DataSource {
double dataMax;
double dataMin;
Map<String, List<LocusScore>> values;
Map<String, String> chrAliasMap;
List<LocusScore> wholeGenomeScores;
private int sampleIndex = 0;
/** Constructor for files with multiple samples. Cufflinks files have multiple
* columns at end (just FPKM files as of this writing) representing each sample
* @param sampleIndex
* @param allValues
* @param genome
*/
public CufflinksDataSource(int sampleIndex, List<FPKMValue> allValues, Genome genome){
this(getSampleValues(sampleIndex, allValues), genome);
this.sampleIndex = sampleIndex;
}
private static List<? extends LocusScore> getSampleValues(int sampleIndex, List<FPKMValue> allValues) {
List<FPKMSampleValue> sampleValueList = new ArrayList<FPKMSampleValue>(allValues.size());
for(FPKMValue value: allValues){
sampleValueList.add(value.getSampleValue(sampleIndex));
}
return sampleValueList;
}
public CufflinksDataSource(List<? extends LocusScore> valueList, Genome genome) {
chrAliasMap = new HashMap<String, String>();
values = new HashMap<String, List<LocusScore>>();
DownsampledDoubleArrayList sampledData = sampleValues(valueList, genome);
// Sort
for (List<LocusScore> chrValues : values.values()) {
FeatureUtils.sortFeatureList(chrValues);
}
double[] sd = sampledData.toArray();
if (sd.length > 0) {
dataMin = Math.min(0, StatUtils.percentile(sd, 5));
dataMax = StatUtils.percentile(sd, 95);
} else {
dataMin = 0;
dataMax = 100;
}
calculateWholeGenomeScores(genome);
}
private void calculateWholeGenomeScores(Genome genome){
GenomeSummaryData genomeSummaryData = new GenomeSummaryData(genome, new String[]{"*"});
for (Map.Entry<String, List<LocusScore>> entry : values.entrySet()) {
String chr = entry.getKey();
List<LocusScore> scores = entry.getValue();
int[] positions = new int[scores.size()];
float[] values = new float[scores.size()];
for (int i = 0; i < scores.size(); i++) {
LocusScore s = scores.get(i);
positions[i] = s.getStart();
values[i] = s.getScore();
}
Map<String, float[]> tmp = new HashMap<String, float[]>(1);
tmp.put("*", values);
genomeSummaryData.addData(chr, positions, tmp);
}
int[] positions = genomeSummaryData.getLocations();
float[] values = genomeSummaryData.getData("*");
wholeGenomeScores = new ArrayList<LocusScore>(positions.length);
for (int i = 0; i < positions.length; i++) {
wholeGenomeScores.add(new BasicScore(positions[i], positions[i] + 1, values[i]));
}
}
/**
* Sample the first 10,000 values to set scale
* Also separate data into chromosomes
* @param valueList
* @param genome
*/
private DownsampledDoubleArrayList sampleValues(List<? extends LocusScore> valueList, Genome genome){
DownsampledDoubleArrayList sampledData = new DownsampledDoubleArrayList(5000, 10000);
for (LocusScore val : valueList) {
String chr = val.getChr();
List<LocusScore> chrValues = values.get(chr);
if (chrValues == null) {
chrValues = new ArrayList<LocusScore>();
values.put(chr, chrValues);
if (genome != null) {
String alias = genome.getCanonicalChrName(chr);
chrAliasMap.put(alias, chr);
}
}
sampledData.add(val.getScore());
chrValues.add(val);
}
return sampledData;
}
@Override
public double getDataMax() {
return dataMax;
}
@Override
public double getDataMin() {
return dataMin;
}
@Override
public List<LocusScore> getSummaryScoresForRange(String chr, int startLocation, int endLocation, int zoom) {
if (chr.equals(Globals.CHR_ALL)) {
return wholeGenomeScores;
}
if (chrAliasMap.containsKey(chr)) {
return values.get(chrAliasMap.get(chr));
} else {
return values.get(chr);
}
}
@Override
public TrackType getTrackType() {
return TrackType.FPKM;
}
@Override
public void setWindowFunction(WindowFunction statType) {
// Ignored
}
@Override
public boolean isLogNormalized() {
return false;
}
@Override
public WindowFunction getWindowFunction() {
return null;
}
@Override
public Collection<WindowFunction> getAvailableWindowFunctions() {
return Arrays.asList(WindowFunction.none);
}
@Override
public void dispose() {
}
}