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* Copyright (c) 2007-2015 Broad Institute
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* of this software and associated documentation files (the "Software"), to deal
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* The above copyright notice and this permission notice shall be included in
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*
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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package org.broad.igv.data;
import org.apache.log4j.Logger;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.tdf.Accumulator;
import org.broad.igv.track.WindowFunction;
import org.broad.igv.util.collections.FloatArrayList;
import org.broad.igv.util.collections.IntArrayList;
import java.util.*;
/**
* Summarize (using a windowing function) numeric data points which are associated
* with locations on a genome. Stored by chromosome
* @author jrobinso
*/
public class GenomeSummaryData {
private static Logger log = Logger.getLogger(GenomeSummaryData.class);
// Genome coordinates are in kilobases
private static final double locationUnit = 1000.0;
/**
* Number of virtual pixels
*/
int nPixels = 1000;
Genome genome;
String[] samples;
/**
* Chromosome name -> [sample name -> list of data values]
*/
Map<String, Map<String, FloatArrayList>> dataMap = new HashMap<String, Map<String, FloatArrayList>>();
/**
* Chromosome name -> list of start locations
*/
Map<String, IntArrayList> locationMap;
/**
* start locations of currently relevant ordered list of chromosomes, spanning whole genomes
*/
int[] locations;
/**
* sample name -> list of sample data
*/
Map<String, float[]> data;
int nDataPts = 0;
Set<String> skippedChromosomes = new HashSet<String>();
/**
* Scale in kilobases / pixel
*/
double scale;
public GenomeSummaryData(Genome genome, String[] samples) {
this.genome = genome;
this.samples = samples;
scale = (genome.getNominalLength() / locationUnit) / nPixels;
List<String> chrNames = genome.getLongChromosomeNames();
locationMap = new HashMap<String, IntArrayList>();
dataMap = new HashMap<String, Map<String, FloatArrayList>>();
for (String chr : chrNames) {
locationMap.put(chr, new IntArrayList(nPixels / 10));
dataMap.put(chr, new HashMap<String, FloatArrayList>());
for (String s : samples) {
dataMap.get(chr).put(s, new FloatArrayList(nPixels / 10));
}
}
}
/**
* Changes scale of summary, ie zoom in or out
* Mainly for testing, can't use after adding any data
* @param scale
*/
void setScale(double scale){
if(nDataPts > 0) throw new IllegalStateException("Can't alter scale after adding data");
this.scale = scale;
nPixels = (int) (((double) this.genome.getNominalLength() / locationUnit) / scale);
}
/**
* Add data to be condensed for the whole genome view
*
* @param chr
* @param locs Genomic positions
* @param sampleData Map of sample name -> array of values.
*/
public void addData(String chr, int[] locs, Map<String, float[]> sampleData) {
IntArrayList locations = locationMap.get(chr);
if (locations == null) {
if (!skippedChromosomes.contains(chr)) {
skippedChromosomes.add(chr);
log.info("Skipping data for: " + chr);
}
return;
}
int lastPixel = -1;
int lastGenomeLocation = -1;
Map<String, Accumulator> dataPoints = new HashMap<String, Accumulator>();
for (int i = 0; i < locs.length; i++) {
int genomeLocation = genome.getGenomeCoordinate(chr, locs[i]);
int pixel = (int) (genomeLocation / scale);
if (lastPixel >= 0 && pixel != lastPixel) {
locations.add(lastGenomeLocation);
finishLastLocation(chr, dataPoints);
}
for (String s : samples) {
float[] data = sampleData.get(s);
Accumulator dp = dataPoints.get(s);
if (dp == null) {
dp = new Accumulator(WindowFunction.mean);
dataPoints.put(s, dp);
}
try {
dp.add(1, data[i], null);
} catch (Exception e) {
log.error("Error adding to GenomeSummaryData", e);
}
}
lastPixel = pixel;
lastGenomeLocation = genomeLocation;
}
locations.add(lastGenomeLocation);
finishLastLocation(chr, dataPoints);
}
/**
* Mark the previous genomic location as having been completely summarized
* @param chr
* @param dataPoints Map sample -> accumulator, which stored data temporarily being accumulated at a given genome location
*/
private void finishLastLocation(String chr, Map<String, Accumulator> dataPoints) {
nDataPts++;
for (String s : dataMap.get(chr).keySet()) {
Accumulator dp = dataPoints.get(s);
dp.finish();
dataMap.get(chr).get(s).add(dp.getValue());
}
dataPoints.clear();
}
public int[] getLocations() {
if (locations == null) {
createDataArrays();
}
return locations;
}
public float[] getData(String sample) {
if (!data.containsKey(sample)) {
createDataArrays();
}
return data.get(sample);
}
/**
* Recalculate:
* 0. Start locations for plotting. Shared across all samples
* 1. Summary data for a given sample, across all stored chromosomes
*/
private synchronized void createDataArrays() {
locations = new int[nDataPts];
int offset = 0;
List<String> chrNames = genome.getLongChromosomeNames();
for (String chr : chrNames) {
int[] chrLocs = locationMap.get(chr).toArray();
System.arraycopy(chrLocs, 0, locations, offset, chrLocs.length);
offset += chrLocs.length;
}
data = new HashMap<String, float[]>();
for (String s : samples) {
float[] sampleData = new float[nDataPts];
offset = 0;
for (String chr : chrNames) {
float[] chrData = dataMap.get(chr).get(s).toArray();
System.arraycopy(chrData, 0, sampleData, offset, chrData.length);
offset += chrData.length;
}
data.put(s, sampleData);
}
locationMap.clear();
dataMap.clear();
}
}