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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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package org.broad.igv.data;
//~--- non-JDK imports --------------------------------------------------------
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.track.TrackProperties;
import org.broad.igv.track.TrackType;
import org.broad.igv.util.ArrayHeapIntSorter;
import org.broad.igv.util.IntComparator;
import org.broad.igv.util.collections.FloatArrayList;
import org.broad.igv.util.collections.IntArrayList;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
/**
* @author jrobinso
*/
public class WiggleDataset implements Dataset {
Genome genome;
private String name;
private TrackProperties trackProperties;
Map<String, IntArrayList> startLocationsMap = new HashMap();
Map<String, IntArrayList> endLocationsMap = new HashMap();
Map<String, FloatArrayList> dataMap = new HashMap();
float dataMin = 0;
float dataMax = 0;
float percent90 = 0;
float percent10 = 0;
private Map<String, Integer> longestFeatureMap;
private TrackType type = TrackType.OTHER;
public WiggleDataset(Genome genome, String name) {
this.genome = genome;
this.name = name;
this.trackProperties = new TrackProperties();
}
public void sort(Set<String> unsortedChromosomes) {
for (String c : unsortedChromosomes) {
String chr = genome.getCanonicalChrName(c);
final IntArrayList starts = startLocationsMap.get(chr);
int sz = starts.size();
int[] indices = new int[sz];
for (int i = 0; i < indices.length; i++) {
indices[i] = i;
}
(new ArrayHeapIntSorter()).sort(indices, new IntComparator() {
public int compare(int arg0, int arg1) {
return starts.get(arg0) - starts.get(arg1);
}
});
int[] sortedStarts = reorder(indices, startLocationsMap.get(chr));
int[] sortedEnds = reorder(indices, endLocationsMap.get(chr));
float[] sortedData = reorder(indices, dataMap.get(chr));
startLocationsMap.put(chr, new IntArrayList(sortedStarts));
endLocationsMap.put(chr, new IntArrayList(sortedEnds));
dataMap.put(chr, new FloatArrayList(sortedData));
}
}
private float[] reorder(int[] indices, FloatArrayList values) {
int size = values.size();
if (indices.length != size) {
throw new IllegalArgumentException(
"Index array length not equal to size");
}
float[] reorderedValues = new float[size];
for (int i = 0; i < size; i++) {
reorderedValues[i] = values.get(indices[i]);
}
return reorderedValues;
}
private int[] reorder(int[] indices, IntArrayList values) {
int size = values.size();
if (indices.length != size) {
throw new IllegalArgumentException(
"Index array length not equal to size");
}
int[] reorderedValues = new int[size];
for (int i = 0; i < size; i++) {
reorderedValues[i] = values.get(indices[i]);
}
return reorderedValues;
}
public void addDataChunk(String chr, IntArrayList starts, IntArrayList ends, FloatArrayList data) {
IntArrayList startLocations = this.startLocationsMap.get(chr);
if (startLocations == null) {
this.startLocationsMap.put(chr, starts);
} else {
startLocations.addAll(starts);
}
if (ends != null) {
IntArrayList endLocations = this.endLocationsMap.get(chr);
if (endLocations == null) {
this.endLocationsMap.put(chr, ends);
} else {
endLocations.addAll(ends);
}
}
FloatArrayList dataArray = this.dataMap.get(chr);
if (dataArray == null) {
this.dataMap.put(chr, data);
} else {
dataArray.addAll(data);
}
float[] d = data.toArray();
for (int i = 0; i < d.length; i++) {
dataMax = Math.max(dataMax, d[i]);
dataMin = Math.min(dataMin, d[i]);
}
}
public float getDataMin() {
return dataMin;
}
public float getDataMax() {
return dataMax;
}
public String getName() {
return name;
}
public TrackType getType() {
return type;
}
public String[] getChromosomes() {
return startLocationsMap.keySet().toArray(new String[]{});
}
boolean containsChromosome(String chr){
String datChr = this.genome != null ? genome.getCanonicalChrName(chr) : chr;
return startLocationsMap.containsKey(datChr);
}
public String[] getTrackNames() {
return new String[]{getName()};
}
public int[] getStartLocations(String chr) {
IntArrayList startLocations = this.startLocationsMap.get(chr);
if (startLocations == null) {
return null;
} else {
return startLocations.toArray();
}
}
public int[] getEndLocations(String chr) {
IntArrayList endLocations = this.endLocationsMap.get(chr);
if (endLocations == null) {
return null;
} else {
return endLocations.toArray();
}
}
public float[] getData(String heading, String chr) {
FloatArrayList data = this.dataMap.get(chr);
if (data == null) {
return null;
} else {
return data.toArray();
}
}
public String[] getFeatureNames(String chr) {
return null;
}
public boolean isLogNormalized() {
return false;
}
public void setName(String name) {
this.name = name;
}
public TrackProperties getTrackProperties() {
return trackProperties;
}
public Integer getLongestFeature(String chr) {
return longestFeatureMap == null ? 1000 :
longestFeatureMap.containsKey(chr) ? longestFeatureMap.get(chr) : 1;
}
public void setLongestFeatureMap(Map<String, Integer> longestFeatureMap) {
this.longestFeatureMap = longestFeatureMap;
}
public void setType(TrackType type) {
this.type = type;
}
public void setPercent10(float percent10) {
this.percent10 = percent10;
}
public float getPercent10() {
return percent10;
}
public void setPercent90(float percent90) {
this.percent90 = percent90;
}
public float getPercent90() {
return percent90;
}
}