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* The MIT License (MIT)
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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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* copies of the Software, and to permit persons to whom the Software is
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*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
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*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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package org.broad.igv.data.seg;
import org.apache.log4j.Logger;
import org.broad.igv.data.CharArrayList;
import java.io.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
/**
* This class encapuslates data for a single chromosome from a segmented
* dataset. Its batch purpose is to provide a single object that can
* easily be serialized and passed from server to IGV clients.
*
* @author jrobinso
*/
public class SegmentedChromosomeData {
private static Logger log = Logger.getLogger(SegmentedChromosomeData.class);
private String[] sampleNames;
Map<String, int[]> startLocations;
Map<String, int[]> endLocations;
Map<String, float[]> valueMap;
public SegmentedChromosomeData() {
}
public SegmentedChromosomeData(
String[] sampleNames,
Map<String, int[]> startLocations,
Map<String, int[]> endLocations,
Map<String, float[]> valueMap) {
this.sampleNames = sampleNames;
this.startLocations = startLocations;
this.endLocations = endLocations;
this.valueMap = valueMap;
}
/**
* Serialize this instance to a stream.
* <p/>
* Format:
* Sample names as a string :
* sample1 tab sample2 tabnetc... line-feed
* Followed by (for each sample)
* numberOfPoints (int)
* start locations (int array)
* end locations (int array)
* values (float array)
*
* @param stream stream to serialize to
*/
public void serialize(OutputStream stream) {
try {
DataOutputStream os = new DataOutputStream(new BufferedOutputStream(stream));
for (String sample : getSampleNames()) {
os.writeChars(sample);
os.writeChar('\t');
}
os.writeChar('\n');
for (String sample : getSampleNames()) {
int[] starts = startLocations.get(sample);
int[] ends = endLocations.get(sample);
float[] values = valueMap.get(sample);
int nPts = starts.length;
assert ends.length == nPts;
assert values.length == nPts;
os.writeInt(nPts);
for (int i = 0; i < nPts; i++) {
os.writeInt(starts[i]);
}
for (int i = 0; i < nPts; i++) {
os.writeInt(ends[i]);
}
for (int i = 0; i < nPts; i++) {
os.writeFloat(values[i]);
}
}
os.flush();
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* Initialize the object by deserializing the stream.
*
* @param stream
* @see #serialize
*/
public void deserialize(InputStream stream) {
startLocations = new HashMap();
endLocations = new HashMap();
valueMap = new HashMap();
try {
DataInputStream is = new DataInputStream(new BufferedInputStream(stream));
ArrayList<String> tmp = new ArrayList(100);
char c = 0;
try {
c = is.readChar();
} catch (EOFException e) {
// This is expected when there is no data available for this chromosome.
return;
}
while (c != '\n') {
CharArrayList chars = new CharArrayList(10);
while (c != '\t') {
chars.add(c);
c = is.readChar();
}
String nm = new String(chars.toArray()).trim();
tmp.add(nm);
c = is.readChar();
}
sampleNames = tmp.toArray(new String[]{});
for (String sample : sampleNames) {
int nPts = is.readInt();
int[] starts = new int[nPts];
for (int i = 0; i < nPts; i++) {
starts[i] = is.readInt();
}
int[] ends = new int[nPts];
for (int i = 0; i < nPts; i++) {
ends[i] = is.readInt();
}
float[] values = new float[nPts];
for (int i = 0; i < nPts; i++) {
values[i] = is.readFloat();
}
startLocations.put(sample, starts);
endLocations.put(sample, ends);
valueMap.put(sample, values);
}
}
catch (IOException e) {
log.error("Error loading segmented data", e);
}
}
public String[] getSampleNames() {
return sampleNames;
}
public int[] getStartLocations(String sampleName) {
return startLocations.get(sampleName);
}
public int[] getEndLocations(String sampleName) {
return endLocations.get(sampleName);
}
public float[] getValues(String sampleName) {
return valueMap.get(sampleName);
}
}