/*
* 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.data.seg;
import java.io.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
/**
* @author jrobinso
*/
public class SegmentedBinaryLocalReader implements SegmentedBinaryReader {
String filePath;
List<String> chromosomes;
List<String> sampleNames;
Map<String, String> dataFileMap = new HashMap();
Map<String, String> attrs;
public SegmentedBinaryLocalReader(String filePath) {
this.filePath = filePath;
}
/**
* Return the set of sample names in this data set
*
* @return
*/
public List<String> getSampleNames() {
if (sampleNames == null) {
sampleNames = readAsStrings("data/samples.txt");
}
return sampleNames;
}
public String getStringAttribute(String key) {
return getAttributes().get(key);
}
public Map<String, String> getAttributes() {
if (attrs == null) {
attrs = new HashMap();
List<String> lines = readAsStrings("data/attributes.txt");
if (lines != null) {
for (String kv : lines) {
String[] tokens = kv.split("=");
attrs.put(tokens[0], tokens[1]);
}
}
}
return attrs;
}
public SegmentedChromosomeData getChromosomeData(String chr) {
return readChromosomeData(chr);
}
/**
* Return the segment start locations for the sample and chromosome
*
* @param sample the sample name
* @param chr the chromosome name
* @return array of end locations
*/
public int[] getStartLocations(String sample, String chr) {
String entryName = "data/" + sample + "/" + chr + "/starts.bin";
return readAsInts(entryName);
}
/**
* Return the segment end locations for the sample and chromosome
*
* @param sample the sample name
* @param chr the chromosome name
* @return array of end locations
*/
public int[] getEndLocations(String sample, String chr) {
String entryName = "data/" + sample + "/" + chr + "/ends.bin";
return readAsInts(entryName);
}
/**
* Return the data values for the given sample and chromosom
*
* @param sample the sample name
* @param chr the chromosome name
* @return data values
*/
public float[] getValues(String sample, String chr) {
String entryName = "data/" + sample + "/" + chr + "/values.bin";
return readAsFloats(entryName);
}
private List<String> readAsStrings(String entryName) {
List<String> strings = new ArrayList();
ZipFile zipFile = null;
try {
zipFile = new ZipFile(new File(filePath));
ZipEntry entry = zipFile.getEntry(entryName);
if (entry == null) {
return null;
}
BufferedReader br = new BufferedReader(new InputStreamReader(zipFile.getInputStream(entry)));
String nextLine = null;
while ((nextLine = br.readLine()) != null) {
strings.add(nextLine.trim());
}
} catch (IOException e) {
e.printStackTrace();
} finally {
try {
zipFile.close();
} catch (IOException e) {
// Close quietly
}
}
return strings;
}
private SegmentedChromosomeData readChromosomeData(String chr) {
ZipFile zipFile = null;
BufferedInputStream is = null;
try {
String entryName = "data/" + chr + ".bin";
zipFile = new ZipFile(new File(filePath));
ZipEntry entry = zipFile.getEntry(entryName);
if (entry == null) {
return null;
}
is = new BufferedInputStream(zipFile.getInputStream(entry));
SegmentedChromosomeData cd = new SegmentedChromosomeData();
cd.deserialize(is);
return cd;
} catch (IOException e) {
e.printStackTrace();
return null;
} finally {
try {
zipFile.close();
} catch (IOException e) {
// Close quietly
}
}
}
/**
* Read the contents of a zip entry as an array of ints.
*
* @param entryName name of the entry
* @return array of ints
*/
private int[] readAsInts(String entryName) {
ZipFile zipFile = null;
try {
zipFile = new ZipFile(new File(filePath));
ZipEntry entry = zipFile.getEntry(entryName);
if (entry == null) {
return null;
}
DataInputStream is = new DataInputStream(
new BufferedInputStream(zipFile.getInputStream(entry)));
int nInts = (int) (entry.getSize() / 4);
int[] ints = new int[nInts];
for (int i = 0; i <
nInts; i++) {
ints[i] = is.readInt();
}
return ints;
} catch (IOException e) {
e.printStackTrace();
return null;
} finally {
try {
zipFile.close();
} catch (IOException e) {
// close quietly
}
}
}
/**
* Read the content of a zip entry as an array of floats.
*
* @param entryName name of the entry
* @return contents as an array of floats
*/
private float[] readAsFloats(String entryName) {
ZipFile zipFile = null;
try {
zipFile = new ZipFile(new File(filePath));
ZipEntry entry = zipFile.getEntry(entryName);
if (entry == null) {
return null;
}
DataInputStream is = new DataInputStream(
new BufferedInputStream(zipFile.getInputStream(entry)));
int nInts = (int) (entry.getSize() / 4);
float[] values = new float[nInts];
for (int i = 0; i <
nInts; i++) {
values[i] = is.readFloat();
}
return values;
} catch (IOException e) {
e.printStackTrace();
return null;
} finally {
try {
zipFile.close();
} catch (IOException e) {
}
}
}
}