/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.feature.genome;
import htsjdk.samtools.seekablestream.SeekableStream;
import org.apache.log4j.Logger;
import org.broad.igv.feature.Cytoband;
import org.broad.igv.util.stream.IGVSeekableStreamFactory;
import java.io.IOException;
import java.util.*;
/**
* Represents a sequence database composed of plain text files with no white space, one per chromosome, in a directory.
* This is the original IGV "sequence" format, replaced in favor of indexed fasta files.
*
* @author jrobinso
* @Date 8/8/11
*/
public class IGVSequence implements Sequence {
private static Logger log = Logger.getLogger(IGVSequence.class);
private String dirPath;
private Map<String, String> chrFileNameCache = new HashMap();
private HashMap<String, Integer> chromosomeLengths;
private List<String> chromosomeNames;
public IGVSequence(String dirPath) {
if (!dirPath.endsWith("/")) {
dirPath = dirPath + "/";
}
this.dirPath = dirPath;
}
public byte[] getSequence(String chr, int start, int end) {
String fn = getChrFileName(chr);
String seqFile = dirPath + fn;
SeekableStream is = null;
try {
is = IGVSeekableStreamFactory.getInstance().getStreamFor(seqFile);
byte[] bytes = new byte[end - start];
is.seek(start);
is.read(bytes);
return bytes;
} catch (Exception ex) {
log.error("Error reading genome sequence from: " + seqFile, ex);
return null;
} finally {
if (is != null) {
try {
is.close();
} catch (IOException ex) {
log.error("Error closing sequence file.", ex);
}
}
}
}
@Override
public byte getBase(String chr, int position) {
throw new RuntimeException("getBase() is not implemented for class " + FastaIndexedSequence.class.getName());
}
@Override
public List<String> getChromosomeNames() {
return chromosomeNames;
}
@Override
public int getChromosomeLength(String chrname) {
return chromosomeLengths.get(chrname);
}
/**
* Get a "legal" chromosome file name from the chr name. This method supports "old" style .genome
* files.
*
* @param chr
* @return
*/
private String getChrFileName(String chr) {
String chrFN = chrFileNameCache.get(chr);
if (chrFN == null) {
chrFN = chr;
for (Map.Entry<String, String> entry : illegalChar.entrySet()) {
chrFN = chrFN.replaceAll(entry.getValue(), entry.getKey());
}
chrFN += ".txt";
chrFileNameCache.put(chr, chrFN);
}
return chrFN;
}
/**
* Generate chromosomes from the list of cytobands. This method is provided for backward compatibility for
* pre V2.1 genomes.
*
* @param chrCytoMap
* @param chromosomesAreOrdered
*/
public void generateChromosomes(LinkedHashMap<String, List<Cytoband>> chrCytoMap, boolean chromosomesAreOrdered) {
chromosomeLengths = new HashMap<String, Integer>();
chromosomeNames = new ArrayList<String>(chrCytoMap.size());
for (Map.Entry<String, List<Cytoband>> entry : chrCytoMap.entrySet()) {
String chr = entry.getKey();
chromosomeNames.add(chr);
List<Cytoband> cytobands = entry.getValue();
int length = cytobands.get(cytobands.size() - 1).getEnd();
chromosomeLengths.put(chr, length);
}
if (!chromosomesAreOrdered) {
Collections.sort(chromosomeNames, ChromosomeNameComparator.get());
}
}
static Map<String, String> illegalChar = new HashMap();
static {
illegalChar.put("_qm_", "\\?");
illegalChar.put("_fbr_", "\\[");
illegalChar.put("_rbr_", "]");
illegalChar.put("_fsl_", "/");
illegalChar.put("_bsl_", "\\\\");
illegalChar.put("_eq_", "=");
illegalChar.put("_pl_", "\\+");
illegalChar.put("_lt_", "<");
illegalChar.put("_gt_", ">");
illegalChar.put("_co_", ":");
illegalChar.put("_sc_", ";");
illegalChar.put("_dq_", "\"");
illegalChar.put("_sq_", "'");
illegalChar.put("_st_", "\\*");
illegalChar.put("_pp_", "\\|");
}
}