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* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
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* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
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* 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.
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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,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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package org.broad.igv.feature;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.exceptions.ParserException;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.tribble.CodecFactory;
import org.broad.igv.feature.tribble.FeatureFileHeader;
import org.broad.igv.track.FeatureCollectionSource;
import org.broad.igv.track.FeatureTrack;
import org.broad.igv.track.TrackProperties;
import org.broad.igv.track.TrackType;
import org.broad.igv.ui.IGV;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import htsjdk.tribble.AbstractFeatureReader;
import htsjdk.tribble.AsciiFeatureCodec;
import htsjdk.tribble.Feature;
import htsjdk.tribble.FeatureCodec;
import java.io.BufferedReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
/**
* @author jrobinso
*/
public abstract class AbstractFeatureParser implements FeatureParser {
private static Logger log = Logger.getLogger(IGV.class);
protected int startBase = 0;
boolean gffTags = false;
/* An object to collection track properties, if specified in the feature file. */
protected TrackProperties trackProperties = null;
public static boolean canParse(ResourceLocator locator) {
return CodecFactory.getCodec(locator, null) != null;
}
/**
* Return an parser instance appropriate the the file type. Currently the filename
* is used to determine file type, this is fragile obviously but what is the alternative?
*/
public static FeatureParser getInstanceFor(ResourceLocator locator, Genome genome) {
FeatureCodec codec = CodecFactory.getCodec(locator, genome);
if (codec != null && codec instanceof AsciiFeatureCodec) {
return new FeatureCodecParser((AsciiFeatureCodec) codec, genome);
} else {
return null;
}
}
/**
*
* @param reader
* @return
*/
public List<htsjdk.tribble.Feature> loadFeatures(BufferedReader reader, Genome genome) {
return loadFeatures(reader, genome, -1);
}
/**
* Load all features in this file.
*
* @param reader
* @param genome
* @param maxLines
* @return
*/
public List<htsjdk.tribble.Feature> loadFeatures(BufferedReader reader, Genome genome, int maxLines) {
List<htsjdk.tribble.Feature> features = new ArrayList<htsjdk.tribble.Feature>();
String nextLine = null;
int maxLogErrors = 10;
int nErrors = 0;
int nLines = 0;
try {
while ((nextLine = reader.readLine()) != null) {
nextLine = nextLine.trim();
if (nextLine.length() == 0) continue;
nLines++;
if ((maxLines > 0) && (nLines > maxLines)) {
break;
}
try {
if (nextLine.startsWith("#")) {
if (nextLine.startsWith("#type")) {
String[] tokens = Globals.equalPattern.split(nextLine);
if (tokens.length > 1) {
try {
// TODO: type is not currently used, is there any reason to keep this?
TrackType type = TrackType.valueOf(tokens[1]);
} catch (Exception e) {
log.error("Error converting track type: " + tokens[1]);
}
}
} else if (nextLine.startsWith("#track") || nextLine.startsWith("track")) {
TrackProperties tp = new TrackProperties();
ParsingUtils.parseTrackLine(nextLine, tp);
setTrackProperties(tp);
if (tp.isGffTags()) {
gffTags = true;
}
} else if (nextLine.startsWith("#coords")) {
try {
String[] tokens = Globals.equalPattern.split(nextLine);
startBase = Integer.parseInt(tokens[1]);
} catch (Exception e) {
log.error("Error parsing coords line: " + nextLine, e);
}
} else if (nextLine.startsWith("#gffTags")) {
gffTags = true;
}
} else {
Feature feature = parseLine(nextLine);
if (feature != null) {
features.add(feature);
}
}
} catch (NumberFormatException e) {
if (nErrors < maxLogErrors) {
log.error("Number format error parsing line: " + nextLine, e);
}
nErrors++;
}
}
} catch (java.io.EOFException e) {
// This exception is due to a known bug with java zip library. Not
// in general a real error, and nothing we can do about it in any
// event.
return features;
} catch (Exception e) {
if (nextLine != null && nLines != 0) {
throw new ParserException(e.getMessage(), e, nLines, nextLine);
} else {
throw new RuntimeException(e);
}
}
// TODO -- why is this test here? This will break igvtools processing of expression files
//if (IGV.hasInstance() || Globals.isTesting()) {
FeatureDB.addFeatures(features, genome);
//}
return features;
}
abstract protected Feature parseLine(String nextLine);
/**
* Convenience method. Write a list of features out as a BED file
*
* @param features
* @param outputfile
*/
public static void dumpFeatures(List<IGVFeature> features, String outputfile) {
PrintWriter pw = null;
try {
pw = new PrintWriter(new FileWriter(outputfile));
pw.println("Header row");
for (IGVFeature gene : features) {
pw.print(gene.getName() + "\t");
pw.print(gene.getIdentifier() + "\t");
pw.print(gene.getChr() + "\t");
if (gene.getStrand() == Strand.POSITIVE) {
pw.print("+\t");
} else if (gene.getStrand() == Strand.NEGATIVE) {
pw.print("-\t");
} else {
pw.print(" \t");
}
pw.print(gene.getStart() + "\t");
pw.print(gene.getEnd() + "\t");
List<Exon> regions = gene.getExons();
pw.print(regions.size() + "\t");
for (Exon exon : regions) {
pw.print(exon.getStart() + ",");
}
pw.print("\t");
for (Exon exon : regions) {
pw.print(exon.getEnd() + ",");
}
pw.println();
}
} catch (IOException e) {
e.printStackTrace();
} finally {
if (pw != null) {
pw.close();
}
}
}
protected void setTrackProperties(TrackProperties trackProperties) {
this.trackProperties = trackProperties;
}
public TrackProperties getTrackProperties() {
return trackProperties;
}
}