/*
* 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.
*/
package org.broad.igv.feature.tribble;
import org.broad.igv.feature.FeatureType;
import org.broad.igv.renderer.SpliceJunctionRenderer;
import org.broad.igv.track.TrackProperties;
import org.broad.igv.track.TrackType;
import org.broad.igv.util.ParsingUtils;
import htsjdk.tribble.AsciiFeatureCodec;
import htsjdk.tribble.Feature;
import htsjdk.tribble.exception.CodecLineParsingException;
import htsjdk.tribble.readers.LineIterator;
/**
* @author jrobinso
* @date Aug 5, 2010
*/
public abstract class UCSCCodec<T extends Feature> extends AsciiFeatureCodec<T> {
GFFCodec.GFF3Helper tagHelper = new GFFCodec.GFF3Helper();
protected boolean gffTags = false;
FeatureFileHeader header;
FeatureType featureType;
protected UCSCCodec(Class myClass) {
super(myClass);
}
protected UCSCCodec(Class myClass, FeatureType featureType) {
super(myClass);
this.featureType = featureType;
}
/**
* @param reader
* @return
*/
@Override
public Object readActualHeader(LineIterator reader) {
String line;
try {
while (reader.hasNext()) {
line = reader.peek();
if (line.startsWith("#") || line.startsWith("track") ||
line.startsWith("browser")) {
readHeaderLine(line);
reader.next();
} else {
break;
}
}
return header;
} catch (Exception e) {
throw new CodecLineParsingException("Error parsing header", e);
}
}
/**
* Extract information from the header line.
* Side effects: Calling this will create a new header field
* if one is null. In general, should check whether the line
* is a header line or not first.
*
* @param line
* @return True iff any information was retrieved.
*/
protected boolean readHeaderLine(String line) {
//Header line found, may not have any content
if (header == null) {
header = new FeatureFileHeader();
}
if (line.startsWith("#type")) {
String[] tokens = line.split("=");
if (tokens.length > 1) {
try {
header.setTrackType(TrackType.valueOf(tokens[1]));
} catch (Exception e) {
// log.error("Error converting track type: " + tokens[1]);
}
}
} else if (line.startsWith("#track") || line.startsWith("track")) {
TrackProperties tp = new TrackProperties();
ParsingUtils.parseTrackLine(line, tp);
header.setTrackProperties(tp);
if(gffTags == false) gffTags = tp.isGffTags();
Class rendererClass = tp.getRendererClass();
if (rendererClass != null && rendererClass.isAssignableFrom(SpliceJunctionRenderer.class)) {
featureType = FeatureType.SPLICE_JUNCTION ;
}
} else if (line.toLowerCase().contains("#gfftags")) {
gffTags = true;
} else {
return false;
}
return true;
}
public Feature decodeLoc(String line) {
return decode(line);
}
public void setGffTags(boolean gffTags) {
this.gffTags = gffTags;
}
public boolean isGffTags() {
return this.gffTags;
}
public void setFeatureType(org.broad.igv.feature.FeatureType featureType) {
this.featureType = featureType;
}
}