/*
* 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.track;
import org.apache.log4j.Logger;
import org.broad.igv.feature.AbstractFeatureParser;
import org.broad.igv.feature.FeatureParser;
import org.broad.igv.feature.IGVFeature;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.HttpUtils;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.collections.LRUCache;
import htsjdk.tribble.Feature;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Properties;
/**
* User: jrobinso
* Date: Jan 31, 2010
*/
public class FeatureDirSource implements FeatureSource {
static Logger log = Logger.getLogger(FeatureDirSource.class);
LRUCache<String, List<Feature>> featureCache;
Properties fileMap;
String rootDir;
ResourceLocator rootLocator;
Genome genome;
public FeatureDirSource(ResourceLocator locator, Genome genome) throws IOException {
this.genome = genome;
featureCache = new LRUCache(3);
rootLocator = locator;
setRootDir(locator.getPath());
fileMap = new Properties();
InputStream propStream = ParsingUtils.openInputStreamGZ(locator);
fileMap.load(propStream);
propStream.close();
}
public Class getFeatureClass() {
return IGVFeature.class;
}
public List<Feature> getFeatures(final String chr) {
List<Feature> features = featureCache.get(chr);
if (features == null) {
final String filename = fileMap.getProperty(chr);
if (filename != null) {
BufferedReader reader = null;
String path = rootDir + "/" + filename;
try {
log.info("Loading " + path);
// Load features here
ResourceLocator loc = new ResourceLocator(path);
FeatureParser fp = AbstractFeatureParser.getInstanceFor(loc, genome);
reader = ParsingUtils.openBufferedReader(loc);
features = fp.loadFeatures(reader, genome);
featureCache.put(chr, features);
} catch (IOException ex) {
MessageUtils.showMessage("Error loading file: " + path + " (" + ex.toString() + ")");
log.info("Error loading feature file: " + filename, ex);
} finally {
if (reader != null) {
try {
reader.close();
} catch (IOException e) {
}
}
}
}
}
return featureCache.get(chr);
}
public List<LocusScore> getCoverageScores(String chr, int i, int i1, int zoom) {
return null;
}
public int getFeatureWindowSize() {
return 0;
}
public void setFeatureWindowSize(int size) {
// ignored
}
public Iterator<Feature> getFeatures(String chr, int start, int end) {
List<Feature> features = getFeatures(chr);
return features == null ? Collections.<Feature>emptyList().iterator() : features.iterator();
}
private void setRootDir(String path) {
if (HttpUtils.isRemoteURL(path)) {
int idx = path.lastIndexOf('/');
rootDir = path.substring(0, idx);
} else {
rootDir = (new File(path)).getParent();
}
}
}