/*
* Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
*
* 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.
*
* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
* WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
* WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
* PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
* OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
* TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
* OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
* ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
* THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
* SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*/
package org.broad.igv.sam.reader;
import org.broad.igv.PreferenceManager;
import org.broad.igv.sam.Alignment;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import htsjdk.tribble.readers.AsciiLineReader;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
/**
* Created by IntelliJ IDEA.
* User: jrobinso
* Date: Oct 1, 2009
* Time: 7:09:37 PM
* To change this template use File | Settings | File Templates.
*/
public class ReadGroupFilter {
private Set<String> filteredReadGroups;
private ReadGroupFilter(Set<String> filteredReadGroups) {
this.filteredReadGroups = filteredReadGroups;
}
public boolean filterAlignment(Alignment alignment) {
return filteredReadGroups.contains(alignment.getReadGroup());
}
static Map<String, ReadGroupFilter> filterCache = new HashMap();
public static synchronized ReadGroupFilter getFilter() {
PreferenceManager samPrefs = PreferenceManager.getInstance();
if (samPrefs.getAsBoolean(PreferenceManager.SAM_FILTER_ALIGNMENTS)) {
String filterURL = samPrefs.get(PreferenceManager.SAM_FILTER_URL);
ReadGroupFilter filter = filterURL == null ? null : filterCache.get(filterURL);
if (filter == null && filterURL != null && filterURL.trim().length() > 0) {
Set<String> readGroups = new HashSet();
AsciiLineReader reader = null;
try {
reader = ParsingUtils.openAsciiReader(new ResourceLocator(filterURL));
String nextLine;
while ((nextLine = reader.readLine()) != null) {
readGroups.add(nextLine.trim());
}
filter = new ReadGroupFilter(readGroups);
filterCache.put(filterURL, filter);
}
catch (Exception e) {
MessageUtils.showMessage("Error reading read filter list: " + e.getMessage());
}
}
return filter;
}
return null;
}
}