/*
* 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 org.broad.igv.feature.Chromosome;
import java.util.Collections;
import java.util.Comparator;
import java.util.LinkedHashMap;
import java.util.List;
/**
* For comparing chromosomes. We order by "important" vs "unimportant".
* The idea being there are main chromosomes (chr1...chrX, chrM) and
* sometimes many smaller contigs. "important" is determined
* by size, set in the constructor, or else by the name.
* <p/>
* If one chromosome is important and the other is not, it is
* considered "less" (so it is sorted earlier), otherwise
* they are sorted by name.
* User: jacob
* Date: 2012-Aug-16
*/
public class ChromosomeComparator implements Comparator<Chromosome> {
/**
*
*/
private final int minSizeImportant;
/**
* @param minSizeImportant The minimum size to be considered "important" by default.
* Note that a contig might still be considered important if it is named chrXXX
*/
public ChromosomeComparator(int minSizeImportant) {
this.minSizeImportant = minSizeImportant;
}
@Override
public int compare(Chromosome o1, Chromosome o2) {
boolean o1import = isImportant(o1);
boolean o2import = isImportant(o2);
boolean checkNames = (o1import == o2import);
if (checkNames) {
return ChromosomeNameComparator.get().compare(o1.getName(), o2.getName());
} else if (o1import) {
return -1;
} else {
return +1;
}
}
private boolean isImportant(Chromosome chromo) {
if (chromo.getLength() > minSizeImportant) return true;
if (chromo.getName().toLowerCase().startsWith("chr") &&
chromo.getName().length() <= 6) return true;
return false;
}
public static LinkedHashMap<String, Chromosome> sortChromosomeList(List<Chromosome> tmpChromos, int minBig,
LinkedHashMap<String, Chromosome> chromosomeMap) {
chromosomeMap.clear();
Collections.sort(tmpChromos, new ChromosomeComparator(minBig));
for (int ii = 0; ii < tmpChromos.size(); ii++) {
Chromosome chromo = tmpChromos.get(ii);
chromo.setIndex(ii);
chromosomeMap.put(chromo.getName(), chromo);
}
return chromosomeMap;
}
}