/*
* 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
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.data.rnai;
//~--- JDK imports ------------------------------------------------------------
import java.util.*;
/**
* A singleton class for managing RNAi haripin scores. The class provides a structure to store
* hairpin scores keyed by batch ID and gene name, and a method to retrieve them. Hairpin scores
* are typically added during parsing of the hairpin file, and retrieved to render a RNAi track
* or populate popup text.
*
* @author jrobinso
*/
public class RNAIHairpinCache {
private static RNAIHairpinCache theInstance = new RNAIHairpinCache();
/**
* A map for containing hairpin scores keyd by batchId and gene name.
* The first key (outer map) is batchId. Inner key is gene name.
* Each gene can multiple hairpin scores (often 5) which are help in
* a list.
*/
Map<String, Map<String, Collection<RNAIHairpinValue>>> hairpinScores;
private RNAIHairpinCache() {
hairpinScores = new HashMap();
}
/**
* Method description
*
* @return
*/
public static RNAIHairpinCache getInstance() {
return theInstance;
}
/**
* Add a haripin score for a particular batch and gene to the hairpin data
* structure.
*
* @param batchId
* @param geneName
* @param score
*/
public void addHairpinScore(String batchId, String geneName, RNAIHairpinValue score) {
Map<String, Collection<RNAIHairpinValue>> scoresForBatch = hairpinScores.get(batchId);
if (scoresForBatch == null) {
scoresForBatch = new HashMap();
hairpinScores.put(batchId, scoresForBatch);
}
Collection<RNAIHairpinValue> scoresForGene = scoresForBatch.get(geneName);
if (scoresForGene == null) {
scoresForGene = new TreeSet(new RNAIHairpinNameComparator());
scoresForBatch.put(geneName, scoresForGene);
}
scoresForGene.add(score);
}
/**
* Return the list of scores associated with the specified batch and gene.
*
* @param batchId
* @param geneName
* @return the scores, or null if there are no matches.
*/
public Collection<RNAIHairpinValue> getHairpinScores(String batchId, String geneName) {
Map<String, Collection<RNAIHairpinValue>> scoresForBatch = hairpinScores.get(batchId);
if (scoresForBatch == null) {
return null;
} else {
return scoresForBatch.get(geneName);
}
}
private class RNAIHairpinNameComparator implements Comparator<RNAIHairpinValue> {
public int compare(RNAIHairpinValue hp1, RNAIHairpinValue hp2) {
if (hp1.getName().length() < hp2.getName().length())
return -1;
return hp1.getName().compareTo(hp2.getName());
}
}
}