/*
* The MIT License
*
* Copyright (c) 2009 The 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 picard.sam.markduplicates.util;
import java.util.List;
import java.util.Map;
import java.util.ArrayList;
import java.util.HashMap;
/**
* Map from String to ReadEnds object. Memory-based implementation. Used for MarkDuplicates.
*
* @author alecw@broadinstitute.org
*/
class MemoryBasedReadEndsForMarkDuplicatesMap implements ReadEndsForMarkDuplicatesMap {
/**
* Index of this list is sequence index. Value is map from String {read group id:read name} to ReadEnds.
* When a ReadEnds is put into this container, it is stored according to the sequenceIndex of the mate
*/
private final List<Map<String, ReadEndsForMarkDuplicates>> mapPerSequence = new ArrayList<Map<String, ReadEndsForMarkDuplicates>>();
public ReadEndsForMarkDuplicates remove(int mateSequenceIndex, String key) {
if (mateSequenceIndex >= mapPerSequence.size()) {
return null;
}
return mapPerSequence.get(mateSequenceIndex).remove(key);
}
public void put(int mateSequenceIndex, String key, ReadEndsForMarkDuplicates readEnds) {
while (mateSequenceIndex >= mapPerSequence.size()) {
mapPerSequence.add(new HashMap<String, ReadEndsForMarkDuplicates>());
}
mapPerSequence.get(mateSequenceIndex).put(key, readEnds);
}
public int size() {
int total = 0;
for (Map<String, ReadEndsForMarkDuplicates> map : mapPerSequence) {
total += map.size();
}
return total;
}
/**
* @return number of elements stored in RAM. Always <= size()
*/
public int sizeInRam() {
return size();
}
}