/*
* 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.sam;
import org.broad.igv.feature.Range;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
/**
* Convenience class for storing map from group -> list of alignments packed into rows
* Can contain discontinuous regions
* @author jacob
* @date 2014-Jan-10
*/
public class PackedAlignments extends LinkedHashMap<String, List<Row>> {
/**
* Set of ranges covered by this instance.
*/
private List<? extends Range> ranges;
PackedAlignments(List<? extends Range> ranges, Map<String, List<Row>> packedAlignments){
super(packedAlignments);
this.ranges = ranges;
}
/**
* Calculate the total number of levels across all groups.
* Since groups are stacked vertically, this is used to calculate height
* @return
*/
public int getNLevels() {
int intervalNLevels = 0;
for (List<Row> rows : this.values()) {
intervalNLevels += rows.size();
}
return intervalNLevels;
}
/**
* Whether any of the ranges contain this interval
* @param chr
* @param start
* @param end
* @return
*/
public boolean contains(String chr, int start, int end) {
for(Range range: this.ranges){
if(range.contains(chr, start, end)){
return true;
}
}
return false;
}
}