/*
* 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.synteny;
//~--- non-JDK imports --------------------------------------------------------
import org.broad.igv.feature.BasicFeature;
import org.broad.igv.feature.Strand;
/**
* // TODO -- consider implementing feature interface
*
* @author jrobinso
*/
public class BlastMapping extends BasicFeature {
private Block queryBlock;
private Block subjectBlock;
/**
* Constructs ...
*
* @param queryBlock
* @param subjectBlock
* @param percentIden
*/
public BlastMapping(Block queryBlock, Block subjectBlock, float percentIden) {
this.queryBlock = queryBlock;
this.subjectBlock = subjectBlock;
this.setStart(Math.min(queryBlock.getStart(), queryBlock.getEnd()));
this.setEnd(Math.max(queryBlock.getStart(), queryBlock.getEnd()));
this.setName("[" + subjectBlock.getContig() + ":" + subjectBlock.getStart() + "-" + subjectBlock.getEnd() + "]");
this.setScore(percentIden);
}
public Block getQueryBlock() {
return queryBlock;
}
public Block getSubjectBlock() {
return subjectBlock;
}
@Override
public String getChr() {
return queryBlock.getContig();
}
public Strand getStrand() {
return subjectBlock.getStrand();
}
public boolean containsQueryPosition(String contig, int position) {
return queryBlock.containsPosition(contig, position);
}
/**
* @author jrobinso
*/
public static class Block {
private String contig;
private int start;
private int end;
Strand strand;
/**
* Constructs ...
*
* @param contig
* @param start
* @param end
*/
public Block(String contig, int start, int end, Strand strand) {
this.contig = contig;
this.start = start;
this.end = end;
this.strand = strand;
}
public String getContig() {
return contig;
}
public int getStart() {
return start;
}
public int getEnd() {
return end;
}
public Strand getStrand() {
return strand;
}
public boolean containsPosition(String contig, int position) {
return this.contig.equals(contig) && position >= start && position < end;
}
}
}