/*
* 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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* THE SOFTWARE.
*/
package org.broad.igv.methyl;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.Strand;
import org.broad.igv.track.WindowFunction;
/**
* @author Jim Robinson
* @date 4/19/12
*/
public class MethylScore implements LocusScore {
String chr;
int start;
int end;
Strand strand;
float percentMethylated;
int totalCount;
public MethylScore(String chr, int start, int end, Strand strand, float percentMethylated, int totalCount) {
this.chr = chr;
this.start = start;
this.end = end;
this.strand = strand;
this.percentMethylated = percentMethylated;
this.totalCount = totalCount;
}
public String getChr() {
return chr;
}
@Override
public String getContig() {
return chr;
}
public int getStart() {
return start;
}
public int getEnd() {
return end;
}
public Strand getStrand() {
return strand;
}
public float getScore() {
return percentMethylated;
}
public int getCount() {
return totalCount;
}
public void setStart(int start) {
this.start = start;
}
public void setEnd(int end) {
this.end = end;
}
/**
* Return a string to be used for popup text. The WindowFunction is passed
* in so it can be used t annotate the value. The LocusScore object itself
* does not "know" from what window function it was derived
*
* @param position Zero-based genome position
* @param mouseX
* @param windowFunction
* @return
*/
public String getValueString(double position, int mouseX, WindowFunction windowFunction) {
return percentMethylated + "%" + " [" + totalCount + "]" +
(strand == Strand.POSITIVE ? " (+)" : (strand == Strand.NEGATIVE ? " (-)" : ""));
}
}