/*
* 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.sam.AlignmentTrack.BisulfiteContext;
import java.awt.*;
/**
* @author benb
*
*/
public class BisulfiteBaseInfoNOMeseq extends BisulfiteBaseInfo {
public static Color GC_METH_COLOR = new Color(0,204,153);
public static Color GC_UNMETH_COLOR = new Color(255,127,191);
public static Color CG_METH_COLOR = Color.black;
public static Color CG_UNMETH_COLOR = Color.white;
public static final BisulfiteContext[] BISULFITE_CONTEXTS = new BisulfiteContext[]{BisulfiteContext.HCG, BisulfiteContext.GCH};
/**
* @param inReference
* @param baseAlignment
* @param block
* @param bisulfiteContext
*/
public BisulfiteBaseInfoNOMeseq(byte[] inReference, Alignment baseAlignment, AlignmentBlock block,
BisulfiteContext bisulfiteContext) {
super(inReference, baseAlignment, block, bisulfiteContext);
}
@Override
protected Color getContextColor(byte readbase,
BisulfiteContext bisulfiteContext) {
Color out = null;
if (bisulfiteContext.equals(BisulfiteContext.HCG))
{
out = (AlignmentUtils.compareBases((byte) 'T', readbase)) ? CG_UNMETH_COLOR : CG_METH_COLOR;
}
else
{
out = (AlignmentUtils.compareBases((byte) 'T', readbase)) ? GC_UNMETH_COLOR : GC_METH_COLOR;
}
return out;
}
@Override
protected BisulfiteContext contextIsMatching(byte[] reference, byte[] read, int idx,
BisulfiteContext bisulfiteContext) {
for (BisulfiteContext context : BISULFITE_CONTEXTS)
{
if (super.contextIsMatching(reference, read, idx,context) != null) return context;
}
return null;
}
@Override
protected double getBisulfiteSymmetricCytosineShift(BisulfiteContext item) {
// TODO Auto-generated method stub
return 0.0;
}
}