SnpPanel.java 6.57 KiB
/* SnpPanel
*
* created: 2010
*
* This file is part of Artemis
*
* Copyright(C) 2010 Genome Research Limited
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or(at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
*/
package uk.ac.sanger.artemis.components.alignment;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.geom.GeneralPath;
import java.util.List;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JTextField;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import net.sf.samtools.AlignmentBlock;
import net.sf.samtools.SAMRecord;
public class SnpPanel extends AbstractGraphPanel
{
private static final long serialVersionUID = 1L;
private Bases bases;
private float minBaseQualityFilter = 0;
private int snpCount[];
public SnpPanel(final BamView bamView, Bases bases)
{
super();
this.bamView = bamView;
this.bases = bases;
initPopupMenu(popup);
JMenuItem configure = new JMenuItem("Filter by Base Quality...");
configure.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// filter by base quality
JTextField filterField = new JTextField(Float.toString(minBaseQualityFilter));
int status = JOptionPane.showConfirmDialog(SnpPanel.this, filterField, "Base Quality Filter",
JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE);
if(status == JOptionPane.CANCEL_OPTION)
return;
try
{
minBaseQualityFilter = Float.parseFloat(filterField.getText());
}
catch(NumberFormatException nfe)
{
JOptionPane.showMessageDialog(SnpPanel.this, nfe.getMessage(),
"Number Format", JOptionPane.WARNING_MESSAGE);
}
}
});
popup.add(configure);
}
/**
* Override
*/
protected void paintComponent(Graphics g)
{
super.paintComponent(g);
Graphics2D g2 = (Graphics2D)g;
if(bases == null || nBins == 0 || snpCount == null)
return;
drawSelectionRange(g2, pixPerBase, start, end, getHeight(), Color.PINK);
draw(g2);
drawMax(g2);
}
protected void init(BamView bamView, float pixPerBase, int start, int end)
{
this.bamView = bamView;
setPixPerBase(pixPerBase);
setStartAndEnd(start, end);
if(autoWinSize)
{
windowSize = (bamView.getBasesInView()/300);
userWinSize = windowSize;
}
else
windowSize = userWinSize;
if(windowSize < 1)
windowSize = 1;
nBins = Math.round((end-start+1.f)/windowSize);
max = 0;
snpCount = null;
}
protected void draw(Graphics2D g2)
{
g2.setColor(Color.red);
g2.setStroke(new BasicStroke(1.f));
if(windowSize == 1)
{
GeneralPath shape = new GeneralPath();
shape.moveTo(0,getHeight());
for(int i=0; i<snpCount.length; i++)
{
float xpos1 = ((i*windowSize) )*pixPerBase;
float xpos2 = ((i*windowSize) + windowSize)*pixPerBase;
shape.lineTo(xpos1,getHeight());
shape.lineTo(xpos1, getHeight() - (((float)snpCount[i]/(float)max)*getHeight()));
shape.lineTo(xpos2,
getHeight() - (((float)snpCount[i]/(float)max)*getHeight()));
shape.lineTo(xpos2,getHeight());
}
shape.lineTo(getWidth(),getHeight());
g2.fill(shape);
}
else
{
for(int i=1; i<snpCount.length; i++)
{
int x0 = (int) (((i*windowSize) - windowSize/2.f)*pixPerBase);
int y0 = (int) (getHeight() - (((float)snpCount[i-1]/(float)max)*getHeight()));
int x1 = (int) ((((i+1)*windowSize) - windowSize/2.f)*pixPerBase);
int y1 = (int) (getHeight() - (((float)snpCount[i]/(float)max)*getHeight()));
g2.drawLine(x0, y0, x1, y1);
}
}
}
/**
* Display the SNPs for the given read.
* @param g2
* @param thisRead
* @param pixPerBase
* @param ypos
*/
protected void addRecord(SAMRecord thisRead, int offset)
{
if(snpCount == null)
{
snpCount = new int[nBins];
for(int i=0; i<snpCount.length; i++)
snpCount[i] = 0;
}
int thisStart = thisRead.getAlignmentStart();
int thisEnd = thisRead.getAlignmentEnd();
// use alignment blocks of the contiguous alignment of
// subsets of read bases to a reference sequence
List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
byte[] phredQuality = thisRead.getBaseQualities();
try
{
char[] refSeq = bases.getSubSequenceC(
new Range(thisStart+offset, thisEnd+offset), Bases.FORWARD);
byte[] readSeq = thisRead.getReadBases();
offset = offset - bamView.getBaseAtStartOfView();
for(int i=0; i<blocks.size(); i++)
{
AlignmentBlock block = blocks.get(i);
for(int j=0; j<block.getLength(); j++)
{
int readPos = block.getReadStart()-1+j;
int refPos = block.getReferenceStart()+j;
if (Character.toUpperCase(refSeq[refPos-thisStart]) != readSeq[readPos])
{
if(phredQuality[readPos] < minBaseQualityFilter)
continue;
int bin = (int)((refPos+offset) / windowSize);
if(bin < 0 || bin > nBins-1)
continue;
snpCount[bin]+=1;
if(snpCount[bin] > max)
max = snpCount[bin];
}
}
}
}
catch (OutOfRangeException e)
{
e.printStackTrace();
}
}
}