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Commit 5bb4ff53 authored by tjc's avatar tjc
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jam updates 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11660 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 31957638
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uk/ac/sanger/artemis/components/alignment/JamView.java
+ 107
− 33
View file @ 5bb4ff53
......@@ -35,6 +35,8 @@ import java.awt.GridBagLayout;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.Stroke;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusEvent;
import java.awt.event.FocusListener;
import java.awt.event.ItemEvent;
......@@ -43,6 +45,8 @@ import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.WindowEvent;
import java.awt.event.WindowFocusListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
......@@ -53,6 +57,7 @@ import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JOptionPane;
......@@ -87,6 +92,7 @@ public class JamView extends JPanel
private EntryGroup entryGroup;
private JScrollPane jspView;
private JComboBox combo;
private JCheckBox checkBoxSingle;
private int nbasesInView;
private int laststart;
private int lastend;
......@@ -134,8 +140,6 @@ public class JamView extends JPanel
}
FontMetrics fm = getFontMetrics(getFont());
ALIGNMENT_PIX_PER_BASE = (int) (fm.stringWidth("A")*1.1);
System.out.println("Font size "+getFont().getSize());
}
/**
......@@ -200,8 +204,10 @@ public class JamView extends JPanel
String samtoolCmd = "";
if(System.getProperty("samtoolDir") != null)
samtoolCmd = System.getProperty("samtoolDir");
String cmd[] = { samtoolCmd+File.separator+"samtools",
"view", bam, refName+":"+start+"-"+end };
"view",
bam, refName+":"+start+"-"+end };
for(int i=0; i<cmd.length;i++)
System.out.print(cmd[i]+" ");
......@@ -339,49 +345,96 @@ public class JamView extends JPanel
Stroke originalStroke = g2.getStroke();
Stroke stroke =
new BasicStroke (2.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
new BasicStroke (1.2f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
int scaleHeight = 15;
for(int i=0; i<readsInView.size(); i++)
{
Read thisRead = readsInView.get(i);
Read nextRead = null;
if( (thisRead.flag & 0x0001) != 0x0001 ||
(thisRead.flag & 0x0008) == 0x0008 ) // not single read
Read nextRead = null;
if( (thisRead.flag & 0x0001) != 0x0001 || // read is not paired in sequencing
(thisRead.flag & 0x0008) == 0x0008 ) // mate is unmapped
{
if(checkBoxSingle.isSelected())
{
System.out.println("HERE "+thisRead.qname+
"\t\t pos "+thisRead.pos+"\tseq length "+thisRead.seq.length()+
"\tisize "+thisRead.isize);
int ypos = (getHeight() - scaleHeight) - thisRead.seq.length();
g2.setColor(Color.orange);
drawRead(g2, thisRead, pixPerBase, stroke, ypos);
}
continue;
}
int ypos = (getHeight() - scaleHeight) - ( Math.abs(thisRead.isize) );
if(i < readsInView.size()-1)
{
nextRead = readsInView.get(i+1);
i++;
}
if(nextRead != null &&
(nextRead.flag & 0x0001) == 0x0001 &&
(nextRead.flag & 0x0008) != 0x0008 )
{
nextRead = readsInView.get(++i);
if(thisRead.qname.equals(nextRead.qname))
{
if( (thisRead.flag & 0x0010) == 0x0010 &&
if( (thisRead.flag & 0x0010) == 0x0010 && // strand of the query (1 for reverse)
(nextRead.flag & 0x0010) == 0x0010 )
g2.setColor(Color.red);
else
g2.setColor(Color.blue);
int thisEnd = drawRead(g2, thisRead, pixPerBase, stroke, ypos)[1];
int nextStart = drawRead(g2, nextRead, pixPerBase, stroke, ypos)[0];
int ypos = (getHeight() - scaleHeight) - ( Math.abs(thisRead.isize) );
int thisStart = drawRead(g2, thisRead, pixPerBase, stroke, ypos);
int nextStart = drawRead(g2, nextRead, pixPerBase, stroke, ypos);
g2.setStroke(originalStroke);
g2.setColor(Color.LIGHT_GRAY);
g2.drawLine(thisStart, ypos, nextStart, ypos);
if(thisEnd < nextStart && (nextStart-thisEnd)*pixPerBase > 2.f)
{
g2.setStroke(originalStroke);
g2.setColor(Color.LIGHT_GRAY);
g2.drawLine((int)(thisEnd*pixPerBase), ypos, (int)(nextStart*pixPerBase), ypos);
}
}
else
{
drawLoneRead(g2, thisRead, ypos, pixPerBase, originalStroke, stroke);
i--;
}
}
else
{
drawLoneRead(g2, thisRead, ypos, pixPerBase, originalStroke, stroke);
}
}
}
/**
* Draw a read that apparently has a read mate that is not in view.
* @param g2
* @param thisRead
* @param ypos
* @param pixPerBase
* @param originalStroke
* @param stroke
*/
private void drawLoneRead(Graphics2D g2, Read thisRead, int ypos,
float pixPerBase, Stroke originalStroke, Stroke stroke)
{
boolean drawLine = true;
g2.setColor(Color.blue);
if(ypos <= 0)
{
ypos = thisRead.seq.length();
drawLine = false;
g2.setColor(Color.orange);
}
int thisEnd = drawRead(g2, thisRead, pixPerBase, stroke, ypos)[1];
if(drawLine)
{
g2.setStroke(originalStroke);
g2.setColor(Color.LIGHT_GRAY);
int nextStart = (int) ((thisRead.mpos-1)*pixPerBase);
g2.drawLine((int)(thisEnd*pixPerBase), ypos, nextStart, ypos);
}
}
private void drawBaseScale(Graphics2D g2, int start, int end, int ypos)
{
int startMark = (((int)(start/10))*10)+1;
......@@ -444,14 +497,14 @@ public class JamView extends JPanel
}
}
private int drawRead(Graphics2D g2, Read read,
private int[] drawRead(Graphics2D g2, Read read,
float pixPerBase, Stroke stroke, int ypos)
{
int thisStart = (int) ((read.pos-1)*pixPerBase);
int thisEnd = (int) (thisStart + (read.seq.length()*pixPerBase));
int thisStart = read.pos-1;
int thisEnd = thisStart + read.seq.length();
g2.setStroke(stroke);
g2.drawLine(thisStart, ypos, thisEnd, ypos);
return thisStart;
g2.drawLine((int)(thisStart*pixPerBase), ypos, (int)(thisEnd*pixPerBase), ypos);
return new int[] { thisStart, thisEnd };
}
public void addToPanel(final JPanel panel)
......@@ -474,6 +527,16 @@ public class JamView extends JPanel
gc.anchor = GridBagConstraints.FIRST_LINE_START;
topPanel.add(combo, gc);
checkBoxSingle = new JCheckBox("Single Reads");
checkBoxSingle.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
repaint();
}
});
topPanel.add(checkBoxSingle, gc);
panel.setPreferredSize(new Dimension(1000,500));
setLength(nbasesInView);
......@@ -486,10 +549,7 @@ public class JamView extends JPanel
jspView.getVerticalScrollBar().setValue(
jspView.getVerticalScrollBar().getMaximum());
setFocusable(true);
requestFocusInWindow();
addMouseListener(new MouseAdapter()
{
public void mouseClicked(MouseEvent e)
......@@ -522,6 +582,8 @@ public class JamView extends JPanel
}
});
setFocusable(true);
requestFocusInWindow();
addFocusListener(new FocusListener()
{
public void focusGained(FocusEvent fe) {}
......@@ -721,10 +783,22 @@ public class JamView extends JPanel
}
}
JamView view = new JamView(bam, reference, nbasesInView);
final JamView view = new JamView(bam, reference, nbasesInView);
JFrame frame = new JFrame("JAM");
frame.addWindowFocusListener(new WindowFocusListener()
{
public void windowGainedFocus(WindowEvent e)
{
view.requestFocus();
}
public void windowLostFocus(WindowEvent e){}
});
view.addToPanel((JPanel)frame.getContentPane());
frame.pack();
view.jspView.getVerticalScrollBar().setValue(
view.jspView.getVerticalScrollBar().getMaximum());
frame.setVisible(true);
}
}
uk/ac/sanger/artemis/components/alignment/Read.java
+ 14
− 0
View file @ 5bb4ff53
......@@ -35,4 +35,18 @@ class Read
int mpos; // leftmost Mate POSition
int isize; // inferred Insert SIZE
String seq; // query SEQuence; Ò=Ó for a match to the reference; n/N/. for ambiguity
public String toString()
{
return qname+"\t"+
flag+"\t"+
rname+"\t"+
pos+"\t"+
mapq+"\t"+
cigar+"\t"+
mrnm+"\t"+
mpos+"\t"+
isize+"\t"+
seq;
}
}
\ No newline at end of file
uk/ac/sanger/artemis/components/alignment/RunSamTools.java
+ 2
− 0
View file @ 5bb4ff53
......@@ -162,6 +162,8 @@ public class RunSamTools
pread.rname = fields[2];
pread.pos = Integer.parseInt(fields[3]);
pread.mapq = Short.parseShort(fields[4]);
pread.cigar = fields[5];
pread.mrnm = fields[6];
pread.mpos = Integer.parseInt(fields[7]);
pread.isize = Integer.parseInt(fields[8]);
pread.seq = fields[9];
......
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