From 5bb4ff532f2b650ab558fea7cc17ef9cbec1a1e2 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 27 Aug 2009 13:59:25 +0000
Subject: [PATCH] jam updates
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11660 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/JamView.java | 140 +++++++++++++-----
.../artemis/components/alignment/Read.java | 14 ++
.../components/alignment/RunSamTools.java | 2 +
3 files changed, 123 insertions(+), 33 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/JamView.java b/uk/ac/sanger/artemis/components/alignment/JamView.java
index db4ed9d49..dc34be498 100644
--- a/uk/ac/sanger/artemis/components/alignment/JamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/JamView.java
@@ -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);
}
}
diff --git a/uk/ac/sanger/artemis/components/alignment/Read.java b/uk/ac/sanger/artemis/components/alignment/Read.java
index 02d765664..56d701165 100644
--- a/uk/ac/sanger/artemis/components/alignment/Read.java
+++ b/uk/ac/sanger/artemis/components/alignment/Read.java
@@ -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
diff --git a/uk/ac/sanger/artemis/components/alignment/RunSamTools.java b/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
index 47dda18fc..ddad42a32 100644
--- a/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
+++ b/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
@@ -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];
--
GitLab