From 6a6281b474d48e9b7686bded5ab9a8d9c9d3c1ef Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 26 Aug 2009 11:36:05 +0000
Subject: [PATCH] update
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11649 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/JamView.java | 191 +++++++++++++-----
1 file changed, 139 insertions(+), 52 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/JamView.java b/uk/ac/sanger/artemis/components/alignment/JamView.java
index 8d8f33cde..b196ba9a5 100644
--- a/uk/ac/sanger/artemis/components/alignment/JamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/JamView.java
@@ -8,6 +8,8 @@ import java.awt.Dimension;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.Stroke;
@@ -17,7 +19,10 @@ import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
import java.io.BufferedReader;
+import java.io.File;
import java.io.IOException;
import java.io.StringReader;
import java.util.Collections;
@@ -28,6 +33,7 @@ import java.util.Vector;
import javax.swing.JComboBox;
import javax.swing.JFrame;
+import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.Scrollable;
@@ -87,10 +93,14 @@ public class JamView extends JPanel
e.printStackTrace();
}
}
+
readHeader();
+ // set font size
+ setFont(getFont().deriveFont(12.f));
final javax.swing.plaf.FontUIResource font_ui_resource =
- Options.getOptions().getFontUIResource();
+ new javax.swing.plaf.FontUIResource(getFont());
+ // Options.getOptions().getFontUIResource();
java.util.Enumeration keys = UIManager.getDefaults().keys();
while(keys.hasMoreElements())
@@ -101,12 +111,14 @@ public class JamView extends JPanel
UIManager.put(key, font_ui_resource);
}
FontMetrics fm = getFontMetrics(getFont());
- int boundWidth = fm.stringWidth("A")/5;
- ALIGNMENT_PIX_PER_BASE = fm.stringWidth("A")+boundWidth;
-
- System.out.println(getFont().getFontName());
+ ALIGNMENT_PIX_PER_BASE = (int) (fm.stringWidth("A")*1.1);
+
+ System.out.println("Font size "+getFont().getSize());
}
+ /**
+ * Read the BAM/SAM header
+ */
private void readHeader()
{
String cmd[] = { "/Users/tjc/BAM/samtools-0.1.5c/samtools",
@@ -150,10 +162,20 @@ public class JamView extends JPanel
}
}
- private void readFromBam(int start, int end, boolean pair_sort)
+ /**
+ * Read data from BAM/SAM file for a region.
+ * @param start
+ * @param end
+ * @param pair_sort
+ */
+ private void readFromBam(int start, int end)
{
String refName = (String) combo.getSelectedItem();
- String cmd[] = { "/Users/tjc/BAM/samtools-0.1.5c/samtools",
+
+ String samtoolCmd = "";
+ if(System.getProperty("samtoolDir") != null)
+ samtoolCmd = System.getProperty("samtoolDir");
+ String cmd[] = { samtoolCmd+File.separator+"samtools",
"view", bam, refName+":"+start+"-"+end };
for(int i=0; i<cmd.length;i++)
@@ -190,9 +212,6 @@ public class JamView extends JPanel
pread.seq = fields[9];
readsInView.add(pread);
}
-
- if(pair_sort)
- Collections.sort(readsInView, new ReadComparator());
}
catch (IOException e)
{
@@ -213,38 +232,54 @@ public class JamView extends JPanel
float pixPerBase = ((float)getWidth())/(float)(seqLength);
- if(pixPerBase >= ALIGNMENT_PIX_PER_BASE)
- drawAlignment(g2, seqLength, pixPerBase);
- else
- drawLineView(g2, seqLength, pixPerBase);
- }
-
- private void drawAlignment(Graphics2D g2, int seqLength, float pixPerBase)
- {
double x = jspView.getViewport().getViewRect().getX();
int start = (int) (seqLength * ( (float)x / (float)getWidth()));
int end = (int) (start + ((float)jspView.getViewport().getWidth() /
(float)pixPerBase));
if(laststart != start ||
- lastend != end)
- readFromBam(start, end, false);
+ lastend != end)
+ {
+ try
+ {
+ readFromBam(start, end);
+ if(pixPerBase < ALIGNMENT_PIX_PER_BASE)
+ Collections.sort(readsInView, new ReadComparator());
+ }
+ catch(OutOfMemoryError ome)
+ {
+ JOptionPane.showMessageDialog(this, "Out of Memory");
+ return;
+ }
+ }
laststart = start;
lastend = end;
+ if(pixPerBase >= ALIGNMENT_PIX_PER_BASE)
+ drawBaseAlignment(g2, seqLength, pixPerBase, start, end);
+ else
+ drawLineView(g2, seqLength, pixPerBase, start, end);
+ }
+
+ private void drawBaseAlignment(Graphics2D g2, int seqLength,
+ float pixPerBase, int start, int end)
+ {
+ FontMetrics fm = getFontMetrics(getFont());
+ int ypos = fm.getHeight();
- int ypos = 1;
-
+ drawBaseScale(g2, start, end, ypos);
boolean draw[] = new boolean[readsInView.size()];
for(int i=0; i<readsInView.size(); i++)
draw[i] = false;
+ ypos+=6;
+
for(int i=0; i<readsInView.size(); i++)
{
if (!draw[i])
{
Read thisRead = readsInView.get(i);
- ypos = ypos + 10;
+ ypos+=10;
drawSequence(g2, thisRead, pixPerBase, ypos);
draw[i] = true;
@@ -259,14 +294,27 @@ public class JamView extends JPanel
{
drawSequence(g2, nextRead, pixPerBase, ypos);
draw[j] = true;
- break;
+ thisEnd = nextRead.pos+nextRead.seq.length();
}
}
}
}
}
+
+ if(ypos > getHeight())
+ {
+ setPreferredSize(new Dimension(getWidth(), ypos));
+ revalidate();
+ }
}
+ /**
+ * Draw the query sequence
+ * @param g2
+ * @param read
+ * @param pixPerBase
+ * @param ypos
+ */
private void drawSequence(Graphics2D g2, Read read, float pixPerBase, int ypos)
{
if ((read.flag & 0x0001) != 0x0001 ||
@@ -285,20 +333,8 @@ public class JamView extends JPanel
}
- private void drawLineView(Graphics2D g2, int seqLength, float pixPerBase)
- {
- double x = jspView.getViewport().getViewRect().getX();
- int start = (int) (seqLength * ( (float)x / (float)getWidth()));
- int end = (int) (start + ((float)jspView.getViewport().getWidth() /
- (float)pixPerBase));
-
- if(laststart != start ||
- lastend != end)
- readFromBam(start, end, true);
-
- laststart = start;
- lastend = end;
-
+ private void drawLineView(Graphics2D g2, int seqLength, float pixPerBase, int start, int end)
+ {
drawScale(g2, start, end, pixPerBase);
Stroke originalStroke = g2.getStroke();
@@ -346,6 +382,19 @@ public class JamView extends JPanel
}
}
+ private void drawBaseScale(Graphics2D g2, int start, int end, int ypos)
+ {
+ int startMark = (((int)(start/10))*10)+1;
+
+ for(int i=startMark; i<end; i+=10)
+ {
+ int xpos = (i-1)*ALIGNMENT_PIX_PER_BASE;
+ g2.drawString(Integer.toString(i), xpos, ypos);
+
+ xpos+=(ALIGNMENT_PIX_PER_BASE/2);
+ g2.drawLine(xpos, ypos+1, xpos, ypos+5);
+ }
+ }
private void drawScale(Graphics2D g2, int start, int end, float pixPerBase)
{
@@ -405,10 +454,11 @@ public class JamView extends JPanel
return thisStart;
}
- public void showJFrame()
+ public void addToPanel(final JPanel panel)
{
- JFrame frame = new JFrame("JamTool");
-
+ JPanel topPanel = new JPanel(new GridBagLayout());
+ GridBagConstraints gc = new GridBagConstraints();
+
combo = new JComboBox(seqNames);
combo.setEditable(false);
combo.addItemListener(new ItemListener()
@@ -418,23 +468,35 @@ public class JamView extends JPanel
setZoomLevel(JamView.this.nbasesInView);
}
});
+ gc.fill = GridBagConstraints.NONE;
+ gc.anchor = GridBagConstraints.FIRST_LINE_START;
+ topPanel.add(combo, gc);
- frame.setPreferredSize(new Dimension(1000,500));
+ panel.setPreferredSize(new Dimension(1000,500));
setLength(nbasesInView);
jspView = new JScrollPane(this, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
- JPanel panel = (JPanel) frame.getContentPane();
-
panel.setLayout(new BorderLayout());
- panel.add(combo, BorderLayout.NORTH);
+ panel.add(topPanel, BorderLayout.NORTH);
panel.add(jspView, BorderLayout.CENTER);
- frame.pack();
+
+ jspView.getVerticalScrollBar().setValue(
+ jspView.getVerticalScrollBar().getMaximum());
setFocusable(true);
requestFocusInWindow();
+ addMouseListener(new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent e)
+ {
+ System.out.println("CLICK");
+ JamView.this.requestFocus();
+ }
+ });
+
addKeyListener(new KeyAdapter()
{
public void keyPressed(final KeyEvent event)
@@ -464,8 +526,6 @@ public class JamView extends JPanel
public void focusGained(FocusEvent fe) {}
public void focusLost(FocusEvent fe) {}
});
-
- frame.setVisible(true);
}
private int getBaseAtStartOfView()
@@ -515,7 +575,10 @@ public class JamView extends JPanel
System.out.println(pixPerBase+" "+ALIGNMENT_PIX_PER_BASE);
if(pixPerBase > ALIGNMENT_PIX_PER_BASE)
+ {
pixPerBase = ALIGNMENT_PIX_PER_BASE;
+ jspView.getVerticalScrollBar().setValue(0);
+ }
Dimension d = new Dimension();
d.setSize((seqLength*pixPerBase), 800.d);
setPreferredSize(d);
@@ -645,12 +708,36 @@ public class JamView extends JPanel
public static void main(String[] args)
{
String bam = args[0];
- int nbasesInView = Integer.parseInt(args[1]);
+ int nbasesInView = 1000;
String reference = null;
- //if(args.length > 2)
- // reference = args[2];
+ for(int i=0;i<args.length; i++)
+ {
+ if(args[i].equals("-a"))
+ bam = args[++i];
+ else if(args[i].equals("-r"))
+ reference = args[++i];
+ else if(args[i].equals("-v"))
+ nbasesInView = Integer.parseInt(args[++i]);
+ else if(args[i].equals("-s"))
+ System.setProperty("samtoolDir", args[++i]);
+ else if(args[i].startsWith("-h"))
+ {
+ System.out.println("-h\t show help");
+
+ System.out.println("-a\t BAM/SAM file to display");
+ System.out.println("-r\t reference file (optional)");
+ System.out.println("-v\t number of bases to display in the view (optional)");
+ System.out.println("-s\t samtool directory");
+
+ System.exit(0);
+ }
+ }
+
JamView view = new JamView(bam, reference, nbasesInView);
- view.showJFrame();
+ JFrame frame = new JFrame("JAM");
+ view.addToPanel((JPanel)frame.getContentPane());
+ frame.pack();
+ frame.setVisible(true);
}
}
--
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