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Commit 6a6281b4 authored by tjc's avatar tjc
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update 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11649 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 661e27f3
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uk/ac/sanger/artemis/components/alignment/JamView.java
+ 139
− 52
View file @ 6a6281b4
......@@ -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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