From 68f450749289a7a42847d22ad3dddfa168b49f85 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 23 Sep 2009 14:47:32 +0000
Subject: [PATCH] provide an alternative stack view of the reads
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11882 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/JamView.java | 112 +++++++++++++++---
1 file changed, 96 insertions(+), 16 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/JamView.java b/uk/ac/sanger/artemis/components/alignment/JamView.java
index 9ce145ac2..0b07938ba 100644
--- a/uk/ac/sanger/artemis/components/alignment/JamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/JamView.java
@@ -120,6 +120,7 @@ public class JamView extends JPanel
private JComboBox combo;
private JCheckBox checkBoxSingle;
private JCheckBox checkBoxSNPs;
+ private JCheckBox checkBoxStackView;
private FeatureDisplay feature_display;
private Selection selection;
@@ -144,8 +145,6 @@ public class JamView extends JPanel
private JPopupMenu popup;
// use the picard library otherwise call samtools
public static boolean PICARD = true;
-
- private boolean painting = true;
public JamView(String bam,
@@ -338,9 +337,6 @@ public class JamView extends JPanel
*/
protected void paintComponent(Graphics g)
{
- if(!painting)
- return;
-
super.paintComponent(g);
Graphics2D g2 = (Graphics2D)g;
@@ -384,7 +380,8 @@ public class JamView extends JPanel
else
readFromBam(start, end);
- Collections.sort(readsInView, new SAMRecordComparator());
+ if(!checkBoxStackView.isSelected())
+ Collections.sort(readsInView, new SAMRecordComparator());
setCursor(cdone);
}
catch(OutOfMemoryError ome)
@@ -399,7 +396,12 @@ public class JamView extends JPanel
if(pixPerBase*3 >= ALIGNMENT_PIX_PER_BASE)
drawBaseAlignment(g2, seqLength, pixPerBase, start, end);
else
- drawLineView(g2, seqLength, pixPerBase, start, end);
+ {
+ if(!checkBoxStackView.isSelected())
+ drawLineView(g2, seqLength, pixPerBase, start, end);
+ else
+ drawStackView(g2, seqLength, pixPerBase, start, end);
+ }
}
@@ -435,8 +437,11 @@ public class JamView extends JPanel
* @param start
* @param end
*/
- private void drawBaseAlignment(Graphics2D g2, int seqLength,
- float pixPerBase, final int start, final int end)
+ private void drawBaseAlignment(Graphics2D g2,
+ int seqLength,
+ float pixPerBase,
+ final int start,
+ final int end)
{
ruler.start = start;
ruler.end = end;
@@ -655,6 +660,69 @@ public class JamView extends JPanel
drawYScale(g2, start, pixPerBase);
}
+
+ private void drawStackView(Graphics2D g2,
+ int seqLength,
+ float pixPerBase,
+ int start,
+ int end)
+ {
+ drawSelectionRange(g2, pixPerBase,start, end);
+ if(isShowScale())
+ drawScale(g2, start, end, pixPerBase);
+
+ BasicStroke stroke = new BasicStroke(
+ 1.3f,
+ BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_MITER);
+
+ int scaleHeight;
+ if(isShowScale())
+ scaleHeight = 15;
+ else
+ scaleHeight = 0;
+
+ int ypos = (getHeight() - scaleHeight);
+ int lastEnd = 0;
+
+ g2.setColor(Color.blue);
+ for(int i=0; i<readsInView.size(); i++)
+ {
+ SAMRecord samRecord = readsInView.get(i);
+
+ int recordStart;
+ int recordEnd;
+ if(samRecord.getAlignmentEnd() > samRecord.getAlignmentStart())
+ {
+ recordStart = samRecord.getAlignmentStart();
+ recordEnd = samRecord.getAlignmentEnd();
+ }
+ else
+ {
+ recordStart = samRecord.getAlignmentEnd();
+ recordEnd = samRecord.getAlignmentStart();
+ }
+
+ if(lastEnd < recordStart)
+ {
+ ypos = (getHeight() - scaleHeight)-2;
+ lastEnd = recordEnd;
+ }
+ else
+ ypos = ypos-2;
+
+ drawRead(g2, samRecord, pixPerBase, stroke, ypos);
+
+ if(ypos > getHeight())
+ {
+ Dimension d = getPreferredSize();
+ d.setSize(getPreferredSize().getWidth(), ypos);
+ setPreferredSize(d);
+ revalidate();
+ }
+ }
+ }
+
/**
* Draw a read that apparently has a read mate that is not in view.
* @param g2
@@ -848,8 +916,8 @@ public class JamView extends JPanel
if (Character.toUpperCase(refSeq[refPos-thisStart]) != readSeq[readPos])
{
- g2.drawLine((int) ((thisStart + i) * pixPerBase), ypos + 2,
- (int) ((thisStart + i) * pixPerBase), ypos - 2);
+ g2.drawLine((int) ((refPos) * pixPerBase), ypos + 2,
+ (int) ((refPos) * pixPerBase), ypos - 2);
}
}
@@ -885,7 +953,8 @@ public class JamView extends JPanel
GridBagConstraints gc = new GridBagConstraints();
// auto hide top panel
- final JCheckBox buttonAutoHide = new JCheckBox("Auto-hide", autohide);
+ final JCheckBox buttonAutoHide = new JCheckBox("Hide", autohide);
+ buttonAutoHide.setToolTipText("Auto-Hide");
final MouseMotionListener mouseMotionListener = new MouseMotionListener()
{
public void mouseDragged(MouseEvent event)
@@ -957,8 +1026,20 @@ public class JamView extends JPanel
}
});
topPanel.add(checkBoxSNPs, gc);
+
+ checkBoxStackView = new JCheckBox("Stack");
+ checkBoxStackView.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ laststart = -1;
+ lastend = -1;
+ repaint();
+ }
+ });
+ topPanel.add(checkBoxStackView, gc);
- if (feature_display == null)
+ if(feature_display == null)
{
final JTextField baseText = new JTextField(10);
JButton goTo = new JButton("GoTo:");
@@ -1392,14 +1473,13 @@ public class JamView extends JPanel
SAMRecord pr2 = (SAMRecord) o2;
int cmp = pr1.getReadName().compareTo(pr2.getReadName());
-
if(cmp == 0)
{
if(pr1.getAlignmentStart() < pr2.getAlignmentStart())
return -1;
else
return 1;
- }
+ }
return cmp;
}
}
@@ -1507,7 +1587,7 @@ public class JamView extends JPanel
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.out.println("-s\t samtool directory");*/
System.exit(0);
}
--
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