From 99d232760cad85a580551c576cf7705726c28568 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Sat, 3 Oct 2009 13:23:32 +0000
Subject: [PATCH] rename JamView and fix zooming-in when running bam viewer
outside artemis interface
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11937 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../alignment/{JamView.java => BamView.java} | 37 ++++++++++---------
.../components/alignment/CoveragePanel.java | 4 +-
.../alignment/PairedReadComparator.java | 2 +-
3 files changed, 22 insertions(+), 21 deletions(-)
rename uk/ac/sanger/artemis/components/alignment/{JamView.java => BamView.java} (98%)
diff --git a/uk/ac/sanger/artemis/components/alignment/JamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
similarity index 98%
rename from uk/ac/sanger/artemis/components/alignment/JamView.java
rename to uk/ac/sanger/artemis/components/alignment/BamView.java
index 5556e681d..6329e244b 100644
--- a/uk/ac/sanger/artemis/components/alignment/JamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -112,7 +112,7 @@ import uk.ac.sanger.artemis.util.Document;
import uk.ac.sanger.artemis.util.DocumentFactory;
import uk.ac.sanger.artemis.util.OutOfRangeException;
-public class JamView extends JPanel
+public class BamView extends JPanel
implements Scrollable, DisplayAdjustmentListener, SelectionChangeListener
{
private static final long serialVersionUID = 1L;
@@ -171,7 +171,7 @@ public class JamView extends JPanel
private JPopupMenu popup;
- public JamView(String bam,
+ public BamView(String bam,
String reference,
int nbasesInView)
{
@@ -478,7 +478,7 @@ public class JamView extends JPanel
try
{
readFromBamPicard(start, end);
- if(!isStackView || pixPerBase*3 >= ALIGNMENT_PIX_PER_BASE)
+ if(!isStackView || pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
Collections.sort(readsInView, new SAMRecordComparator());
setCursor(cdone);
@@ -492,7 +492,7 @@ public class JamView extends JPanel
laststart = start;
lastend = end;
- if(pixPerBase*3 >= ALIGNMENT_PIX_PER_BASE)
+ if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
drawBaseAlignment(g2, seqLength, pixPerBase, start, end);
else
{
@@ -521,7 +521,7 @@ public class JamView extends JPanel
private int getMaxBasesInPanel(int seqLength)
{
if(feature_display == null)
- return seqLength+nbasesInView/2;
+ return seqLength+nbasesInView/3;
else
return seqLength+nbasesInView;
}
@@ -564,8 +564,6 @@ public class JamView extends JPanel
refSeq =
bases.getSubSequence(new Range(refSeqStart, seqEnd), Bases.FORWARD).toUpperCase();
- System.out.println(refSeqStart +" "+ seqEnd+" "+refSeq);
-
g2.setColor(lightGrey);
g2.fillRect(0, ypos-11, getPreferredSize().width, 11);
drawSelectionRange(g2, pixPerBase, start, end);
@@ -1335,7 +1333,7 @@ public class JamView extends JPanel
{
laststart = -1;
lastend = -1;
- setZoomLevel(JamView.this.nbasesInView);
+ setZoomLevel(BamView.this.nbasesInView);
}
});
topPanel.add(combo);
@@ -1356,7 +1354,7 @@ public class JamView extends JPanel
}
catch (NumberFormatException nfe)
{
- JOptionPane.showMessageDialog(JamView.this,
+ JOptionPane.showMessageDialog(BamView.this,
"Expecting a base number!", "Number Format",
JOptionPane.WARNING_MESSAGE);
}
@@ -1372,7 +1370,7 @@ public class JamView extends JPanel
{
public void actionPerformed(ActionEvent e)
{
- setZoomLevel((int) (JamView.this.nbasesInView * 1.1));
+ setZoomLevel((int) (BamView.this.nbasesInView * 1.1));
}
});
topPanel.add(zoomIn);
@@ -1385,7 +1383,7 @@ public class JamView extends JPanel
{
if (showBaseAlignment)
return;
- setZoomLevel((int) (JamView.this.nbasesInView * .9));
+ setZoomLevel((int) (BamView.this.nbasesInView * .9));
}
});
topPanel.add(zoomOut);
@@ -1416,6 +1414,7 @@ public class JamView extends JPanel
{
scrollBar = new JScrollBar(JScrollBar.HORIZONTAL, 1, nbasesInView, 1,
getMaxBasesInPanel(getSequenceLength()));
+ scrollBar.setUnitIncrement(nbasesInView/20);
scrollBar.addAdjustmentListener(new AdjustmentListener()
{
public void adjustmentValueChanged(AdjustmentEvent e)
@@ -1442,12 +1441,12 @@ public class JamView extends JPanel
switch (event.getKeyCode())
{
case KeyEvent.VK_UP:
- setZoomLevel((int) (JamView.this.nbasesInView * 1.1));
+ setZoomLevel((int) (BamView.this.nbasesInView * 1.1));
break;
case KeyEvent.VK_DOWN:
if (showBaseAlignment)
break;
- setZoomLevel((int) (JamView.this.nbasesInView * .9));
+ setZoomLevel((int) (BamView.this.nbasesInView * .9));
break;
default:
break;
@@ -1601,10 +1600,9 @@ public class JamView extends JPanel
{
int startValue = getBaseAtStartOfView();
this.nbasesInView = nbasesInView;
-
float pixPerBase = getPixPerBaseByWidth();
- if(pixPerBase*3 > ALIGNMENT_PIX_PER_BASE)
+ if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
{
pixPerBase = ALIGNMENT_PIX_PER_BASE;
this.nbasesInView = (int)(getPreferredSize().getWidth()/pixPerBase);
@@ -1621,8 +1619,11 @@ public class JamView extends JPanel
}
if(scrollBar != null)
+ {
scrollBar.setValues(startValue, nbasesInView, 1,
getMaxBasesInPanel(getSequenceLength()));
+ scrollBar.setUnitIncrement(nbasesInView/20);
+ }
}
@@ -1653,7 +1654,7 @@ public class JamView extends JPanel
pixPerBase = feature_display.getWidth()/(float)(end-start+1);
}
- if(pixPerBase*3 > ALIGNMENT_PIX_PER_BASE)
+ if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
{
pixPerBase = ALIGNMENT_PIX_PER_BASE;
jspView.getVerticalScrollBar().setValue(0);
@@ -1934,7 +1935,7 @@ public class JamView extends JPanel
{
public void mouseClicked(MouseEvent e)
{
- JamView.this.requestFocus();
+ BamView.this.requestFocus();
handleCanvasMouseDragOrClick(e);
}
@@ -1999,7 +2000,7 @@ public class JamView extends JPanel
}
}
- final JamView view = new JamView(bam, reference, nbasesInView);
+ final BamView view = new BamView(bam, reference, nbasesInView);
JFrame frame = new JFrame("JAM");
// translucent
diff --git a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
index 46a488a58..42875b732 100644
--- a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
@@ -43,9 +43,9 @@ import net.sf.samtools.SAMRecord;
private int end;
private float pixPerBase;
private Color lightBlue = new Color(30,144,255);
- private JamView jamView;
+ private BamView jamView;
- public CoveragePanel(JamView jamView)
+ public CoveragePanel(BamView jamView)
{
super();
setBackground(Color.white);
diff --git a/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java b/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
index 1b652b1b8..b8c655b3c 100644
--- a/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
+++ b/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
@@ -26,7 +26,7 @@ package uk.ac.sanger.artemis.components.alignment;
import java.util.Comparator;
-import uk.ac.sanger.artemis.components.alignment.JamView.PairedRead;
+import uk.ac.sanger.artemis.components.alignment.BamView.PairedRead;
class PairedReadComparator implements Comparator<Object>
--
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