diff --git a/uk/ac/sanger/artemis/components/alignment/JamView.java b/uk/ac/sanger/artemis/components/alignment/JamView.java
index 1a2c96fb5b21f97148c07898cd1ad44f3f666aab..5c9c49f69783a530294c770bec95725d82d36ea6 100644
--- a/uk/ac/sanger/artemis/components/alignment/JamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/JamView.java
@@ -144,6 +144,8 @@ 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,
@@ -328,7 +330,7 @@ public class JamView extends JPanel
}
}
inputSam.close();
- //System.out.println("readFromBamPicard "+start+".."+end);
+ System.out.println("readFromBamPicard "+start+".."+end);
}
/**
@@ -336,12 +338,15 @@ public class JamView extends JPanel
*/
protected void paintComponent(Graphics g)
{
+ if(!painting)
+ return;
+
super.paintComponent(g);
Graphics2D g2 = (Graphics2D)g;
String refName = (String) combo.getSelectedItem();
int seqLength = seqLengths.get(refName);
- float pixPerBase = ((float)getWidth())/((float)seqLength);
+ float pixPerBase = getPixPerBaseByWidth();
int start;
final int end;
@@ -351,7 +356,7 @@ public class JamView extends JPanel
else
{
double x = jspView.getViewport().getViewRect().getX();
- start = 1 + (int) (seqLength * ( (float)x / (float)getWidth()));
+ start = 1 + (int) (seqLength * ( (float)x / (float)getPreferredSize().getWidth()));
}
if(endBase > 0)
@@ -364,7 +369,8 @@ public class JamView extends JPanel
end = (int) (start + ((float)width / (float)pixPerBase));
}
- //System.out.println("paintComponent "+start+".."+end+" "+startBase+".."+endBase+" pixPerBase="+pixPerBase);
+ System.out.println("paintComponent "+start+".."+end+" "+startBase+".."+endBase+
+ " pixPerBase="+pixPerBase+" getPreferredSize().getWidth()="+getPreferredSize().getWidth());
if(laststart != start ||
lastend != end)
@@ -390,12 +396,30 @@ public class JamView extends JPanel
laststart = start;
lastend = end;
- if(pixPerBase*2 >= ALIGNMENT_PIX_PER_BASE)
+ if(pixPerBase*3 >= ALIGNMENT_PIX_PER_BASE)
drawBaseAlignment(g2, seqLength, pixPerBase, start, end);
else
drawLineView(g2, seqLength, pixPerBase, start, end);
}
+
+ private float getPixPerBaseByWidth()
+ {
+ String refName = (String) combo.getSelectedItem();
+ int seqLength = seqLengths.get(refName);
+ return ((float)getPreferredSize().getWidth())/((float)seqLength);
+ }
+
+ private float getPixPerBaseByBasesInView()
+ {
+ int width = jspView.getViewport().getViewRect().width;
+ if(jspView.getVerticalScrollBar() != null)
+ width += jspView.getVerticalScrollBar().getWidth();
+
+ return ((float)width)/(float)(nbasesInView);
+ }
+
+
/**
* Draw the zoomed-in base view.
* @param g2
@@ -493,7 +517,9 @@ public class JamView extends JPanel
if(ypos > getHeight())
{
- setPreferredSize(new Dimension(getWidth(), ypos));
+ Dimension d = getPreferredSize();
+ d.setSize(getPreferredSize().getWidth(), ypos);
+ setPreferredSize(d);
revalidate();
}
}
@@ -937,7 +963,6 @@ public class JamView extends JPanel
{
int startBase = getBaseAtStartOfView();
setZoomLevel((int) (JamView.this.nbasesInView * 1.1));
- revalidate();
goToBasePosition(startBase);
}
});
@@ -952,7 +977,6 @@ public class JamView extends JPanel
return;
int startBase = getBaseAtStartOfView();
setZoomLevel((int) (JamView.this.nbasesInView * .9));
- revalidate();
goToBasePosition(startBase);
}
});
@@ -962,7 +986,9 @@ public class JamView extends JPanel
topPanel.add(buttonAutoHide, gc);
mainPanel.setPreferredSize(new Dimension(900, 400));
- jspView = new JScrollPane(this, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
+
+ jspView = new JScrollPane(this,
+ JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
setDisplay(1, nbasesInView, null);
@@ -985,7 +1011,6 @@ public class JamView extends JPanel
case KeyEvent.VK_UP:
int startBase = getBaseAtStartOfView();
setZoomLevel((int) (JamView.this.nbasesInView * 1.1));
- revalidate();
goToBasePosition(startBase);
break;
case KeyEvent.VK_DOWN:
@@ -1051,18 +1076,13 @@ public class JamView extends JPanel
private void setZoomLevel(final int nbasesInView)
{
this.nbasesInView = nbasesInView;
- int start = getBaseAtStartOfView();
- System.out.println("setZoomLevel "+start);
+ System.out.println("setZoomLevel "+nbasesInView+" "+getBaseAtStartOfView());
String refName = (String) combo.getSelectedItem();
int seqLength = seqLengths.get(refName);
- int width = jspView.getViewport().getViewRect().width;
- if(jspView.getVerticalScrollBar() != null)
- width += jspView.getVerticalScrollBar().getWidth();
-
- float pixPerBase = ((float)width)/(float)(nbasesInView);
-
- if(pixPerBase*2 > ALIGNMENT_PIX_PER_BASE)
+ float pixPerBase = getPixPerBaseByBasesInView();
+
+ if(pixPerBase*3 > ALIGNMENT_PIX_PER_BASE)
{
pixPerBase = ALIGNMENT_PIX_PER_BASE;
checkBoxSingle.setVisible(false);
@@ -1080,9 +1100,9 @@ public class JamView extends JPanel
Dimension d = new Dimension();
d.setSize((seqLength*pixPerBase), 800.d);
setPreferredSize(d);
+ painting = false;
revalidate();
-
- repaint();
+ painting = true;
}
/**
@@ -1095,9 +1115,10 @@ public class JamView extends JPanel
String refName = (String) combo.getSelectedItem();
int seqLength = seqLengths.get(refName);
- int width = getPreferredSize().width;
+ float width = (float) getPreferredSize().getWidth();
- p.x = Math.round((float)width*((float)(base-1)/(float)seqLength));
+ p.x = Math.round(width*((float)(base-1)/(float)seqLength));
+ System.out.println("goToBasePosition "+base);
jspView.getViewport().setViewPosition(p);
}
@@ -1113,12 +1134,23 @@ public class JamView extends JPanel
{
this.startBase = start;
this.endBase = end;
+ this.nbasesInView = end-start+1;
String refName = (String) combo.getSelectedItem();
int seqLength = seqLengths.get(refName);
- double pixPerBase = getPixPerBase(start, end);
- if(pixPerBase*2 > ALIGNMENT_PIX_PER_BASE)
+ float pixPerBase;
+ if(jspView.getViewport().getViewRect().width > 0)
+ pixPerBase = getPixPerBaseByBasesInView();
+ else
+ {
+ if(feature_display == null)
+ pixPerBase = 1000.f/(float)(end-start+1);
+ else
+ pixPerBase = feature_display.getWidth()/(float)(end-start+1);
+ }
+
+ if(pixPerBase*3 > ALIGNMENT_PIX_PER_BASE)
{
pixPerBase = ALIGNMENT_PIX_PER_BASE;
checkBoxSingle.setVisible(false);
@@ -1145,13 +1177,7 @@ public class JamView extends JPanel
}
}
- private double getPixPerBase(int start, int end)
- {
- if(feature_display == null)
- return 1000.d/(double)(end-start+1);
- else
- return feature_display.getWidth()/(double)(end-start+1);
- }
+
/**
* Return an Artemis entry from a file
@@ -1292,7 +1318,7 @@ public class JamView extends JPanel
for(int i=startMark; i<end; i+=10)
{
- int xpos = (i-1-start)*ALIGNMENT_PIX_PER_BASE;
+ int xpos = (i-start)*ALIGNMENT_PIX_PER_BASE;
g2.drawString(Integer.toString(i), xpos, ypos);
xpos+=(ALIGNMENT_PIX_PER_BASE/2);
@@ -1410,14 +1436,23 @@ public class JamView extends JPanel
{
if(event.getType() == DisplayAdjustmentEvent.SCALE_ADJUST_EVENT)
{
- this.nbasesInView = event.getWidthInBases();
+ laststart = -1;
+ lastend = -1;
+ this.startBase = event.getStart();
+ this.endBase = event.getEnd();
+
+ int width = event.getEnd()-event.getStart()+1;
+ System.out.println("displayAdjustmentValueChanged() "+event.getStart()+".."+event.getEnd()+" +width");
+
+ setZoomLevel(width);
+ goToBasePosition(event.getStart());
setDisplay(event.getStart(), event.getEnd(), event);
- revalidate();
repaint();
}
else
{
setDisplay(event.getStart(), event.getEnd(), event);
+ repaint();
}
}