diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 8a0ed8a88e973cf09bade5d464828b3ab6b5b903..00da171d7e817b2a37801d4fe3cf3666c4c608e3 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -36,6 +36,7 @@ import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Insets;
import java.awt.Point;
+import java.awt.Rectangle;
import java.awt.Stroke;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
@@ -800,16 +801,19 @@ public class BamView extends JPanel
if(showScale)
drawScale(g2, start, end, pixPerBase, getHeight());
- Stroke originalStroke =
- new BasicStroke (1.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
Stroke stroke =
new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
+ g2.setStroke(stroke);
+
int scaleHeight;
if(isShowScale())
scaleHeight = 15;
else
scaleHeight = 0;
+ int baseAtStartOfView = getBaseAtStartOfView();
+ Rectangle r = jspView.getViewport().getVisibleRect();
+
for(int i=0; i<readsInView.size(); i++)
{
SAMRecord samRecord = readsInView.get(i);
@@ -821,13 +825,19 @@ public class BamView extends JPanel
if(isSingle)
{
int ypos = (getHeight() - scaleHeight) - samRecord.getReadString().length();
+ if(ypos > r.getMaxX() || ypos < r.getMinY())
+ continue;
+
g2.setColor(Color.black);
- drawRead(g2, samRecord, pixPerBase, stroke, ypos);
+ drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
}
continue;
}
int ypos = (getHeight() - scaleHeight) - ( Math.abs(samRecord.getInferredInsertSize()) );
+ if(ypos > r.getMaxX() || ypos < r.getMinY())
+ continue;
+
if(i < readsInView.size()-1)
{
samNextRecord = readsInView.get(++i);
@@ -838,7 +848,6 @@ public class BamView extends JPanel
if(samRecord.getAlignmentEnd() < samNextRecord.getAlignmentStart() &&
(samNextRecord.getAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
{
- g2.setStroke(originalStroke);
g2.setColor(Color.LIGHT_GRAY);
drawTranslucentLine(g2,
@@ -852,18 +861,18 @@ public class BamView extends JPanel
else
g2.setColor(Color.blue);
- drawRead(g2, samRecord, pixPerBase, stroke, ypos);
- drawRead(g2, samNextRecord, pixPerBase, stroke, ypos);
+ drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
+ drawRead(g2, samNextRecord, pixPerBase, ypos, baseAtStartOfView);
}
else
{
- drawLoneRead(g2, samRecord, ypos, pixPerBase, originalStroke, stroke);
+ drawLoneRead(g2, samRecord, ypos, pixPerBase, baseAtStartOfView);
i--;
}
}
else
{
- drawLoneRead(g2, samRecord, ypos, pixPerBase, originalStroke, stroke);
+ drawLoneRead(g2, samRecord, ypos, pixPerBase, baseAtStartOfView);
}
}
@@ -898,6 +907,7 @@ public class BamView extends JPanel
1.3f,
BasicStroke.CAP_BUTT,
BasicStroke.JOIN_MITER);
+ g2.setStroke(stroke);
int scaleHeight;
if(isShowScale())
@@ -909,8 +919,10 @@ public class BamView extends JPanel
int maxEnd = 0;
int lstStart = 0;
int lstEnd = 0;
-
+ int baseAtStartOfView = getBaseAtStartOfView();
g2.setColor(Color.blue);
+ Rectangle r = jspView.getViewport().getVisibleRect();
+
for(int i=0; i<readsInView.size(); i++)
{
SAMRecord samRecord = readsInView.get(i);
@@ -940,7 +952,10 @@ public class BamView extends JPanel
lstStart = recordStart;
lstEnd = recordEnd;
- drawRead(g2, samRecord, pixPerBase, stroke, ypos);
+
+ if(ypos > r.getMaxX() || ypos < r.getMinY())
+ continue;
+ drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
}
}
@@ -993,8 +1008,9 @@ public class BamView extends JPanel
int maxEnd = 0;
int lstStart = 0;
int lstEnd = 0;
-
+ int baseAtStartOfView = getBaseAtStartOfView();
g2.setColor(Color.blue);
+ Rectangle r = jspView.getViewport().getVisibleRect();
for(int i=0; i<readsInView.size(); i++)
{
@@ -1027,7 +1043,10 @@ public class BamView extends JPanel
lstStart = recordStart;
lstEnd = recordEnd;
- drawRead(g2, samRecord, pixPerBase, stroke, ypos);
+
+ if(ypos > r.getMaxX() || ypos < r.getMinY())
+ continue;
+ drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
}
}
}
@@ -1098,6 +1117,8 @@ public class BamView extends JPanel
Stroke originalStroke = new BasicStroke (1.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
Stroke stroke =
new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
+ g2.setStroke(stroke);
+
int scaleHeight;
if(isShowScale())
scaleHeight = 15;
@@ -1106,6 +1127,8 @@ public class BamView extends JPanel
int ypos = getHeight() - scaleHeight - 3;
int lastEnd = 0;
+ int baseAtStartOfView = getBaseAtStartOfView();
+ Rectangle r = jspView.getViewport().getVisibleRect();
for(int i=0; i<pairedReads.size(); i++)
{
@@ -1125,6 +1148,9 @@ public class BamView extends JPanel
else
ypos = ypos - 3;
+ if(ypos > r.getMaxX() || ypos < r.getMinY())
+ continue;
+
g2.setStroke(originalStroke);
g2.setColor(Color.LIGHT_GRAY);
@@ -1156,10 +1182,10 @@ public class BamView extends JPanel
g2.setColor(Color.red);
else
g2.setColor(Color.blue);
- drawRead(g2, pr.sam1, pixPerBase, stroke, ypos);
+ drawRead(g2, pr.sam1, pixPerBase, ypos, baseAtStartOfView);
if(pr.sam2 != null)
- drawRead(g2, pr.sam2, pixPerBase, stroke, ypos);
+ drawRead(g2, pr.sam2, pixPerBase, ypos, baseAtStartOfView);
}
}
@@ -1174,7 +1200,7 @@ public class BamView extends JPanel
* @param stroke
*/
private void drawLoneRead(Graphics2D g2, SAMRecord samRecord, int ypos,
- float pixPerBase, Stroke originalStroke, Stroke stroke)
+ float pixPerBase, int baseAtStartOfView)
{
boolean offTheTop = false;
int offset = getSequenceOffset(samRecord.getReferenceName());
@@ -1189,7 +1215,6 @@ public class BamView extends JPanel
if(Math.abs(samRecord.getMateAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
{
- g2.setStroke(originalStroke);
g2.setColor(Color.LIGHT_GRAY);
if(samRecord.getAlignmentEnd() < samRecord.getMateAlignmentStart())
@@ -1216,7 +1241,7 @@ public class BamView extends JPanel
g2.setColor(Color.blue);
- drawRead(g2, samRecord, pixPerBase, stroke, ypos);
+ drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
if (isSNPs)
showSNPsOnReads(g2, samRecord, pixPerBase, ypos, offset);
@@ -1301,31 +1326,34 @@ public class BamView extends JPanel
* @param g2
* @param thisRead
* @param pixPerBase
- * @param stroke
* @param ypos
+ * @param baseAtStartOfView
*/
private void drawRead(Graphics2D g2, SAMRecord thisRead,
- float pixPerBase, Stroke stroke, int ypos)
+ float pixPerBase,
+ int ypos,
+ int baseAtStartOfView)
{
int offset = getSequenceOffset(thisRead.getReferenceName());
-
- int thisStart = thisRead.getAlignmentStart()+offset-getBaseAtStartOfView();
- int thisEnd = thisRead.getAlignmentEnd()+offset-getBaseAtStartOfView();
+
+ int thisStart = thisRead.getAlignmentStart()+offset-baseAtStartOfView;
+ int thisEnd = thisRead.getAlignmentEnd()+offset-baseAtStartOfView;
if(highlightSAMRecord != null &&
highlightSAMRecord.getReadName().equals(thisRead.getReadName()))
{
- Stroke stroke2 =
+ Stroke originalStroke = g2.getStroke();
+ Stroke stroke =
new BasicStroke (3.f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
- g2.setStroke(stroke2);
+ g2.setStroke(stroke);
Color c = g2.getColor();
g2.setColor(Color.black);
g2.drawLine((int)( thisStart * pixPerBase), ypos,
(int)( thisEnd * pixPerBase), ypos);
g2.setColor(c);
+ g2.setStroke(originalStroke);
}
-
- g2.setStroke(stroke);
+
g2.drawLine((int)( thisStart * pixPerBase), ypos,
(int)( thisEnd * pixPerBase), ypos);
@@ -1435,6 +1463,7 @@ public class BamView extends JPanel
Color col = g2.getColor();
g2.setColor(Color.red);
+ offset = offset - getBaseAtStartOfView();
for(int i=0; i<blocks.size(); i++)
{
AlignmentBlock block = blocks.get(i);
@@ -1445,8 +1474,8 @@ public class BamView extends JPanel
if (Character.toUpperCase(refSeq[refPos-thisStart]) != readSeq[readPos])
{
- g2.drawLine((int) ((refPos+offset-getBaseAtStartOfView()) * pixPerBase), ypos + 2,
- (int) ((refPos+offset-getBaseAtStartOfView()) * pixPerBase), ypos - 2);
+ g2.drawLine((int) ((refPos+offset) * pixPerBase), ypos + 2,
+ (int) ((refPos+offset) * pixPerBase), ypos - 2);
}
}
@@ -1703,11 +1732,12 @@ public class BamView extends JPanel
});
view.add(checkBoxSNPs);
view.add(new JSeparator());
-
+
ButtonGroup group = new ButtonGroup();
final JCheckBoxMenuItem checkBoxPairedStackView = new JCheckBoxMenuItem("Paired Stack View");
final JCheckBoxMenuItem checkBoxStrandStackView = new JCheckBoxMenuItem("Strand Stack View");
final JCheckBoxMenuItem checkIsizeStackView = new JCheckBoxMenuItem("Inferred Size View", true);
+ checkBoxStackView.setFont(checkIsizeStackView.getFont());
group.add(checkBoxStackView);
group.add(checkBoxPairedStackView);
group.add(checkBoxStrandStackView);