diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 2ef2f7b7534b3c51172ca2cfc641ad371bc5fc38..19a308179838740251d3c41cb113c4527fe9dbac 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -122,6 +122,7 @@ public class BamView extends JPanel
private static final long serialVersionUID = 1L;
private List<SAMRecord> readsInView;
private Hashtable<String, Integer> seqLengths = new Hashtable<String, Integer>();
+ private Hashtable<String, Integer> offsetLengths;
private Vector<String> seqNames = new Vector<String>();
private String bam;
@@ -477,16 +478,19 @@ public class BamView extends JPanel
{
if(!concatSequences)
return 0;
- int offset = 0;
- for(int i=0; i<combo.getItemCount(); i++)
- {
- String thisSeqName = (String) combo.getItemAt(i);
- if(refName.equals(thisSeqName))
- return offset;
-
- offset += seqLengths.get(combo.getItemAt(i));
+
+ if(offsetLengths == null)
+ {
+ offsetLengths = new Hashtable<String, Integer>(combo.getItemCount());
+ int offset = 0;
+ for(int i=0; i<combo.getItemCount(); i++)
+ {
+ String thisSeqName = (String) combo.getItemAt(i);
+ offsetLengths.put(thisSeqName, offset);
+ offset += seqLengths.get(combo.getItemAt(i));
+ }
}
- return offset;
+ return offsetLengths.get(refName);
}
/**
@@ -517,11 +521,6 @@ public class BamView extends JPanel
if(end > seqLength)
end = seqLength;
}
-
-
- //System.out.println(start+".."+end+" " +
- // "sequence length = "+getSequenceLength()+
- // " pixPerBase="+pixPerBase);
boolean changeToStackView = false;
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
@@ -529,42 +528,49 @@ public class BamView extends JPanel
lastend != end)
{
setCursor(cbusy);
- try
+ synchronized (this)
{
- float heapFractionUsedBefore = (float)((float)memory.getHeapMemoryUsage().getUsed()/(float)memory.getHeapMemoryUsage().getMax());
- //System.out.println("Heap memory used before "+heapFractionUsedBefore+"\n");
-
- readFromBamPicard(start, end);
+ try
+ {
+ float heapFractionUsedBefore = (float) ((float) memory.getHeapMemoryUsage().getUsed() /
+ (float) memory.getHeapMemoryUsage().getMax());
+ readFromBamPicard(start, end);
+ float heapFractionUsedAfter = (float) ((float) memory.getHeapMemoryUsage().getUsed() /
+ (float) memory.getHeapMemoryUsage().getMax());
+
+ // System.out.println("Heap Max : "+memory.getHeapMemoryUsage().getMax());
+ // System.out.println("Heap Used : "+memory.getHeapMemoryUsage().getUsed());
+ // System.out.println("Heap memory used "+heapFractionUsedAfter);
+
+ if ((heapFractionUsedAfter - heapFractionUsedBefore) > 0.06
+ && !isStackView && heapFractionUsedAfter > 0.8)
+ {
+ checkBoxStackView.setSelected(true);
+ isStackView = true;
+ changeToStackView = true;
+ }
- float heapFractionUsedAfter =
- (float)((float)memory.getHeapMemoryUsage().getUsed()/
- (float)memory.getHeapMemoryUsage().getMax());
-
- //System.out.println("Heap Max : "+memory.getHeapMemoryUsage().getMax());
- //System.out.println("Heap Used : "+memory.getHeapMemoryUsage().getUsed());
- //System.out.println("Heap memory used "+heapFractionUsedAfter);
+ if ((!isStackView && !isStrandStackView)
+ || pixPerBase * 1.08f >= ALIGNMENT_PIX_PER_BASE)
+ {
+ Collections.sort(readsInView, new SAMRecordComparator());
+ }
- if((heapFractionUsedAfter-heapFractionUsedBefore) > 0.06 && !isStackView &&
- heapFractionUsedAfter > 0.8)
+ setCursor(cdone);
+ }
+ catch (OutOfMemoryError ome)
{
- checkBoxStackView.setSelected(true);
- isStackView = true;
- changeToStackView = true;
+ JOptionPane.showMessageDialog(this, "Out of Memory");
+ readsInView.clear();
+ return;
}
-
- if((!isStackView && !isStrandStackView) || pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
- Collections.sort(readsInView, new SAMRecordComparator());
-
- setCursor(cdone);
- }
- catch(OutOfMemoryError ome)
- {
- JOptionPane.showMessageDialog(this, "Out of Memory");
- readsInView.clear();
- return;
}
}
+ //System.out.println(start+".."+end+" " +
+ // "sequence length = "+getSequenceLength()+
+ // " pixPerBase="+pixPerBase);
+
laststart = start;
lastend = end;
if(showBaseAlignment)
@@ -674,33 +680,42 @@ public class BamView extends JPanel
for(int i=0; i<readsInView.size(); i++)
drawn[i] = false;
- for(int i=0; i<readsInView.size(); i++)
+ Rectangle r = jspView.getViewport().getViewRect();
+ int nreads = readsInView.size();
+
+ for(int i=0; i<nreads; i++)
{
if (!drawn[i])
{
- SAMRecord thisRead = readsInView.get(i);
ypos+=11;
-
- drawSequence(g2, thisRead, ypos, refSeq, refSeqStart);
+
+ SAMRecord thisRead = readsInView.get(i);
+ if(ypos < r.getMaxY() || ypos > r.getMinY())
+ drawSequence(g2, thisRead, ypos, refSeq, refSeqStart);
drawn[i] = true;
int thisEnd = thisRead.getAlignmentEnd();
if(thisEnd == 0)
thisEnd = thisRead.getAlignmentStart()+thisRead.getReadLength();
- for(int j=i+1; j<readsInView.size(); j++)
+ for(int j=i+1; j<nreads; j++)
{
if (!drawn[j])
{
SAMRecord nextRead = readsInView.get(j);
- if(nextRead.getAlignmentStart() > thisEnd+1)
+ int nextStart = nextRead.getAlignmentStart();
+ if(nextStart > thisEnd+1)
{
- drawSequence(g2, nextRead, ypos, refSeq, refSeqStart);
+ if(ypos < r.getMaxY() || ypos > r.getMinY())
+ drawSequence(g2, nextRead, ypos, refSeq, refSeqStart);
+
drawn[j] = true;
thisEnd = nextRead.getAlignmentEnd();
if(thisEnd == 0)
- thisEnd = nextRead.getAlignmentStart()+nextRead.getReadLength();
+ thisEnd = nextStart+nextRead.getReadLength();
}
+ else if(ypos > r.getMaxY() || ypos < r.getMinY())
+ break;
}
}
}
@@ -813,7 +828,7 @@ public class BamView extends JPanel
scaleHeight = 0;
int baseAtStartOfView = getBaseAtStartOfView();
- Rectangle r = jspView.getViewport().getVisibleRect();
+ Rectangle r = jspView.getViewport().getViewRect();
for(int i=0; i<readsInView.size(); i++)
{
@@ -826,7 +841,7 @@ public class BamView extends JPanel
if(isSingle)
{
int ypos = (getHeight() - scaleHeight) - samRecord.getReadString().length();
- if(ypos > r.getMaxX() || ypos < r.getMinY())
+ if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
g2.setColor(Color.black);
@@ -836,7 +851,7 @@ public class BamView extends JPanel
}
int ypos = (getHeight() - scaleHeight) - ( Math.abs(samRecord.getInferredInsertSize()) );
- if(ypos > r.getMaxX() || ypos < r.getMinY())
+ if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
if(i < readsInView.size()-1)
@@ -922,7 +937,7 @@ public class BamView extends JPanel
int lstEnd = 0;
int baseAtStartOfView = getBaseAtStartOfView();
g2.setColor(Color.blue);
- Rectangle r = jspView.getViewport().getVisibleRect();
+ Rectangle r = jspView.getViewport().getViewRect();
for(int i=0; i<readsInView.size(); i++)
{
@@ -954,7 +969,7 @@ public class BamView extends JPanel
lstStart = recordStart;
lstEnd = recordEnd;
- if(ypos > r.getMaxX() || ypos < r.getMinY())
+ if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
}
@@ -1011,7 +1026,7 @@ public class BamView extends JPanel
int lstEnd = 0;
int baseAtStartOfView = getBaseAtStartOfView();
g2.setColor(Color.blue);
- Rectangle r = jspView.getViewport().getVisibleRect();
+ Rectangle r = jspView.getViewport().getViewRect();
for(int i=0; i<readsInView.size(); i++)
{
@@ -1045,7 +1060,7 @@ public class BamView extends JPanel
lstStart = recordStart;
lstEnd = recordEnd;
- if(ypos > r.getMaxX() || ypos < r.getMinY())
+ if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
}
@@ -1129,7 +1144,7 @@ public class BamView extends JPanel
int ypos = getHeight() - scaleHeight - 3;
int lastEnd = 0;
int baseAtStartOfView = getBaseAtStartOfView();
- Rectangle r = jspView.getViewport().getVisibleRect();
+ Rectangle r = jspView.getViewport().getViewRect();
for(int i=0; i<pairedReads.size(); i++)
{
@@ -1149,7 +1164,7 @@ public class BamView extends JPanel
else
ypos = ypos - 3;
- if(ypos > r.getMaxX() || ypos < r.getMinY())
+ if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
g2.setStroke(originalStroke);
@@ -2160,7 +2175,7 @@ public class BamView extends JPanel
else
{
setDisplay(event.getStart(),
- event.getStart()+feature_display.getMaxVisibleBases(), event);
+ event.getStart()+feature_display.getMaxVisibleBases(), event);
repaint();
}
return null;
diff --git a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
index 42875b732a0e50f6615b61f2e74bdb5d0e97cc93..497ea1df63d1d3e9edc0c81dcbedf50d5f070a38 100644
--- a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
@@ -80,7 +80,7 @@ import net.sf.samtools.SAMRecord;
for(int j=0; j<length;j++)
{
int bin =
- Math.round(((thisRead.getAlignmentStart()-start) + j + offset) / windowSize);
+ (int)(((thisRead.getAlignmentStart()-start) + j + offset) / windowSize);
if(bin < 0 || bin > coverage.length-1)
continue;