diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 1378391cae4bc695b3420ba176848a0cd04a85bf..3ef3b269c73ac0fb22b802ca95eba3318408968b 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -148,7 +148,7 @@ public class BamView extends JPanel
{
private static final long serialVersionUID = 1L;
- private List<SAMRecord> readsInView;
+ private List<BamViewRecord> readsInView;
private Hashtable<String, SAMFileReader> samFileReaderHash = new Hashtable<String, SAMFileReader>();
private HashMap<String, Integer> seqLengths = new HashMap<String, Integer>();
@@ -548,7 +548,7 @@ public class BamView extends JPanel
* Read a SAM or BAM file.
* @throws IOException
*/
- private void readFromBamPicard(int start, int end, int bamIndex, float pixPerBase)
+ private void readFromBamPicard(int start, int end, short bamIndex, float pixPerBase)
throws IOException
{
// Open the input file. Automatically detects whether input is SAM or BAM
@@ -599,20 +599,17 @@ public class BamView extends JPanel
* @param end
*/
private void iterateOverBam(final SAMFileReader inputSam,
- String refName, int start, int end,
- int bamIndex, float pixPerBase,
- String bam)
+ final String refName, final int start, final int end,
+ final short bamIndex, final float pixPerBase,
+ final String bam)
{
- boolean multipleBAM = false;
- if(bamList.size() > 1)
- multipleBAM = true;
-
- CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
+ final CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
int checkMemAfter = 8000;
int cnt = 0;
- int seqOffset = getSequenceOffset(refName);
- int offset = seqOffset- getBaseAtStartOfView();
+ final int seqOffset = getSequenceOffset(refName);
+ final int offset = seqOffset- getBaseAtStartOfView();
+ final boolean isCoverageView = isCoverageView(pixPerBase);
while ( it.hasNext() )
{
@@ -627,10 +624,7 @@ public class BamView extends JPanel
if(samRecordMapQPredicate == null ||
samRecordMapQPredicate.testPredicate(samRecord))
{
- if(multipleBAM)
- samRecord.setAttribute("FL", bamIndex);
-
- if(isCoverageView(pixPerBase))
+ if(isCoverageView)
coverageView.addRecord(samRecord, offset, bam);
if(isCoverage)
@@ -639,8 +633,8 @@ public class BamView extends JPanel
if(isSNPplot)
snpPanel.addRecord(samRecord, seqOffset);
- if(!isCoverageView(pixPerBase))
- readsInView.add(samRecord);
+ if(!isCoverageView)
+ readsInView.add(new BamViewRecord(samRecord, bamIndex));
}
}
@@ -817,11 +811,11 @@ public class BamView extends JPanel
(float) memory.getHeapMemoryUsage().getMax());
if(readsInView == null)
- readsInView = new Vector<SAMRecord>();
+ readsInView = new Vector<BamViewRecord>();
else
readsInView.clear();
- for(int i=0; i<bamList.size(); i++)
+ for(short i=0; i<bamList.size(); i++)
{
if(!hideBamList.contains(i))
readFromBamPicard(start, end, i, pixPerBase);
@@ -984,7 +978,7 @@ public class BamView extends JPanel
{
ypos += 11;
- SAMRecord thisRead = readsInView.get(i);
+ SAMRecord thisRead = readsInView.get(i).sam;
if (ypos < r.getMaxY() || ypos > r.getMinY())
drawSequence(g2, thisRead, ypos, refSeq, refSeqStart);
drawn[i] = true;
@@ -997,7 +991,7 @@ public class BamView extends JPanel
{
if (!drawn[j])
{
- SAMRecord nextRead = readsInView.get(j);
+ SAMRecord nextRead = readsInView.get(j).sam;
int nextStart = nextRead.getAlignmentStart();
if (nextStart > thisEnd + 1)
{
@@ -1213,7 +1207,8 @@ public class BamView extends JPanel
for(int i=0; i<readsInView.size(); i++)
{
- SAMRecord samRecord = readsInView.get(i);
+ BamViewRecord bamViewRecord = readsInView.get(i);
+ SAMRecord samRecord = bamViewRecord.sam;
SAMRecord samNextRecord = null;
if( !samRecord.getReadPairedFlag() || // read is not paired in sequencing
@@ -1237,7 +1232,7 @@ public class BamView extends JPanel
if(i < readsInView.size()-1)
{
- samNextRecord = readsInView.get(++i);
+ samNextRecord = readsInView.get(++i).sam;
if(samRecord.getReadName().equals(samNextRecord.getReadName()))
{
@@ -1258,7 +1253,7 @@ public class BamView extends JPanel
}
if(colourByCoverageColour.isSelected())
- g2.setColor(getColourByCoverageColour(samRecord));
+ g2.setColor(getColourByCoverageColour(bamViewRecord));
else if( (samRecord.getReadNegativeStrandFlag() && // strand of the query (1 for reverse)
samNextRecord.getReadNegativeStrandFlag()) ||
(!samRecord.getReadNegativeStrandFlag() &&
@@ -1272,13 +1267,13 @@ public class BamView extends JPanel
}
else
{
- drawLoneRead(g2, samRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight);
+ drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight);
i--;
}
}
else
{
- drawLoneRead(g2, samRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight);
+ drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight);
}
}
@@ -1349,7 +1344,8 @@ public class BamView extends JPanel
for(int i=0; i<readsInView.size(); i++)
{
- SAMRecord samRecord = readsInView.get(i);
+ BamViewRecord bamViewRecord = readsInView.get(i);
+ SAMRecord samRecord = bamViewRecord.sam;
int offset = getSequenceOffset(samRecord.getReferenceName());
int recordStart = samRecord.getAlignmentStart()+offset;
@@ -1359,7 +1355,7 @@ public class BamView extends JPanel
lstStart != recordStart || lstEnd != recordEnd)
{
if(colourByCoverageColour.isSelected())
- g2.setColor(getColourByCoverageColour(samRecord));
+ g2.setColor(getColourByCoverageColour(bamViewRecord));
else if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
g2.setColor(Color.black);
@@ -1445,8 +1441,8 @@ public class BamView extends JPanel
for(int i=0; i<readsInView.size(); i++)
{
- SAMRecord samRecord = readsInView.get(i);
-
+ BamViewRecord bamViewRecord = readsInView.get(i);
+ SAMRecord samRecord = bamViewRecord.sam;
if( samRecord.getReadNegativeStrandFlag() == isStrandNegative )
{
int offset = getSequenceOffset(samRecord.getReferenceName());
@@ -1457,7 +1453,7 @@ public class BamView extends JPanel
lstStart != recordStart || lstEnd != recordEnd)
{
if(colourByCoverageColour.isSelected())
- g2.setColor(getColourByCoverageColour(samRecord));
+ g2.setColor(getColourByCoverageColour(bamViewRecord));
else if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped
g2.setColor(Color.black);
@@ -1506,34 +1502,37 @@ public class BamView extends JPanel
final Vector<PairedRead> pairedReads = new Vector<PairedRead>();
for(int i=0; i<readsInView.size(); i++)
{
- SAMRecord samRecord = readsInView.get(i);
+ BamViewRecord bamViewRecord = readsInView.get(i);
+ SAMRecord samRecord = bamViewRecord.sam;
if( !samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped
continue;
- SAMRecord samNextRecord = null;
+ BamViewRecord bamViewNextRecord = null;
if(i < readsInView.size()-1)
{
- samNextRecord = readsInView.get(++i);
+ bamViewNextRecord = readsInView.get(++i);
+ SAMRecord samNextRecord = bamViewNextRecord.sam;
+
final PairedRead pr = new PairedRead();
if(samRecord.getReadName().equals(samNextRecord.getReadName()) &&
- isFromSameBamFile(samRecord, samNextRecord, bamList))
+ isFromSameBamFile(bamViewRecord, bamViewNextRecord, bamList))
{
if(samRecord.getAlignmentStart() < samNextRecord.getAlignmentStart())
{
- pr.sam1 = samRecord;
- pr.sam2 = samNextRecord;
+ pr.sam1 = bamViewRecord;
+ pr.sam2 = bamViewNextRecord;
}
else
{
- pr.sam2 = samRecord;
- pr.sam1 = samNextRecord;
+ pr.sam2 = bamViewRecord;
+ pr.sam1 = bamViewNextRecord;
}
}
else
{
--i;
- pr.sam1 = samRecord;
+ pr.sam1 = bamViewRecord;
pr.sam2 = null;
}
@@ -1564,13 +1563,13 @@ public class BamView extends JPanel
for(int i=0; i<pairedReads.size(); i++)
{
PairedRead pr = pairedReads.get(i);
- if(pr.sam1.getAlignmentStart() > lastEnd)
+ if(pr.sam1.sam.getAlignmentStart() > lastEnd)
{
ypos = getHeight() - scaleHeight - ydiff;
if(pr.sam2 != null)
- lastEnd = pr.sam2.getAlignmentEnd();
+ lastEnd = pr.sam2.sam.getAlignmentEnd();
else
- lastEnd = pr.sam1.getAlignmentEnd();
+ lastEnd = pr.sam1.sam.getAlignmentEnd();
}
else
ypos = ypos - ydiff;
@@ -1581,39 +1580,39 @@ public class BamView extends JPanel
g2.setStroke(originalStroke);
if(highlightSAMRecord != null &&
- highlightSAMRecord.getReadName().equals(pr.sam1.getReadName()))
+ highlightSAMRecord.getReadName().equals(pr.sam1.sam.getReadName()))
g2.setColor(Color.black);
else
g2.setColor(Color.gray);
if(pr.sam2 != null)
{
- if(!readsOverlap(pr.sam1, pr.sam2))
+ if(!readsOverlap(pr.sam1.sam, pr.sam2.sam))
{
- int offset1 = getSequenceOffset(pr.sam1.getReferenceName());
- int offset2 = getSequenceOffset(pr.sam2.getReferenceName());
+ int offset1 = getSequenceOffset(pr.sam1.sam.getReferenceName());
+ int offset2 = getSequenceOffset(pr.sam2.sam.getReferenceName());
drawTranslucentJointedLine(g2,
- (int)((pr.sam1.getAlignmentEnd()+offset1-getBaseAtStartOfView())*pixPerBase),
- (int)((pr.sam2.getAlignmentStart()+offset2-getBaseAtStartOfView())*pixPerBase), ypos);
+ (int)((pr.sam1.sam.getAlignmentEnd()+offset1-getBaseAtStartOfView())*pixPerBase),
+ (int)((pr.sam2.sam.getAlignmentStart()+offset2-getBaseAtStartOfView())*pixPerBase), ypos);
}
}
- else if(!pr.sam1.getMateUnmappedFlag() &&
- pr.sam1.getProperPairFlag() &&
- pr.sam1.getMateReferenceName().equals(pr.sam1.getReferenceName()))
+ else if(!pr.sam1.sam.getMateUnmappedFlag() &&
+ pr.sam1.sam.getProperPairFlag() &&
+ pr.sam1.sam.getMateReferenceName().equals(pr.sam1.sam.getReferenceName()))
{
final int prStart, prEnd;
- if(pr.sam1.getAlignmentStart() > pr.sam1.getMateAlignmentStart())
+ if(pr.sam1.sam.getAlignmentStart() > pr.sam1.sam.getMateAlignmentStart())
{
- prStart = pr.sam1.getMateAlignmentStart();
- prEnd = pr.sam1.getAlignmentStart();
+ prStart = pr.sam1.sam.getMateAlignmentStart();
+ prEnd = pr.sam1.sam.getAlignmentStart();
}
else
{
- prStart = pr.sam1.getAlignmentEnd();
- prEnd = pr.sam1.getMateAlignmentStart();
+ prStart = pr.sam1.sam.getAlignmentEnd();
+ prEnd = pr.sam1.sam.getMateAlignmentStart();
}
- int offset = getSequenceOffset(pr.sam1.getReferenceName());
+ int offset = getSequenceOffset(pr.sam1.sam.getReferenceName());
drawTranslucentJointedLine(g2,
(int)( (prStart+offset-getBaseAtStartOfView())*pixPerBase),
(int)( (prEnd +offset-getBaseAtStartOfView())*pixPerBase), ypos);
@@ -1622,15 +1621,15 @@ public class BamView extends JPanel
if(colourByCoverageColour.isSelected())
g2.setColor(getColourByCoverageColour(pr.sam1));
else if( pr.sam2 != null &&
- !( pr.sam1.getReadNegativeStrandFlag() ^ pr.sam2.getReadNegativeStrandFlag() ) )
+ !( pr.sam1.sam.getReadNegativeStrandFlag() ^ pr.sam2.sam.getReadNegativeStrandFlag() ) )
g2.setColor(Color.red);
else
g2.setColor(Color.blue);
- drawRead(g2, pr.sam1, pixPerBase, ypos, baseAtStartOfView);
+ drawRead(g2, pr.sam1.sam, pixPerBase, ypos, baseAtStartOfView);
if(pr.sam2 != null)
- drawRead(g2, pr.sam2, pixPerBase, ypos, baseAtStartOfView);
+ drawRead(g2, pr.sam2.sam, pixPerBase, ypos, baseAtStartOfView);
}
}
@@ -1641,17 +1640,17 @@ public class BamView extends JPanel
* @param bamList
* @return
*/
- private boolean isFromSameBamFile(final SAMRecord sam1,
- final SAMRecord sam2,
+ private boolean isFromSameBamFile(final BamViewRecord sam1,
+ final BamViewRecord sam2,
final List<String> bamList)
{
if(bamList == null || bamList.size()<2)
return true;
- final Object o1 = sam1.getAttribute("FL");
- final Object o2 = sam2.getAttribute("FL");
- if(o1 != null && o2 != null)
- if( (Integer)o1 != (Integer)o2 )
+ final short o1 = sam1.bamIndex;
+ final short o2 = sam2.bamIndex;
+ if(o1 != -1 && o2 != -1)
+ if( o1 != o2 )
return false;
return true;
@@ -1713,9 +1712,10 @@ public class BamView extends JPanel
* @param originalStroke
* @param stroke
*/
- private void drawLoneRead(Graphics2D g2, SAMRecord samRecord, int ypos,
+ private void drawLoneRead(Graphics2D g2, BamViewRecord bamViewRecord, int ypos,
float pixPerBase, int baseAtStartOfView, int scaleHeight)
{
+ SAMRecord samRecord = bamViewRecord.sam;
boolean offTheTop = false;
int offset = getSequenceOffset(samRecord.getReferenceName());
int thisStart = samRecord.getAlignmentStart()+offset;
@@ -1755,7 +1755,7 @@ public class BamView extends JPanel
}
if(colourByCoverageColour.isSelected())
- g2.setColor(getColourByCoverageColour(samRecord));
+ g2.setColor(getColourByCoverageColour(bamViewRecord));
else if(offTheTop)
g2.setColor(DARK_ORANGE);
else if(samRecord.getReadNegativeStrandFlag() &&
@@ -2175,7 +2175,7 @@ public class BamView extends JPanel
jspView.getVerticalScrollBar().getMaximum());
}
- private void addToViewMenu(final int thisBamIndex)
+ private void addToViewMenu(final short thisBamIndex)
{
final File f = new File(bamList.get(thisBamIndex));
final JCheckBoxMenuItem cbBam = new JCheckBoxMenuItem(
@@ -2217,7 +2217,7 @@ public class BamView extends JPanel
protected Color getColorByJCheckBoxMenuItem(JCheckBoxMenuItem cbBam)
{
final String bam = cbBam.getText();
- for(int i=0; i<bamList.size(); i++)
+ for(short i=0; i<bamList.size(); i++)
{
final File f = new File(bamList.get(i));
if(f.getName().equals(bam))
@@ -2251,12 +2251,12 @@ public class BamView extends JPanel
FileSelectionDialog bamFileSelection = new FileSelectionDialog(
null, false, "BamView", "BAM");
List<String> bamFiles = bamFileSelection.getFiles(BAM_SUFFIX);
- int count = bamList.size();
+ short count = (short) bamList.size();
bamList.addAll(bamFileSelection.getFiles(BAM_SUFFIX));
- for(int i=0; i<bamFiles.size(); i++)
- addToViewMenu(i+count);
+ for(short i=0; i<bamFiles.size(); i++)
+ addToViewMenu((short) (i+count));
laststart = -1;
repaint();
}
@@ -2365,7 +2365,7 @@ public class BamView extends JPanel
}
});
- for(int i=0; i<bamList.size(); i++)
+ for(short i=0; i<bamList.size(); i++)
addToViewMenu(i);
menu.add(new JSeparator());
@@ -3155,15 +3155,15 @@ public class BamView extends JPanel
* @param samRecord
* @return
*/
- private Color getColourByCoverageColour(SAMRecord samRecord)
+ private Color getColourByCoverageColour(BamViewRecord samRecord)
{
- int fileIndex = 0;
+ short fileIndex = 0;
if(bamList.size()>1)
- fileIndex = (Integer) samRecord.getAttribute("FL");
+ fileIndex = samRecord.bamIndex;
return getColourByCoverageColour(fileIndex);
}
- private Color getColourByCoverageColour(final int fileIndex)
+ private Color getColourByCoverageColour(final short fileIndex)
{
LineAttributes lines[] = CoveragePanel.getLineAttributes(bamList.size());
return lines[fileIndex].getLineColour();
@@ -3234,7 +3234,7 @@ public class BamView extends JPanel
return selection;
}
- protected List<SAMRecord> getReadsInView()
+ protected List<BamViewRecord> getReadsInView()
{
return readsInView;
}
@@ -3668,8 +3668,8 @@ public class BamView extends JPanel
class PairedRead
{
- SAMRecord sam1;
- SAMRecord sam2;
+ BamViewRecord sam1;
+ BamViewRecord sam2;
}
class CreateFeatures
diff --git a/uk/ac/sanger/artemis/components/alignment/BamViewRecord.java b/uk/ac/sanger/artemis/components/alignment/BamViewRecord.java
new file mode 100644
index 0000000000000000000000000000000000000000..51ae8984e5248360530abf7474585e5bddd0c4fe
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/BamViewRecord.java
@@ -0,0 +1,15 @@
+package uk.ac.sanger.artemis.components.alignment;
+
+import net.sf.samtools.SAMRecord;
+
+
+class BamViewRecord
+{
+ protected SAMRecord sam;
+ protected short bamIndex = -1;
+ BamViewRecord(final SAMRecord sam, final short bamIndex)
+ {
+ this.sam = sam;
+ this.bamIndex = bamIndex;
+ }
+}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
index 37bf2a3df527a92d32a202d4d05faab0caea605c..3d0d6d136bfe7b5eb31c2729a59feb28ea2fd432 100644
--- a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
@@ -195,7 +195,7 @@ import net.sf.samtools.SAMRecord;
col = 1;
else
col = 0;
- List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
+ final List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
for(int j=0; j<blocks.size(); j++)
{
AlignmentBlock block = blocks.get(j);
diff --git a/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java b/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
index b8c655b3c45fc66243227201e1d4dd082cd5c345..4a64e2339da4870b049cc9a249360276da17cd31 100644
--- a/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
+++ b/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
@@ -26,6 +26,8 @@ package uk.ac.sanger.artemis.components.alignment;
import java.util.Comparator;
+import net.sf.samtools.SAMRecord;
+
import uk.ac.sanger.artemis.components.alignment.BamView.PairedRead;
@@ -33,16 +35,16 @@ import uk.ac.sanger.artemis.components.alignment.BamView.PairedRead;
{
public int compare(Object o1, Object o2)
{
- PairedRead pr1 = (PairedRead) o1;
- PairedRead pr2 = (PairedRead) o2;
+ SAMRecord sam1 = ((PairedRead) o1).sam1.sam;
+ SAMRecord sam2 = ((PairedRead) o2).sam1.sam;
- int start1 = pr1.sam1.getAlignmentStart();
- if(pr1.sam1.getAlignmentEnd() < start1)
- start1 = pr1.sam1.getAlignmentEnd();
+ int start1 = sam1.getAlignmentStart();
+ if(sam1.getAlignmentEnd() < start1)
+ start1 = sam1.getAlignmentEnd();
- int start2 = pr2.sam1.getAlignmentStart();
- if(pr2.sam1.getAlignmentEnd() < start2)
- start2 = pr1.sam1.getAlignmentEnd();
+ int start2 = sam2.getAlignmentStart();
+ if(sam2.getAlignmentEnd() < start2)
+ start2 = sam1.getAlignmentEnd();
return start1-start2;
}
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordComparator.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordComparator.java
index 28b8dc6b31a90da71fd864d942c823b17685a980..079993834d0408c52ae7667c8865b680d804244f 100644
--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordComparator.java
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordComparator.java
@@ -26,29 +26,29 @@ package uk.ac.sanger.artemis.components.alignment;
import java.util.Comparator;
-import net.sf.samtools.SAMRecord;
+import uk.ac.sanger.artemis.components.alignment.BamViewRecord;
class SAMRecordComparator implements Comparator<Object>
{
public int compare(Object o1, Object o2)
{
- SAMRecord pr1 = (SAMRecord) o1;
- SAMRecord pr2 = (SAMRecord) o2;
+ BamViewRecord pr1 = (BamViewRecord) o1;
+ BamViewRecord pr2 = (BamViewRecord) o2;
- int cmp = pr1.getReadName().compareTo(pr2.getReadName());
+ int cmp = pr1.sam.getReadName().compareTo(pr2.sam.getReadName());
if(cmp == 0)
{
- Object fl1 = pr1.getAttribute("FL"); // bam file index
- Object fl2 = pr2.getAttribute("FL");
- if(fl1 != null && fl2 != null)
+ short fl1 = pr1.bamIndex; // bam file index
+ short fl2 = pr2.bamIndex;
+ if(fl1 != -1 && fl2 != -1)
{
- if((Integer)fl1 < (Integer)fl2)
+ if(fl1 < fl2)
return -1;
- else if((Integer)fl1 > (Integer)fl2)
+ else if(fl1 > fl2)
return 1;
}
- if(pr1.getAlignmentStart() < pr2.getAlignmentStart())
+ if(pr1.sam.getAlignmentStart() < pr2.sam.getAlignmentStart())
return -1;
else
return 1;
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java
index 63384ac89404f04fb086399435e0f648d3eb385f..b35e5e6a0415dfff876aa560b4ec560e77b4f4a9 100644
--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java
@@ -50,6 +50,7 @@ import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.components.DisplayAdjustmentEvent;
import uk.ac.sanger.artemis.components.DisplayAdjustmentListener;
import uk.ac.sanger.artemis.components.SwingWorker;
+import uk.ac.sanger.artemis.components.alignment.BamViewRecord;
import net.sf.samtools.SAMRecord;
@@ -166,7 +167,7 @@ public class SAMRecordList extends JPanel
private void setHighlight()
{
- bamView.setHighlightSAMRecord( bamView.getReadsInView().get(highlight) );
+ bamView.setHighlightSAMRecord( bamView.getReadsInView().get(highlight).sam );
bamView.repaint();
repaint();
}
@@ -176,7 +177,7 @@ public class SAMRecordList extends JPanel
super.paintComponent(g);
int nrecordsShown = getHeight()/font_size;
- List<SAMRecord> readsInView = bamView.getReadsInView();
+ List<BamViewRecord> readsInView = bamView.getReadsInView();
verticalScroll.setMaximum(readsInView.size());
verticalScroll.setVisibleAmount(nrecordsShown);
@@ -192,7 +193,7 @@ public class SAMRecordList extends JPanel
String fmt = getFormatString(fst, lst, readsInView);
for(int i=fst; i<lst; i++)
{
- SAMRecord thisRead = readsInView.get(i);
+ SAMRecord thisRead = readsInView.get(i).sam;
if(highlightedSAMRecord != null && highlightedSAMRecord.equals(thisRead.getReadName()))
{
@@ -211,7 +212,7 @@ public class SAMRecordList extends JPanel
}
}
- private String getFormatString(int fst, int lst, List<SAMRecord> readsInView)
+ private String getFormatString(int fst, int lst, List<BamViewRecord> readsInView)
{
int nameWidth = 10;
int coordWidth = 10;
@@ -220,7 +221,7 @@ public class SAMRecordList extends JPanel
for(int i=fst; i<lst; i++)
{
- SAMRecord thisRead = readsInView.get(i);
+ SAMRecord thisRead = readsInView.get(i).sam;
int thisWidth = thisRead.getReadName().length();
if(thisWidth > nameWidth)
nameWidth = thisWidth;
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java
index 7b42f795010a674a0a06592efe9563801899657b..0f4469945ff06c3140b776057f413470ce95ac27 100644
--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java
@@ -27,6 +27,7 @@ package uk.ac.sanger.artemis.components.alignment;
import java.util.Comparator;
import net.sf.samtools.SAMRecord;
+import uk.ac.sanger.artemis.components.alignment.BamViewRecord;
class SAMRecordPositionComparator implements Comparator<Object>
{
@@ -38,8 +39,8 @@ import net.sf.samtools.SAMRecord;
public int compare(Object o1, Object o2)
{
- SAMRecord pr1 = (SAMRecord) o1;
- SAMRecord pr2 = (SAMRecord) o2;
+ SAMRecord pr1 = ((BamViewRecord) o1).sam;
+ SAMRecord pr2 = ((BamViewRecord) o2).sam;
int offset1 = bamView.getSequenceOffset(pr1.getReferenceName());
int offset2 = bamView.getSequenceOffset(pr2.getReferenceName());