diff --git a/test/build-test.xml b/test/build-test.xml
index b22c9233c4dd29bc309602db2b9e879aba877f74..531da118c4b0cbcf1c7afd265793e75be69e0d79 100644
--- a/test/build-test.xml
+++ b/test/build-test.xml
@@ -350,6 +350,9 @@
<jvmarg value="-Djava.awt.headless=true" />
<batchtest fork="yes" todir="${junit.reports.dir}">
<fileset dir="${evosuite.tests.src.dir}">
+
+ <!--include name="**/*BamView_ESTest.java" if="${do.run.evosuite.tests}" /-->
+
<include name="**/*_ESTest.java" if="${do.run.evosuite.tests}" />
<!-- Exclude classes that currently produce broken tests -->
@@ -382,7 +385,7 @@
</target>
<!-- Create Jacoco reports -->
- <target name="jacoco-coverage-report">
+ <target name="jacoco-coverage-report" depends="run-manual-tests">
<delete dir="${coverage.report.jacoco.dir}" />
<mkdir dir="${coverage.report.jacoco.dir}" />
diff --git a/uk/ac/sanger/artemis/components/alignment/BamUtils.java b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
index f668011963ffdf86cece45a6664daaa5d7878955..b1181e7ce0136170dd9f53824b31a635360ec331 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamUtils.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
@@ -362,5 +362,28 @@ class BamUtils
}
return featureReadCount;
}
+
+ /**
+ * Check whether two SAM records are the same.
+ * @param bamRec1 SamViewRecord
+ * @param bamRec2 SamViewRecord
+ * @return boolean - true if equality holds.
+ */
+ public static boolean samRecordEqualityCheck(SAMRecord rec1, SAMRecord rec2)
+ {
+ boolean result = false;
+
+ if (rec1 == null && rec2 == null)
+ return true;
+
+ result = (
+ (rec1.getReadName().equals(rec2.getReadName())) &&
+ (rec1.getAlignmentStart() == rec2.getAlignmentStart()) &&
+ (rec1.getAlignmentEnd() == rec2.getAlignmentEnd()) &&
+ (rec1.getFlags() == rec2.getFlags())
+ );
+
+ return result;
+ }
}
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 0228a8442e9bf018723f9732dd6a024d16878d53..3a05371409b7311b56740f95ff3710dea7932378 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -220,6 +220,7 @@ public class BamView extends JPanel
private JCheckBoxMenuItem colourByCoverageColour = new JCheckBoxMenuItem("Coverage Plot Colours");
private JCheckBoxMenuItem baseQualityColour = new JCheckBoxMenuItem("Base Quality");
private JCheckBoxMenuItem markInsertions = new JCheckBoxMenuItem("Mark Insertions", true);
+
private AlphaComposite translucent =
AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.6f);
@@ -234,9 +235,11 @@ public class BamView extends JPanel
private static Color DARK_ORANGE = new Color(255,140,0);
private static Color DEEP_PINK = new Color(139,10,80);
+ private static Color NON_SELECTED_READ_HIGHLIGHT_COLOUR = new Color(189,103,107);
+
private Point lastMousePoint = null;
- private BamViewRecord mouseOverSAMRecord = null;
- private BamViewRecord highlightSAMRecord = null;
+ private volatile BamViewRecord mouseOverSAMRecord = null;
+ private volatile BamViewRecord highlightSAMRecord = null;
private String mouseOverInsertion;
// record of where a mouse drag starts
protected int dragStart = -1;
@@ -396,41 +399,41 @@ public class BamView extends JPanel
}
public String getToolTipText()
- {
- if(isCoverageView(getPixPerBaseByWidth()) && lastMousePoint != null)
- return coverageView.getToolTipText(
- lastMousePoint.y-getJspView().getViewport().getViewPosition().y);
-
- if(mouseOverSAMRecord == null)
- return null;
-
- String msg =
- mouseOverSAMRecord.sam.getReadName() + "\n" +
- mouseOverSAMRecord.sam.getAlignmentStart() + ".." +
- mouseOverSAMRecord.sam.getAlignmentEnd() +
- (mouseOverSAMRecord.sam.getReadGroup() != null ? "\nRG="+mouseOverSAMRecord.sam.getReadGroup().getId() : "") +
- "\nisize=" + mouseOverSAMRecord.sam.getInferredInsertSize() +
- "\nmapq=" + mouseOverSAMRecord.sam.getMappingQuality()+
- "\nrname="+ mouseOverSAMRecord.sam.getReferenceName();
-
- if( mouseOverSAMRecord.sam.getReadPairedFlag() &&
- mouseOverSAMRecord.sam.getProperPairFlag() &&
- !mouseOverSAMRecord.sam.getMateUnmappedFlag())
- {
- msg = msg +
- "\nstrand (read/mate): "+
- (mouseOverSAMRecord.sam.getReadNegativeStrandFlag() ? "-" : "+")+" / "+
- (mouseOverSAMRecord.sam.getMateNegativeStrandFlag() ? "-" : "+");
- }
- else
- msg = msg +
- "\nstrand (read/mate): "+
- (mouseOverSAMRecord.sam.getReadNegativeStrandFlag() ? "-" : "+");
-
- if(msg != null && mouseOverInsertion != null)
- msg = msg + "\nInsertion at:" +mouseOverInsertion;
-
- return msg;
+ {
+ if(isCoverageView(getPixPerBaseByWidth()) && lastMousePoint != null)
+ return coverageView.getToolTipText(
+ lastMousePoint.y-getJspView().getViewport().getViewPosition().y);
+
+ if(mouseOverSAMRecord == null)
+ return null;
+
+ String msg =
+ mouseOverSAMRecord.sam.getReadName() + "\n" +
+ mouseOverSAMRecord.sam.getAlignmentStart() + ".." +
+ mouseOverSAMRecord.sam.getAlignmentEnd() +
+ (mouseOverSAMRecord.sam.getReadGroup() != null ? "\nRG="+mouseOverSAMRecord.sam.getReadGroup().getId() : "") +
+ "\nisize=" + mouseOverSAMRecord.sam.getInferredInsertSize() +
+ "\nmapq=" + mouseOverSAMRecord.sam.getMappingQuality()+
+ "\nrname="+ mouseOverSAMRecord.sam.getReferenceName();
+
+ if( mouseOverSAMRecord.sam.getReadPairedFlag() &&
+ mouseOverSAMRecord.sam.getProperPairFlag() &&
+ !mouseOverSAMRecord.sam.getMateUnmappedFlag())
+ {
+ msg = msg +
+ "\nstrand (read/mate): "+
+ (mouseOverSAMRecord.sam.getReadNegativeStrandFlag() ? "-" : "+")+" / "+
+ (mouseOverSAMRecord.sam.getMateNegativeStrandFlag() ? "-" : "+");
+ }
+ else
+ msg = msg +
+ "\nstrand (read/mate): "+
+ (mouseOverSAMRecord.sam.getReadNegativeStrandFlag() ? "-" : "+");
+
+ if(msg != null && mouseOverInsertion != null)
+ msg = msg + "\nInsertion at:" +mouseOverInsertion;
+
+ return msg;
}
/**
@@ -1021,11 +1024,11 @@ public class BamView extends JPanel
if(isCoverageView(pixPerBase))
drawCoverage(g2,start, end, pixPerBase);
else if(isStackView())
- drawStackView(g2, seqLength, pixPerBase, start, end);
+ drawStackView(g2, seqLength, pixPerBase, start, end);
else if(isPairedStackView())
drawPairedStackView(g2, seqLength, pixPerBase, start, end);
else if(isStrandStackView())
- drawStrandStackView(g2, seqLength, pixPerBase, start, end);
+ drawStrandStackView(g2, seqLength, pixPerBase, start, end);
else
drawLineView(g2, seqLength, pixPerBase, start, end);
}
@@ -1202,17 +1205,17 @@ public class BamView extends JPanel
int xpos;
int len = 0;
int refPos = 0;
- final String readSeq = samRecord.getReadString();
+ SAMRecordSequenceString readSeq = new SAMRecordSequenceString(samRecord.getReadString());
final int offset = getSequenceOffset(samRecord.getReferenceName());
byte[] phredQuality = null;
if(baseQualityColour.isSelected())
phredQuality = samRecord.getBaseQualities();
-
+
Hashtable<Integer, String> insertions = null;
List<AlignmentBlock> blocks = samRecord.getAlignmentBlocks();
for(int i=0; i<blocks.size(); i++)
- {
+ {
AlignmentBlock block = blocks.get(i);
int blockStart = block.getReadStart();
len += block.getLength();
@@ -1222,19 +1225,22 @@ public class BamView extends JPanel
xpos = block.getReferenceStart() - 1 + j + offset;
refPos = xpos - refSeqStart + 1;
- if(phredQuality != null)
+ if(phredQuality != null && phredQuality.length > 0)
setColourByBaseQuality(g2, phredQuality[readPos]);
if(isSNPs && refSeq != null && refPos > 0 && refPos < refSeq.length())
{
- if(Character.toUpperCase(readSeq.charAt(readPos)) != refSeq.charAt(refPos))
+ if(
+ (!readSeq.isSecondaryAlignment()) &&
+ (Character.toUpperCase(readSeq.charAt(readPos)) != refSeq.charAt(refPos))
+ )
g2.setColor(Color.red);
else
g2.setColor(col);
}
- g2.drawString(readSeq.substring(readPos, readPos+1),
- refPos*ALIGNMENT_PIX_PER_BASE, ypos);
+ g2.drawString(readSeq.substring(readPos, readPos+1),
+ refPos*ALIGNMENT_PIX_PER_BASE, ypos);
if(isSNPs)
g2.setColor(col);
@@ -1265,16 +1271,27 @@ public class BamView extends JPanel
g2.setColor(col);
}
}
-
- // highlight
- if(highlightSAMRecord != null &&
- highlightSAMRecord.sam.getReadName().equals(samRecord.getReadName()))
+
+ if(highlightSAMRecord != null &&
+ highlightSAMRecord.sam.getReadName().equals(bamViewRecord.sam.getReadName()))
{
refPos = block.getReferenceStart() + offset - refSeqStart;
int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
int width = block.getLength()*ALIGNMENT_PIX_PER_BASE;
Color col1 = g2.getColor();
- g2.setColor(Color.red);
+ //g2.setColor(Color.red);
+
+ if (isThisBamRecordHighlighted(bamViewRecord) )
+ {
+ // Selected read alignment
+ g2.setColor(Color.black);
+ }
+ else
+ {
+ // For a read with the same name as selected one.
+ g2.setColor(NON_SELECTED_READ_HIGHLIGHT_COLOUR);
+ }
+
g2.drawRect(xstart, ypos-BASE_HEIGHT, width, BASE_HEIGHT);
if(i < blocks.size()-1)
{
@@ -1361,7 +1378,7 @@ public class BamView extends JPanel
int baseAtStartOfView = getBaseAtStartOfView();
Rectangle r = jspView.getViewport().getViewRect();
-
+
for(int i=0; i<readsInView.size(); i++)
{
BamViewRecord bamViewRecord = readsInView.get(i);
@@ -1494,8 +1511,6 @@ public class BamView extends JPanel
if(isOrientation)
ydiff= 2*ydiff;
int maxEnd = 0;
- int lstStart = 0;
- int lstEnd = 0;
final int baseAtStartOfView = getBaseAtStartOfView();
g2.setColor(Color.blue);
final Rectangle r = jspView.getViewport().getViewRect();
@@ -1503,6 +1518,7 @@ public class BamView extends JPanel
for(BamViewRecord bamViewRecord: readsInView)
{
SAMRecord samRecord = bamViewRecord.sam;
+
int offset = getSequenceOffset(samRecord.getReferenceName());
int recordStart = samRecord.getAlignmentStart()+offset;
@@ -1510,53 +1526,40 @@ public class BamView extends JPanel
List<Integer> snps = getSNPs(samRecord);
- if(colourByCoverageColour.isSelected() ||
- colourByStrandTag.isSelected() ||
- colourByReadGrp.isSelected() ||
- lstStart != recordStart || lstEnd != recordEnd || snps != null)
- {
- if(colourByStrandTag.isSelected())
- {
- if(samRecord.getAttribute("XS") == null)
- g2.setColor(Color.BLACK);
- else if( ((Character)samRecord.getAttribute("XS")).equals('+') )
- g2.setColor(Color.BLUE);
- else if( ((Character)samRecord.getAttribute("XS")).equals('-') )
- g2.setColor(Color.RED);
- else
- g2.setColor(Color.BLACK);
- }
- else if(colourByCoverageColour.isSelected())
- g2.setColor(getColourByCoverageColour(bamViewRecord));
- else if(colourByReadGrp.isSelected())
- g2.setColor(getReadGroupFrame().getReadGroupColour(readGroups, samRecord.getReadGroup()));
- else if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
- samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
- g2.setColor(Color.black);
- else
- g2.setColor(Color.blue);
-
- if(maxEnd < recordStart || ypos < 0)
- {
- ypos = (getHeight() - scaleHeight)-ydiff;
- maxEnd = recordEnd+2;
- }
- else
- ypos = ypos-ydiff;
- }
- else
- g2.setColor(DARK_GREEN);
+ if(colourByStrandTag.isSelected())
+ {
+ if(samRecord.getAttribute("XS") == null)
+ g2.setColor(Color.BLACK);
+ else if( ((Character)samRecord.getAttribute("XS")).equals('+') )
+ g2.setColor(Color.BLUE);
+ else if( ((Character)samRecord.getAttribute("XS")).equals('-') )
+ g2.setColor(Color.RED);
+ else
+ g2.setColor(Color.BLACK);
+ }
+ else if(colourByCoverageColour.isSelected())
+ g2.setColor(getColourByCoverageColour(bamViewRecord));
+ else if(colourByReadGrp.isSelected())
+ g2.setColor(getReadGroupFrame().getReadGroupColour(readGroups, samRecord.getReadGroup()));
+ else if (samRecord.getDuplicateReadFlag())
+ g2.setColor(DARK_GREEN); // Duplicate
+ else if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
+ samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
+ g2.setColor(Color.black);
+ else
+ g2.setColor(Color.blue);
- if(snps != null)
- lstStart = -1;
- else
+ if(maxEnd < recordStart || ypos < 0)
{
- lstStart = recordStart;
- lstEnd = recordEnd;
+ ypos = (getHeight() - scaleHeight)-ydiff;
+ maxEnd = recordEnd+2;
}
+ else
+ ypos = ypos-ydiff;
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
+
drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps, ydiff);
}
}
@@ -1614,8 +1617,6 @@ public class BamView extends JPanel
int hgt = getHeight();
int ypos = (hgt - scaleHeight);
int maxEnd = 0;
- int lstStart = 0;
- int lstEnd = 0;
int baseAtStartOfView = getBaseAtStartOfView();
g2.setColor(Color.blue);
Rectangle r = jspView.getViewport().getViewRect();
@@ -1623,6 +1624,7 @@ public class BamView extends JPanel
for(BamViewRecord bamViewRecord: readsInView)
{
SAMRecord samRecord = bamViewRecord.sam;
+
if( isNegativeStrand(samRecord, colourByStrandTag.isSelected()) == isStrandNegative )
{
final int offset = getSequenceOffset(samRecord.getReferenceName());
@@ -1630,13 +1632,8 @@ public class BamView extends JPanel
final int recordEnd = samRecord.getAlignmentEnd()+offset;
List<Integer> snps = getSNPs(samRecord);
- if(colourByCoverageColour.isSelected() ||
- colourByStrandTag.isSelected() ||
- colourByReadGrp.isSelected() ||
- lstStart != recordStart || lstEnd != recordEnd || snps != null)
+ if(colourByStrandTag.isSelected())
{
- if(colourByStrandTag.isSelected())
- {
if(samRecord.getAttribute("XS") == null)
g2.setColor(Color.BLACK);
else if( ((Character)samRecord.getAttribute("XS")).equals('+') )
@@ -1645,36 +1642,27 @@ public class BamView extends JPanel
g2.setColor(Color.RED);
else
g2.setColor(Color.BLACK);
- }
- else if(colourByCoverageColour.isSelected())
+ }
+ else if(colourByCoverageColour.isSelected())
g2.setColor(getColourByCoverageColour(bamViewRecord));
- else if(colourByReadGrp.isSelected())
+ else if(colourByReadGrp.isSelected())
g2.setColor(getReadGroupFrame().getReadGroupColour(readGroups, samRecord.getReadGroup()));
- else if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
+ else if (samRecord.getDuplicateReadFlag())
+ g2.setColor(DARK_GREEN); // Duplicate
+ else if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped
g2.setColor(Color.black);
- else
+ else
g2.setColor(Color.blue);
- if(maxEnd < recordStart || ypos < 0 || ypos > hgt)
- {
- ypos = ymid + ystep;
- maxEnd = recordEnd+2;
- }
- else
- ypos = ypos + ystep;
+ if(maxEnd < recordStart || ypos < 0 || ypos > hgt)
+ {
+ ypos = ymid + ystep;
+ maxEnd = recordEnd+2;
}
else
- g2.setColor(DARK_GREEN);
+ ypos = ypos + ystep;
- if(snps != null)
- lstStart = -1;
- else
- {
- lstStart = recordStart;
- lstEnd = recordEnd;
- }
-
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
@@ -1700,7 +1688,7 @@ public class BamView extends JPanel
drawSelectionRange(g2, pixPerBase,start, end, Color.PINK);
if(isShowScale())
drawScale(g2, start, end, pixPerBase, getHeight());
-
+
final Vector<PairedRead> pairedReads = new Vector<PairedRead>();
for(int i=0; i<readsInView.size(); i++)
{
@@ -1779,8 +1767,8 @@ public class BamView extends JPanel
g2.setStroke(originalStroke);
- if(highlightSAMRecord != null &&
- highlightSAMRecord.sam.getReadName().equals(pr.sam1.sam.getReadName()))
+ if( highlightSAMRecord != null &&
+ highlightSAMRecord.sam.getReadName().equals(pr.sam1.sam.getReadName()) )
g2.setColor(Color.black);
else
g2.setColor(Color.gray);
@@ -2133,22 +2121,34 @@ public class BamView extends JPanel
int thisStart = thisRead.getAlignmentStart()+offset-baseAtStartOfView;
int thisEnd = thisRead.getAlignmentEnd()+offset-baseAtStartOfView;
+
+ if(highlightSAMRecord != null &&
+ highlightSAMRecord.sam.getReadName().equals(thisRead.getReadName()))
+ {
+ Stroke originalStroke = g2.getStroke();
+ Stroke stroke =
+ new BasicStroke (readLnHgt*1.6f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
+ g2.setStroke(stroke);
+ Color c = g2.getColor();
+
+ if (isThisBamRecordHighlighted(bamViewRecord) )
+ {
+ // Selected read alignment
+ g2.setColor(Color.black);
+ }
+ else
+ {
+ // For a read with the same name as selected one.
+ g2.setColor(NON_SELECTED_READ_HIGHLIGHT_COLOUR);
+ }
+
+ g2.drawLine((int)( thisStart * pixPerBase), ypos,
+ (int)( thisEnd * pixPerBase), ypos);
+ g2.setColor(c);
+ g2.setStroke(originalStroke);
+ }
+
- if(highlightSAMRecord != null &&
- highlightSAMRecord.sam.getReadName().equals(thisRead.getReadName()))
- {
- Stroke originalStroke = g2.getStroke();
- Stroke stroke =
- new BasicStroke (readLnHgt*1.6f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
- 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);
- }
-
if(thisRead.getCigar().getCigarElements().size() == 1)
g2.drawLine((int)( thisStart * pixPerBase), ypos,
(int)( thisEnd * pixPerBase), ypos);
@@ -2178,19 +2178,21 @@ public class BamView extends JPanel
if(isOrientation)
drawArrow(g2, thisRead, thisStart, thisEnd, pixPerBase, ypos, ydiff);
-
+
// test if the mouse is over this read
if(lastMousePoint != null)
{
- if(lastMousePoint.getY()+2 > ypos && lastMousePoint.getY()-2 < ypos)
- if(lastMousePoint.getX() > thisStart * pixPerBase &&
- lastMousePoint.getX() < thisEnd * pixPerBase)
- {
- mouseOverSAMRecord = bamViewRecord;
- }
+ if(lastMousePoint.getY() > ypos-(Math.abs(ydiff)/2) && lastMousePoint.getY() < ypos+(Math.abs(ydiff)/2))
+ {
+ if(lastMousePoint.getX() > thisStart * pixPerBase &&
+ lastMousePoint.getX() < thisEnd * pixPerBase)
+ {
+ mouseOverSAMRecord = bamViewRecord;
+ }
+ }
}
- if (isSNPs && snps != null)
+ if (isSNPs && snps != null && snps.size() > 0)
showSNPsOnReads(snps, g2, pixPerBase, ypos);
}
@@ -2341,6 +2343,12 @@ public class BamView extends JPanel
new Range(rbeg+offset, rend+offset), Bases.FORWARD);
final byte[] readSeq = samRecord.getReadBases();
+ if (readSeq == null || readSeq.length == 0)
+ {
+ // Can occur for secondary alignments
+ return null;
+ }
+
offset = offset - getBaseAtStartOfView();
final List<AlignmentBlock> blocks = samRecord.getAlignmentBlocks();
for(AlignmentBlock block: blocks)
@@ -2843,8 +2851,12 @@ public class BamView extends JPanel
colourMenu.add(baseQualityColour);
menu.add(colourMenu);
- //
+ // =============
+ // Show Menu
+ // =============
+
JMenu showMenu = new JMenu("Show");
+
JCheckBoxMenuItem checkBoxOrientation = new JCheckBoxMenuItem("Orientation");
checkBoxOrientation.addActionListener(new ActionListener()
{
@@ -3199,6 +3211,10 @@ public class BamView extends JPanel
if (buttonAutoHide.isSelected() && topPanel.isVisible())
topPanel.setVisible(false);
}
+
+ // KJP - added these to make selecting work properly.
+ mainPanel.repaint();
+ mainPanel.revalidate();
}
};
addMouseMotionListener(mouseMotionListener);
@@ -3506,7 +3522,10 @@ public class BamView extends JPanel
if(event.getButton() == MouseEvent.BUTTON3 || bases == null)
return;
- highlightSAMRecord = null;
+ // KJP: Removed this as it causes selection issues and
+ // doesn't seems strictly necessary.
+ // highlightSAMRecord = null;
+
if(event.getClickCount() > 1)
{
getSelection().clear();
@@ -3906,17 +3925,29 @@ public class BamView extends JPanel
if(isCoverageView(getPixPerBaseByWidth()))
coverageView.singleClick(e.isShiftDown(),
e.getPoint().y-getJspView().getViewport().getViewPosition().y);
- else
- highlightSAMRecord = mouseOverSAMRecord;
+ //else
+ //{
+ // mouseHighlightSelectionMade.set(true);
+ // highlightSAMRecord = null;
+ //}
}
else
highlightRange(e, MouseEvent.BUTTON2_DOWN_MASK);
- repaint();
+ //repaint();
}
- public void mousePressed(MouseEvent e)
+ public void mousePressed(final MouseEvent e)
{
- maybeShowPopup(e);
+ highlightSAMRecord = mouseOverSAMRecord;
+
+ repaint();
+
+ javax.swing.SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ maybeShowPopup(e);
+ }
+ });
+
}
public void mouseReleased(MouseEvent e)
@@ -3985,9 +4016,12 @@ public class BamView extends JPanel
popup.remove(showDetails);
if( mouseOverSAMRecord != null &&
- mouseOverSAMRecord.sam.getReadPairedFlag() &&
+ mouseOverSAMRecord.sam.getReadPairedFlag() &&
!mouseOverSAMRecord.sam.getMateUnmappedFlag() )
{
+ // KJP: new
+ highlightSAMRecord = mouseOverSAMRecord;
+
final BamViewRecord thisSAMRecord = mouseOverSAMRecord;
gotoMateMenuItem = new JMenuItem("Go to mate of : "+
thisSAMRecord.sam.getReadName());
@@ -4015,6 +4049,9 @@ public class BamView extends JPanel
if( mouseOverSAMRecord != null)
{
+ // KJP: new
+ highlightSAMRecord = mouseOverSAMRecord;
+
final BamViewRecord thisSAMRecord = mouseOverSAMRecord;
showDetails = new JMenuItem("Show details of : "+
thisSAMRecord.sam.getReadName());
@@ -4194,6 +4231,21 @@ public class BamView extends JPanel
{
return concatSequences;
}
+
+ /**
+ * Check whether the given BAM record is highlighted currently.
+ * @param bamRec BamViewRecord
+ * @return boolean - true if highlighted
+ */
+ protected boolean isThisBamRecordHighlighted(BamViewRecord bamRec)
+ {
+ if (highlightSAMRecord == null)
+ {
+ return false;
+ }
+
+ return BamUtils.samRecordEqualityCheck(highlightSAMRecord.sam, bamRec.sam);
+ }
class PairedRead
{
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordSequenceString.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordSequenceString.java
new file mode 100644
index 0000000000000000000000000000000000000000..5221b92d9e8478c4c03f549d0d7b6f4357637969
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordSequenceString.java
@@ -0,0 +1,74 @@
+package uk.ac.sanger.artemis.components.alignment;
+
+/**
+ * Utility class that handles operations on an alignment block
+ * string taking into account the possibility that it could be
+ * a secondary alignment.
+ *
+ * @author kp11
+ *
+ */
+public class SAMRecordSequenceString
+{
+
+ public final static char SECONDARY_ALIGNMENT_BASE_CHAR = '=';
+ public final static char SECONDARY_ALIGNMENT_MARKER = '*';
+
+ private String sequence;
+ private boolean isSecondaryAlignment;
+
+ public SAMRecordSequenceString(String sequence)
+ {
+ this.sequence = sequence;
+ this.isSecondaryAlignment = (String.valueOf(SECONDARY_ALIGNMENT_MARKER).equals(sequence));
+ }
+
+ public String substring(int beginIdx, int endIdx)
+ {
+
+ String result = null;
+
+ if (!isSecondaryAlignment())
+ {
+ result = sequence.substring(beginIdx, endIdx);
+ }
+ else
+ {
+ result = new String(new char[endIdx-beginIdx]).replace('\0', SECONDARY_ALIGNMENT_BASE_CHAR);
+ }
+
+ return result;
+
+ }
+
+ public char charAt(int idx)
+ {
+
+ char result;
+
+ if (!isSecondaryAlignment())
+ {
+ result = sequence.charAt(idx);
+ }
+ else
+ {
+ result = SECONDARY_ALIGNMENT_BASE_CHAR;
+ }
+
+ return result;
+ }
+
+ public String getSequence()
+ {
+ return sequence;
+ }
+
+ public int length()
+ {
+ return sequence.length();
+ }
+
+ public boolean isSecondaryAlignment() {
+ return isSecondaryAlignment;
+ }
+}