diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index fab7732e850769010ca74c56d5c7bef7dace6a9f..caaa8085c37acb9cc9cc809fd677657843ca2db2 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -135,7 +135,7 @@ public class BamView extends JPanel
private JPanel mainPanel;
private CoveragePanel coveragePanel;
private boolean showScale = true;
- private Ruler ruler = new Ruler();
+ private Ruler ruler;
private int nbasesInView;
private int startBase = -1;
@@ -166,6 +166,7 @@ public class BamView extends JPanel
private boolean concatSequences = false;
private int ALIGNMENT_PIX_PER_BASE;
+ private int BASE_HEIGHT;
private JPopupMenu popup;
@@ -215,6 +216,7 @@ public class BamView extends JPanel
setFont(Options.getOptions().getFont());
FontMetrics fm = getFontMetrics(getFont());
ALIGNMENT_PIX_PER_BASE = fm.charWidth('M');
+ BASE_HEIGHT = fm.getHeight();
selection = new Selection(null);
MultiLineToolTipUI.initialize();
@@ -491,7 +493,7 @@ public class BamView extends JPanel
laststart = start;
lastend = end;
- if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
+ if(showBaseAlignment)
drawBaseAlignment(g2, seqLength, pixPerBase, start, end);
else
{
@@ -513,7 +515,7 @@ public class BamView extends JPanel
private float getPixPerBaseByWidth()
{
- return (float)( getPreferredSize().getWidth() /nbasesInView);
+ return (float)mainPanel.getWidth() / (float)nbasesInView;
}
@@ -537,7 +539,7 @@ public class BamView extends JPanel
int seqLength,
float pixPerBase,
final int start,
- final int end)
+ int end)
{
ruler.start = start;
ruler.end = end;
@@ -547,6 +549,8 @@ public class BamView extends JPanel
String refSeq = null;
int refSeqStart = start;
+
+ end = start + ( mainPanel.getWidth() * ALIGNMENT_PIX_PER_BASE );
if(bases != null)
{
// draw the reference sequence
@@ -564,7 +568,7 @@ public class BamView extends JPanel
bases.getSubSequence(new Range(refSeqStart, seqEnd), Bases.FORWARD).toUpperCase();
g2.setColor(lightGrey);
- g2.fillRect(0, ypos-11, getPreferredSize().width, 11);
+ g2.fillRect(0, ypos-11, mainPanel.getWidth(), 11);
drawSelectionRange(g2, ALIGNMENT_PIX_PER_BASE, start, end);
g2.setColor(Color.black);
g2.drawString(refSeq, 0, ypos);
@@ -670,6 +674,17 @@ public class BamView extends JPanel
}
}
+ // highlight
+ if(highlightSAMRecord != null &&
+ highlightSAMRecord.getReadName().equals(samRecord.getReadName()))
+ {
+ int refPos = blocks.get(0).getReferenceStart()+offset-refSeqStart;
+ int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
+ int width = len*ALIGNMENT_PIX_PER_BASE;
+ g2.setColor(Color.red);
+ g2.drawRect(xstart, ypos-BASE_HEIGHT, width, BASE_HEIGHT);
+ }
+
if(lastMousePoint != null)
{
int refPos = blocks.get(0).getReferenceStart()+offset-refSeqStart;
@@ -990,8 +1005,8 @@ public class BamView extends JPanel
{
boolean offTheTop = false;
int offset = getSequenceOffset(samRecord.getReferenceName());
- int thisStart = samRecord.getAlignmentStart()-1+offset;
- int thisEnd = thisStart + samRecord.getReadString().length();
+ int thisStart = samRecord.getAlignmentStart()+offset;
+ int thisEnd = thisStart + samRecord.getReadString().length() -1;
if(ypos <= 0)
{
@@ -1007,16 +1022,16 @@ public class BamView extends JPanel
if(samRecord.getAlignmentEnd() < samRecord.getMateAlignmentStart())
{
int nextStart =
- (int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
+ (int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
drawTranslucentLine(g2,
- (int)((thisStart-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
+ (int)((thisEnd-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
}
else
{
int nextStart =
(int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
drawTranslucentLine(g2,
- (int)((thisEnd-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
+ (int)((thisStart-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
}
}
@@ -1622,8 +1637,11 @@ public class BamView extends JPanel
if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
{
pixPerBase = ALIGNMENT_PIX_PER_BASE;
- this.nbasesInView = (int)(getPreferredSize().getWidth()/pixPerBase);
+ this.nbasesInView = (int)(mainPanel.getWidth()/pixPerBase);
jspView.getVerticalScrollBar().setValue(0);
+
+ if(ruler == null)
+ ruler = new Ruler();
jspView.setColumnHeaderView(ruler);
showBaseAlignment = true;
}
@@ -1640,6 +1658,7 @@ public class BamView extends JPanel
scrollBar.setValues(startValue, nbasesInView, 1,
getMaxBasesInPanel(getSequenceLength()));
scrollBar.setUnitIncrement(nbasesInView/20);
+ scrollBar.setBlockIncrement(nbasesInView);
}
}
@@ -1777,8 +1796,7 @@ public class BamView extends JPanel
**/
private void handleCanvasMouseDragOrClick(final MouseEvent event)
{
- if(event.isShiftDown() || event.getButton() == MouseEvent.BUTTON3
- || bases == null)
+ if(event.getButton() == MouseEvent.BUTTON3 || bases == null)
return;
highlightSAMRecord = null;
@@ -1789,21 +1807,31 @@ public class BamView extends JPanel
return;
}
- int onmask = MouseEvent.BUTTON1_DOWN_MASK;
+ highlightRange(event,
+ MouseEvent.BUTTON1_DOWN_MASK & MouseEvent.BUTTON2_DOWN_MASK);
+ }
+
+ /**
+ *
+ * @param event
+ * @param onmask
+ */
+ private void highlightRange(MouseEvent event, int onmask)
+ {
int seqLength = getSequenceLength();
float pixPerBase = getPixPerBaseByWidth();
int start = (int) ( ( (event.getPoint().getX())/pixPerBase) + getBaseAtStartOfView() );
- if (dragStart < 0 && (event.getModifiersEx() & onmask) == onmask)
- dragStart = start;
- else if((event.getModifiersEx() & onmask) != onmask)
- dragStart = -1;
-
if(start < 1)
start = 1;
if(start > seqLength)
start = seqLength;
+ if (dragStart < 0 && (event.getModifiersEx() & onmask) == onmask)
+ dragStart = start;
+ else if((event.getModifiersEx() & onmask) != onmask)
+ dragStart = -1;
+
MarkerRange drag_range;
try
{
@@ -1868,7 +1896,7 @@ public class BamView extends JPanel
public Ruler()
{
super();
- setPreferredSize(new Dimension(getPreferredSize().width, 15));
+ setPreferredSize(new Dimension(mainPanel.getWidth(), 15));
setBackground(Color.white);
setFont(getFont().deriveFont(11.f));
}
@@ -1884,6 +1912,9 @@ public class BamView extends JPanel
{
int startMark = (((int)(start/10))*10)+1;
+ if(end > getSequenceLength())
+ end = getSequenceLength();
+
for(int i=startMark; i<end; i+=10)
{
int xpos = (i-start)*ALIGNMENT_PIX_PER_BASE;
@@ -1909,6 +1940,8 @@ public class BamView extends JPanel
getSelection().clear();
else if(e.getButton() == MouseEvent.BUTTON1)
highlightSAMRecord = mouseOverSAMRecord;
+ else
+ highlightRange(e, MouseEvent.BUTTON2_DOWN_MASK);
repaint();
}