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JAL-2556 start to account for wrapped alignments
author
kiramt
<k.mourao@dundee.ac.uk>
Wed, 16 Aug 2017 13:25:03 +0000
(14:25 +0100)
committer
kiramt
<k.mourao@dundee.ac.uk>
Wed, 16 Aug 2017 13:25:03 +0000
(14:25 +0100)
src/jalview/gui/SeqCanvas.java
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diff --git
a/src/jalview/gui/SeqCanvas.java
b/src/jalview/gui/SeqCanvas.java
index
e999e78
..
558c1ca
100755
(executable)
--- a/
src/jalview/gui/SeqCanvas.java
+++ b/
src/jalview/gui/SeqCanvas.java
@@
-936,8
+936,8
@@
public class SeqCanvas extends JComponent implements ViewportListenerI
if (sx < 0)
{
if (sx < 0)
{
- // ex += sx;
- // sx = 0;
+ ex += sx;
+ sx = 0;
}
if (sx + ex > visWidth)
}
if (sx + ex > visWidth)
@@
-1034,6
+1034,16
@@
public class SeqCanvas extends JComponent implements ViewportListenerI
*/
private BufferedImage drawSelectionGroup()
{
*/
private BufferedImage drawSelectionGroup()
{
+ int verticalOffset = 0;
+ if (av.getWrapAlignment())
+ {
+ verticalOffset = charHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ verticalOffset += charHeight;
+ }
+ }
+
// get a new image of the correct size
BufferedImage selectionImage = setupImage();
// get a new image of the correct size
BufferedImage selectionImage = setupImage();
@@
-1051,6
+1061,7
@@
public class SeqCanvas extends JComponent implements ViewportListenerI
// set up drawing colour
Graphics2D g = (Graphics2D) selectionImage.getGraphics();
// set up drawing colour
Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+ g.translate(LABEL_WEST, 0);
// set background to transparent
g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
// set background to transparent
g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
@@
-1079,7
+1090,7
@@
public class SeqCanvas extends JComponent implements ViewportListenerI
int startSeq = av.getRanges().getStartSeq();
for (i = startSeq; i <= av.getRanges().getEndSeq(); ++i)
{
int startSeq = av.getRanges().getStartSeq();
for (i = startSeq; i <= av.getRanges().getEndSeq(); ++i)
{
- int sy = (i - startSeq) * charHeight;
+ int sy = verticalOffset + (i - startSeq) * charHeight;
if (group.getSequences(null)
.contains(av.getAlignment().getSequenceAt(i)))
if (group.getSequences(null)
.contains(av.getAlignment().getSequenceAt(i)))
@@
-1145,7
+1156,7
@@
public class SeqCanvas extends JComponent implements ViewportListenerI
}
if (inGroup)
{
}
if (inGroup)
{
- int sy = (i - startSeq) * charHeight;
+ int sy = verticalOffset + (i - startSeq) * charHeight;
if (startx >= 0 && startx < visWidth)
{
g.drawLine(startx, oldY, startx, sy);
if (startx >= 0 && startx < visWidth)
{
g.drawLine(startx, oldY, startx, sy);
@@
-1175,7
+1186,7
@@
public class SeqCanvas extends JComponent implements ViewportListenerI
inGroup = false;
}
inGroup = false;
}
-
+ g.translate(-LABEL_WEST, 0);
return selectionImage;
}
return selectionImage;
}