git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
59fec9d
)
JAL-3095 account for sequence start when highlighting selections in trimmed VARNA...
author
Jim Procter
<jprocter@issues.jalview.org>
Fri, 31 Aug 2018 15:08:32 +0000
(16:08 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Fri, 31 Aug 2018 15:08:32 +0000
(16:08 +0100)
src/jalview/gui/AppVarna.java
patch
|
blob
|
history
diff --git
a/src/jalview/gui/AppVarna.java
b/src/jalview/gui/AppVarna.java
index
aad4a96
..
3a64716
100644
(file)
--- a/
src/jalview/gui/AppVarna.java
+++ b/
src/jalview/gui/AppVarna.java
@@
-428,15
+428,28
@@
public class AppVarna extends JInternalFrame
{
return;
}
{
return;
}
- if (seqsel != null && seqsel.getSize() > 0)
+
+ RnaModel rnaModel = models.get(rna);
+
+ if (seqsel != null && seqsel.getSize() > 0
+ && seqsel.contains(rnaModel.seq))
{
int start = seqsel.getStartRes(), end = seqsel.getEndRes();
{
int start = seqsel.getStartRes(), end = seqsel.getEndRes();
- ShiftList shift = offsets.get(rna);
- if (shift != null)
+ if (rnaModel.gapped)
+ {
+ ShiftList shift = offsets.get(rna);
+ if (shift != null)
+ {
+ start = shift.shift(start);
+ end = shift.shift(end);
+ }
+ }
+ else
{
{
- start = shift.shift(start);
- end = shift.shift(end);
+ start = rnaModel.seq.findPosition(start) - rnaModel.seq.getStart();
+ end = rnaModel.seq.findPosition(end) - rnaModel.seq.getStart();
}
}
+
selectionHighlighter.highlightRegion(rna, start, end);
selectionHighlighter.getLastHighlight()
.setOutlineColor(seqsel.getOutlineColour());
selectionHighlighter.highlightRegion(rna, start, end);
selectionHighlighter.getLastHighlight()
.setOutlineColor(seqsel.getOutlineColour());