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:
a98cc98
)
(JAL-942) more tweaking mapping between 2-struct and seqs
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Fri, 2 Mar 2012 16:23:20 +0000
(16:23 +0000)
committer
jprocter
<jprocter@compbio.dundee.ac.uk>
Fri, 2 Mar 2012 16:23:20 +0000
(16:23 +0000)
src/jalview/gui/AppVarna.java
patch
|
blob
|
history
diff --git
a/src/jalview/gui/AppVarna.java
b/src/jalview/gui/AppVarna.java
index
06de21f
..
cbb3f95
100644
(file)
--- a/
src/jalview/gui/AppVarna.java
+++ b/
src/jalview/gui/AppVarna.java
@@
-190,7
+190,7
@@
public class AppVarna extends JInternalFrame implements
{
if (ofstart > -1)
{
{
if (ofstart > -1)
{
- offset.addShift(ofstart, ofstart - i);
+ offset.addShift(offset.shift(ofstart), ofstart - i);
ofstart = -1;
}
}
ofstart = -1;
}
}
@@
-198,7
+198,7
@@
public class AppVarna extends JInternalFrame implements
// final gap
if (ofstart > -1)
{
// final gap
if (ofstart > -1)
{
- offset.addShift(ofstart, ofstart - sleng);
+ offset.addShift(offset.shift(ofstart), ofstart - sleng);
ofstart = -1;
}
String newSeq = rnaTrim.getSeq().replace("-", "");
ofstart = -1;
}
String newSeq = rnaTrim.getSeq().replace("-", "");
@@
-327,12
+327,14
@@
public class AppVarna extends JInternalFrame implements
public void mouseOverSequence(SequenceI sequence, int index)
{
RNA rna = vab.getSelectedRNA();
public void mouseOverSequence(SequenceI sequence, int index)
{
RNA rna = vab.getSelectedRNA();
- if (rnas.get(sequence) == rna)
+ if (seqs.get(rna) == sequence)
{
ShiftList shift = offsets.get(rna);
if (shift != null)
{
{
ShiftList shift = offsets.get(rna);
if (shift != null)
{
- index = shift.shift(index);
+ // System.err.print("Orig pos:"+index);
+ index = shift.shift(index);
+ // System.err.println("\nFinal pos:"+index);
}
mouseOverHighlighter.highlightRegion(rna, index, index);
vab.updateSelectedRNA(rna);
}
mouseOverHighlighter.highlightRegion(rna, index, index);
vab.updateSelectedRNA(rna);
@@
-388,9
+390,9
@@
public class AppVarna extends JInternalFrame implements
{
if (shift != null)
{
{
if (shift != null)
{
- int i=shift.shift(arg1.getIndex());
- ssm.mouseOverVamsasSequence(seq,
- i, this);
+ int i = shift.shift(arg1.getIndex());
+ // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
+ ssm.mouseOverVamsasSequence(seq, i, this);
}
else
{
}
else
{