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propagated groups trimmed to correct region on viscontig
author
jprocter
<Jim Procter>
Wed, 5 Jan 2011 15:36:30 +0000
(15:36 +0000)
committer
jprocter
<Jim Procter>
Wed, 5 Jan 2011 15:36:30 +0000
(15:36 +0000)
src/jalview/datamodel/AlignmentView.java
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diff --git
a/src/jalview/datamodel/AlignmentView.java
b/src/jalview/datamodel/AlignmentView.java
index
21b5e7f
..
2a93861
100644
(file)
--- a/
src/jalview/datamodel/AlignmentView.java
+++ b/
src/jalview/datamodel/AlignmentView.java
@@
-351,9
+351,14
@@
public class AlignmentView
continue;
\r
}
\r
}
\r
continue;
\r
}
\r
}
\r
+
\r
+ // clone group properties
\r
+ nsg[g] = new SequenceGroup(sg);
\r
+
\r
// may need to shift/trim start and end ?
\r
if (r && !viscontigs)
\r
{
\r
// may need to shift/trim start and end ?
\r
if (r && !viscontigs)
\r
{
\r
+ // Not fully tested code - routine not yet called with viscontigs==false
\r
if (nsg[g].getStartRes() < gstart)
\r
{
\r
nsg[g].setStartRes(0);
\r
if (nsg[g].getStartRes() < gstart)
\r
{
\r
nsg[g].setStartRes(0);
\r
@@
-363,14
+368,11
@@
public class AlignmentView
nsg[g].setStartRes(nsg[g].getStartRes() - gstart);
\r
nsg[g].setEndRes(nsg[g].getEndRes() - gstart);
\r
}
\r
nsg[g].setStartRes(nsg[g].getStartRes() - gstart);
\r
nsg[g].setEndRes(nsg[g].getEndRes() - gstart);
\r
}
\r
- if (nsg[g].getEndRes() > gend)
\r
+ if (nsg[g].getEndRes() > (gend-gstart))
\r
{
\r
{
\r
- nsg[g].setEndRes(gend);
\r
+ nsg[g].setEndRes(gend-gstart);
\r
}
\r
}
\r
}
\r
}
\r
-
\r
- // clone group properties
\r
- nsg[g] = new SequenceGroup(sg);
\r
}
\r
if (viscontigs)
\r
{
\r
}
\r
if (viscontigs)
\r
{
\r