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[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentView.java
diff --git
a/src/jalview/datamodel/AlignmentView.java
b/src/jalview/datamodel/AlignmentView.java
index
2da7c80
..
ebe8301
100644
(file)
--- a/
src/jalview/datamodel/AlignmentView.java
+++ b/
src/jalview/datamodel/AlignmentView.java
@@
-107,7
+107,7
@@
public class AlignmentView
{
\r
Vector sel = selection.getSequences(null);
\r
this.selected = new Vector();
\r
{
\r
Vector sel = selection.getSequences(null);
\r
this.selected = new Vector();
\r
- selseqs = selection.getSequencesInOrder(alignment, false);
\r
+ selseqs = selection.getSequencesInOrder(alignment, selectedRegionOnly);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
@@
-150,6
+150,9
@@
public class AlignmentView
{
\r
sg.setEndRes(esel);
\r
}
\r
{
\r
sg.setEndRes(esel);
\r
}
\r
+ sg.setStartRes(sg.getStartRes()-ssel+1);
\r
+ sg.setEndRes(sg.getEndRes()-ssel+1);
\r
+
\r
isg.addElement(sg);
\r
}
\r
}
\r
isg.addElement(sg);
\r
}
\r
}
\r
@@
-348,9
+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
@@
-360,14
+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