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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
80319be
..
c1c88c1
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-612,7
+612,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
boolean recalc = false;
if (cs != null)
{
boolean recalc = false;
if (cs != null)
{
- cs.setConservationApplied(recalc = getConservationSelected());
+ recalc = getConservationSelected();
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
@@
-629,6
+629,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
cs.setConsensus(hconsensus);
cs.setConservation(hconservation);
}
cs.setConsensus(hconsensus);
cs.setConservation(hconservation);
}
+ cs.setConservationApplied(getConservationSelected());
cs.alignmentChanged(alignment, hiddenRepSequences);
}
if (getColourAppliesToAllGroups())
cs.alignmentChanged(alignment, hiddenRepSequences);
}
if (getColourAppliesToAllGroups())
@@
-1573,7
+1574,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
public boolean isHiddenRepSequence(SequenceI seq)
{
return (hiddenRepSequences != null && hiddenRepSequences
public boolean isHiddenRepSequence(SequenceI seq)
{
return (hiddenRepSequences != null && hiddenRepSequences
- .containsKey(seq));
+ .containsKey(seq));
}
/**
}
/**
@@
-2796,8
+2797,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
public void expandColSelection(SequenceGroup sg, boolean wholewidth)
{
int sgs, sge;
public void expandColSelection(SequenceGroup sg, boolean wholewidth)
{
int sgs, sge;
- if (sg != null
- && (sgs = sg.getStartRes()) >= 0
+ if (sg != null && (sgs = sg.getStartRes()) >= 0
&& sg.getStartRes() <= (sge = sg.getEndRes())
&& !this.hasSelectedColumns())
{
&& sg.getStartRes() <= (sge = sg.getEndRes())
&& !this.hasSelectedColumns())
{