git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
apply jalview code style
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
eedc863
..
6f713fc
100755
(executable)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-1,5
+1,5
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
@@
-552,8
+552,8
@@
public class AlignViewport implements SelectionSource
consensus.annotations = new Annotation[aWidth];
hconsensus = new Hashtable[aWidth];
consensus.annotations = new Annotation[aWidth];
hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
- .getWidth(), hconsensus, true);
+ AAFrequency.calculate(alignment.getSequencesArray(), 0,
+ alignment.getWidth(), hconsensus, true);
updateAnnotation(true);
if (globalColourScheme != null)
updateAnnotation(true);
if (globalColourScheme != null)
@@
-589,7
+589,8
@@
public class AlignViewport implements SelectionSource
protected void updateAnnotation(boolean immediate)
{
protected void updateAnnotation(boolean immediate)
{
- // TODO: make calls thread-safe, so if another thread calls this method, it will either return or wait until one calculation is finished.
+ // TODO: make calls thread-safe, so if another thread calls this method,
+ // it will either return or wait until one calculation is finished.
if (immediate
|| (!updatingConsensus && consensus != null && hconsensus != null))
{
if (immediate
|| (!updatingConsensus && consensus != null && hconsensus != null))
{
@@
-1852,8
+1853,8
@@
public class AlignViewport implements SelectionSource
{
Alignment al = (Alignment) alignment;
Conservation c = new Conservation("All",
{
Alignment al = (Alignment) alignment;
Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0, al
- .getWidth() - 1);
+ ResidueProperties.propHash, 3, al.getSequences(), 0,
+ al.getWidth() - 1);
c.calculate();
c.verdict(false, ConsPercGaps);
c.calculate();
c.verdict(false, ConsPercGaps);
@@
-1867,8
+1868,8
@@
public class AlignViewport implements SelectionSource
SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
{
SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
{
- ((ClustalxColourScheme) sg.cs).resetClustalX(sg
- .getSequences(hiddenRepSequences), sg.getWidth());
+ ((ClustalxColourScheme) sg.cs).resetClustalX(
+ sg.getSequences(hiddenRepSequences), sg.getWidth());
}
sg.recalcConservation();
}
}
sg.recalcConservation();
}