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Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into develop
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
757175e
..
7849c2d
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-665,8
+665,7
@@
public abstract class AlignmentViewport
* retain any colour thresholds per group while
* changing choice of colour scheme (JAL-2386)
*/
* retain any colour thresholds per group while
* changing choice of colour scheme (JAL-2386)
*/
- sg.setColourScheme(
- cs == null ? null : cs.getInstance(this, sg));
+ sg.setColourScheme(cs == null ? null : cs.getInstance(this, sg));
if (cs != null)
{
sg.getGroupColourScheme().alignmentChanged(sg,
if (cs != null)
{
sg.getGroupColourScheme().alignmentChanged(sg,
@@
-1822,9
+1821,8
@@
public abstract class AlignmentViewport
AlignmentAnnotation clone = new AlignmentAnnotation(annot);
if (selectedOnly && selectionGroup != null)
{
AlignmentAnnotation clone = new AlignmentAnnotation(annot);
if (selectedOnly && selectionGroup != null)
{
- clone.makeVisibleAnnotation(
- selectionGroup.getStartRes(), selectionGroup.getEndRes(),
- alignment.getHiddenColumns());
+ clone.makeVisibleAnnotation(selectionGroup.getStartRes(),
+ selectionGroup.getEndRes(), alignment.getHiddenColumns());
}
else
{
}
else
{
@@
-2994,7
+2992,8
@@
public abstract class AlignmentViewport
}
@Override
}
@Override
- public AlignmentExportData getAlignExportData(AlignExportSettingsI options)
+ public AlignmentExportData getAlignExportData(
+ AlignExportSettingsI options)
{
AlignmentI alignmentToExport = null;
String[] omitHidden = null;
{
AlignmentI alignmentToExport = null;
String[] omitHidden = null;
@@
-3022,7
+3021,7
@@
public abstract class AlignmentViewport
omitHidden, alignmentStartEnd);
return ed;
}
omitHidden, alignmentStartEnd);
return ed;
}
-
+
/**
* flag set to indicate if structure views might be out of sync with sequences
* in the alignment
/**
* flag set to indicate if structure views might be out of sync with sequences
* in the alignment