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Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
6581bef
..
91ee3c1
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-1420,11
+1420,15
@@
public abstract class AlignmentViewport implements AlignViewportI,
protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
boolean visible)
{
protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
boolean visible)
{
- for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+ AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+ if (anns != null)
{
{
- if (ann.sequenceRef == sequenceI)
+ for (AlignmentAnnotation ann : anns)
{
{
- ann.visible = visible;
+ if (ann.sequenceRef == sequenceI)
+ {
+ ann.visible = visible;
+ }
}
}
}
}
}
}
@@
-1588,6
+1592,13
@@
public abstract class AlignmentViewport implements AlignViewportI,
@Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
@Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
+ return getViewAsString(selectedRegionOnly, true);
+ }
+
+ @Override
+ public String[] getViewAsString(boolean selectedRegionOnly,
+ boolean exportHiddenSeqs)
+ {
String[] selection = null;
SequenceI[] seqs = null;
int i, iSize;
String[] selection = null;
SequenceI[] seqs = null;
int i, iSize;
@@
-1601,13
+1612,13
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
else
{
}
else
{
- if (hasHiddenRows() && isExportHiddenSeqs)
+ if (hasHiddenRows() && exportHiddenSeqs)
{
{
- iSize = alignment.getHiddenSequences().getFullAlignment()
- .getHeight();
- seqs = alignment.getHiddenSequences().getFullAlignment()
- .getSequencesArray();
- end = alignment.getHiddenSequences().getFullAlignment().getWidth();
+ AlignmentI fullAlignment = alignment.getHiddenSequences()
+ .getFullAlignment();
+ iSize = fullAlignment.getHeight();
+ seqs = fullAlignment.getSequencesArray();
+ end = fullAlignment.getWidth();
}
else
{
}
else
{
@@
-2720,17
+2731,5
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
}
}
}
- private boolean isExportHiddenSeqs = true;
- @Override
- public void setExportHiddenSeqs(boolean isExportHiddenSeqs)
- {
- this.isExportHiddenSeqs = isExportHiddenSeqs;
- }
-
- @Override
- public boolean isExportHiddenSeqs()
- {
- return isExportHiddenSeqs;
- }
}
}