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Merge branch 'bug/JAL-2791selectVisibleFeatures' into
[jalview.git]
/
src
/
jalview
/
controller
/
AlignViewController.java
diff --git
a/src/jalview/controller/AlignViewController.java
b/src/jalview/controller/AlignViewController.java
index
cc5a184
..
8b001b3
100644
(file)
--- a/
src/jalview/controller/AlignViewController.java
+++ b/
src/jalview/controller/AlignViewController.java
@@
-216,8
+216,9
@@
public class AlignViewController implements AlignViewControllerI
/**
* Sets a bit in the BitSet for each column (base 0) in the sequence
/**
* Sets a bit in the BitSet for each column (base 0) in the sequence
- * collection which includes the specified feature type. Returns the number of
- * sequences which have the feature in the selected range.
+ * collection which includes a visible feature of the specified feature type.
+ * Returns the number of sequences which have the feature visible in the
+ * selected range.
*
* @param featureType
* @param sqcol
*
* @param featureType
* @param sqcol
@@
-227,8
+228,8
@@
public class AlignViewController implements AlignViewControllerI
int findColumnsWithFeature(String featureType,
SequenceCollectionI sqcol, BitSet bs)
{
int findColumnsWithFeature(String featureType,
SequenceCollectionI sqcol, BitSet bs)
{
- FeatureRendererModel fr = (FeatureRendererModel) alignPanel
- .getFeatureRenderer();
+ FeatureRendererModel fr = alignPanel == null ? null
+ : (FeatureRendererModel) alignPanel.getFeatureRenderer();
List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
@@
-243,11
+244,7
@@
public class AlignViewController implements AlignViewControllerI
List<SequenceFeature> sfs = sq.findFeatures(startColumn,
endColumn, featureType);
List<SequenceFeature> sfs = sq.findFeatures(startColumn,
endColumn, featureType);
- if (!sfs.isEmpty())
- {
- nseq++;
- }
-
+ boolean found = false;
for (SequenceFeature sf : sfs)
{
{
for (SequenceFeature sf : sfs)
{
{
@@
-257,6
+254,12
@@
public class AlignViewController implements AlignViewControllerI
continue;
}
}
continue;
}
}
+ if (!found)
+ {
+ nseq++;
+ }
+ found = true;
+
int sfStartCol = sq.findIndex(sf.getBegin());
int sfEndCol = sq.findIndex(sf.getEnd());
int sfStartCol = sq.findIndex(sf.getBegin());
int sfEndCol = sq.findIndex(sf.getEnd());