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JAL-3594 New Jalview Test logos and .icns/.ico creation helper script
[jalview.git]
/
src
/
jalview
/
workers
/
ColumnCounterSetWorker.java
diff --git
a/src/jalview/workers/ColumnCounterSetWorker.java
b/src/jalview/workers/ColumnCounterSetWorker.java
index
2422748
..
74695fe
100644
(file)
--- a/
src/jalview/workers/ColumnCounterSetWorker.java
+++ b/
src/jalview/workers/ColumnCounterSetWorker.java
@@
-57,7
+57,7
@@
class ColumnCounterSetWorker extends AlignCalcWorker
AlignmentViewPanel panel, FeatureSetCounterI counter)
{
super(viewport, panel);
AlignmentViewPanel panel, FeatureSetCounterI counter)
{
super(viewport, panel);
- ourAnnots = new ArrayList<AlignmentAnnotation>();
+ ourAnnots = new ArrayList<>();
this.counter = counter;
calcMan.registerWorker(this);
}
this.counter = counter;
calcMan.registerWorker(this);
}
@@
-116,7
+116,7
@@
class ColumnCounterSetWorker extends AlignCalcWorker
{
ap.adjustAnnotationHeight();
}
{
ap.adjustAnnotationHeight();
}
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
}
}
}
@@
-229,6
+229,7
@@
class ColumnCounterSetWorker extends AlignCalcWorker
*
* @param alignment
* @param col
*
* @param alignment
* @param col
+ * (0..)
* @param row
* @param fr
*/
* @param row
* @param fr
*/
@@
-249,14
+250,12
@@
class ColumnCounterSetWorker extends AlignCalcWorker
{
return null;
}
{
return null;
}
- int pos = seq.findPosition(col);
/*
* compute a count for any displayed features at residue
*/
/*
* compute a count for any displayed features at residue
*/
- // NB have to adjust pos if using AlignmentView.getVisibleAlignment
// see JAL-2075
// see JAL-2075
- List<SequenceFeature> features = fr.findFeaturesAtRes(seq, pos);
+ List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, col + 1);
int[] count = this.counter.count(String.valueOf(res), features);
return count;
}
int[] count = this.counter.count(String.valueOf(res), features);
return count;
}