X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FColumnCounterSetWorker.java;fp=src%2Fjalview%2Fworkers%2FColumnCounterSetWorker.java;h=3a4bcc4c6a155c90def4437dd1b7cb0d58e36536;hb=c3c8eb857e5544602671ea205da67f082de5a306;hp=74695fe2bd494f63ce4d866f3f16b02ee2a8691d;hpb=e9b0f1619b7b33b9d2ebb3f64d7cefe563c24db8;p=jalview.git
diff --git a/src/jalview/workers/ColumnCounterSetWorker.java b/src/jalview/workers/ColumnCounterSetWorker.java
index 74695fe..3a4bcc4 100644
--- a/src/jalview/workers/ColumnCounterSetWorker.java
+++ b/src/jalview/workers/ColumnCounterSetWorker.java
@@ -20,6 +20,10 @@
*/
package jalview.workers;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.List;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
@@ -31,10 +35,6 @@ import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.util.ColorUtils;
import jalview.util.Comparison;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.List;
-
/**
* A class to compute alignment annotations with column counts for a set of
* properties of interest on positions in an alignment.
@@ -223,6 +223,26 @@ class ColumnCounterSetWorker extends AlignCalcWorker
return annotationAdded;
}
+ void removeOldAnnotations(String[] annotDescs)
+ {
+ // TODO use the commented out code once JAL-2075 is fixed
+ // to get adequate performance on genomic length sequence
+ AlignmentI alignment = alignViewport.getAlignment();
+ ArrayList toRemove = new ArrayList();
+ for (String toRemoveDesc : annotDescs)
+ {
+ for (AlignmentAnnotation aa : ourAnnots)
+ {
+ if (toRemoveDesc.equals(aa.getCalcId()))
+ toRemove.add(aa);
+ }
+ }
+ for (AlignmentAnnotation deleted : toRemove)
+ {
+ alignment.deleteAnnotation(deleted);
+ }
+ }
+
/**
* Returns a count of any feature types present at the specified position of
* the alignment