Merge branch 'features/JAL-4071_visibleFeaturesCounter' into features/JAL-3417_sdppre...

[jalview.git] / src / jalview / workers / ColumnCounterSetWorker.java

diff --git a/src/jalview/workers/ColumnCounterSetWorker.java b/src/jalview/workers/ColumnCounterSetWorker.java
index 74695fe..0858527 100644 (file)
--- a/src/jalview/workers/ColumnCounterSetWorker.java
+++ b/src/jalview/workers/ColumnCounterSetWorker.java
@@ -20,21 +20,22 @@
  */
 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;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 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. <br>
@@ -147,11 +148,6 @@ class ColumnCounterSetWorker extends AlignCalcWorker
       max[crow] = 0;
     }
 
-    int[] minC = counter.getMinColour();
-    int[] maxC = counter.getMaxColour();
-    Color minColour = new Color(minC[0], minC[1], minC[2]);
-    Color maxColour = new Color(maxC[0], maxC[1], maxC[2]);
-
     for (int col = 0; col < width; col++)
     {
       int[] count = counts[col];
@@ -181,6 +177,11 @@ class ColumnCounterSetWorker extends AlignCalcWorker
 
     for (int anrow = 0; anrow < rows; anrow++)
     {
+      int[] minC = counter.getMinColour(anrow);
+      int[] maxC = counter.getMaxColour(anrow);
+      Color minColour = new Color(minC[0], minC[1], minC[2]);
+      Color maxColour = new Color(maxC[0], maxC[1], maxC[2]);
+
       Annotation[] anns = new Annotation[width];
       long rmax = 0;
       /*
@@ -223,6 +224,26 @@ 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<AlignmentAnnotation> toRemove = new ArrayList<AlignmentAnnotation>();
+    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
@@ -256,6 +277,12 @@ class ColumnCounterSetWorker extends AlignCalcWorker
      */
     // see JAL-2075
     List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, col + 1);
+    if (fr.hasRenderOrder())
+    {
+      MappedFeatures mappedFeatres = fr.findComplementFeaturesAtResidue(seq,
+              seq.findPosition(col));
+      features.addAll(mappedFeatres.features);
+    }
     int[] count = this.counter.count(String.valueOf(res), features);
     return count;
   }