JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...

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

diff --git a/src/jalview/workers/ColumnCounterSetWorker.java b/src/jalview/workers/ColumnCounterSetWorker.java
index cf6a229..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);
-    ourAnnots = new ArrayList<AlignmentAnnotation>();
+    ourAnnots = new ArrayList<>();
     this.counter = counter;
     calcMan.registerWorker(this);
   }
@@ -69,6 +69,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
   @Override
   public void run()
   {
+    boolean annotationAdded = false;
     try
     {
       calcMan.notifyStart(this);
@@ -93,7 +94,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
       {
         try
         {
-          computeAnnotations();
+          annotationAdded = computeAnnotations();
         } catch (IndexOutOfBoundsException x)
         {
           // probable race condition. just finish and return without any fuss.
@@ -111,8 +112,11 @@ class ColumnCounterSetWorker extends AlignCalcWorker
 
     if (ap != null)
     {
-      ap.adjustAnnotationHeight();
-      ap.paintAlignment(true);
+      if (annotationAdded)
+      {
+        ap.adjustAnnotationHeight();
+      }
+      ap.paintAlignment(true, true);
     }
 
   }
@@ -120,8 +124,10 @@ class ColumnCounterSetWorker extends AlignCalcWorker
   /**
    * Scan each column of the alignment to calculate a count by feature type. Set
    * the count as the value of the alignment annotation for that feature type.
+   * 
+   * @return
    */
-  void computeAnnotations()
+  boolean computeAnnotations()
   {
     FeatureRenderer fr = new FeatureRenderer(alignViewport);
     // TODO use the commented out code once JAL-2075 is fixed
@@ -140,6 +146,12 @@ 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];
@@ -164,43 +176,51 @@ class ColumnCounterSetWorker extends AlignCalcWorker
         max[crow] = Math.max(count[crow], max[crow]);
       }
     }
+
+    boolean annotationAdded = false;
+
     for (int anrow = 0; anrow < rows; anrow++)
     {
       Annotation[] anns = new Annotation[width];
+      long rmax = 0;
       /*
-       * add non-zero counts as annotations
+       * add counts as annotations. zeros are needed since select-by-annotation ignores empty annotation positions
        */
       for (int i = 0; i < counts.length; i++)
       {
         int count = counts[i][anrow];
-        if (count > 0)
-        {
-          Color color = ColorUtils.getGraduatedColour(count, 0, Color.cyan,
-                  max[anrow], Color.blue);
-          String str = String.valueOf(count);
-          anns[i] = new Annotation(str, str, '0', count, color);
-        }
+
+        Color color = ColorUtils.getGraduatedColour(count, 0, minColour,
+                max[anrow], maxColour);
+        String str = String.valueOf(count);
+        anns[i] = new Annotation(str, str, '0', count, color);
+        rmax = Math.max(count, rmax);
       }
 
       /*
        * construct or update the annotation
        */
-      AlignmentAnnotation ann = alignViewport.getAlignment()
-              .findOrCreateAnnotation(counter.getNames()[anrow],
-                      counter.getDescriptions()[anrow], false, null,
-                      null);
-      ann.description = counter.getDescriptions()[anrow];
+      String description = counter.getDescriptions()[anrow];
+      if (!alignment.findAnnotation(description).iterator().hasNext())
+      {
+        annotationAdded = true;
+      }
+      AlignmentAnnotation ann = alignment.findOrCreateAnnotation(
+              counter.getNames()[anrow], description, false, null, null);
+      ann.description = description;
       ann.showAllColLabels = true;
       ann.scaleColLabel = true;
       ann.graph = AlignmentAnnotation.BAR_GRAPH;
       ann.annotations = anns;
-      setGraphMinMax(ann, anns);
+      ann.graphMin = 0f; // minimum always zero count
+      ann.graphMax = rmax; // maximum count from loop over feature columns
       ann.validateRangeAndDisplay();
       if (!ourAnnots.contains(ann))
       {
         ourAnnots.add(ann);
       }
     }
+    return annotationAdded;
   }
 
   /**
@@ -209,6 +229,7 @@ class ColumnCounterSetWorker extends AlignCalcWorker
    * 
    * @param alignment
    * @param col
+   *          (0..)
    * @param row
    * @param fr
    */
@@ -229,14 +250,12 @@ class ColumnCounterSetWorker extends AlignCalcWorker
     {
       return null;
     }
-    int pos = seq.findPosition(col);
 
     /*
      * compute a count for any displayed features at residue
      */
-    // NB have to adjust pos if using AlignmentView.getVisibleAlignment
     // 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;
   }