From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 19 Jul 2016 17:30:24 +0000 (+0100)
Subject: JAL-2068 update rather than recreate AlignmentAnnotation on run()
X-Git-Tag: Release_2_10_0~125^2~15
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f5be72936a417898b982510adf7e23d2f313c59a;p=jalview.git

JAL-2068 update rather than recreate AlignmentAnnotation on run()
---

diff --git a/src/jalview/workers/ColumnCounterWorker.java b/src/jalview/workers/ColumnCounterWorker.java
index 5f61525..4e1a336 100644
--- a/src/jalview/workers/ColumnCounterWorker.java
+++ b/src/jalview/workers/ColumnCounterWorker.java
@@ -89,7 +89,6 @@ class ColumnCounterWorker extends AlignCalcWorker
         return;
       }
 
-      removeAnnotation();
       if (alignViewport.getAlignment() != null)
       {
         try
@@ -159,21 +158,58 @@ class ColumnCounterWorker extends AlignCalcWorker
       {
         Color color = ColorUtils.getGraduatedColour(count, 0, Color.cyan,
                 max, Color.blue);
-        anns[i] = new Annotation(String.valueOf(count),
-                String.valueOf(count), '0', count, color);
+        String str = String.valueOf(count);
+        anns[i] = new Annotation(str, str, '0', count, color);
       }
     }
 
     /*
-     * construct the annotation, save it and add it to the displayed alignment
+     * construct or update the annotation
      */
-    AlignmentAnnotation ann = new AlignmentAnnotation(counter.getName(),
-            counter.getDescription(), anns);
+    AlignmentAnnotation ann = alignViewport.getAlignment()
+            .findOrCreateAnnotation(counter.getName(),
+                    counter.getDescription(), false, null,
+                    null);
+    ann.description = counter.getDescription();
     ann.showAllColLabels = true;
     ann.scaleColLabel = true;
     ann.graph = AlignmentAnnotation.BAR_GRAPH;
-    ourAnnots.add(ann);
-    alignViewport.getAlignment().addAnnotation(ann);
+    ann.annotations = anns;
+    setGraphMinMax(ann, anns);
+    ann.validateRangeAndDisplay();
+    if (!ourAnnots.contains(ann))
+    {
+      ourAnnots.add(ann);
+    }
+  }
+
+  /**
+   * Calculate min and max values of annotations and set as graphMin, graphMax
+   * on the AlignmentAnnotation. This is needed because otherwise, well, bad
+   * things happen.
+   * 
+   * @param ann
+   * @param anns
+   */
+  private void setGraphMinMax(AlignmentAnnotation ann, Annotation[] anns)
+  {
+    // TODO feels like this belongs inside AlignmentAnnotation!
+    float max = Float.MIN_VALUE;
+    float min = Float.MAX_VALUE;
+    boolean set = false;
+    for (Annotation a : anns) {
+      if (a != null) {
+        set = true;
+        float val = a.value;
+        max = Math.max(max, val);
+        min = Math.min(min, val);
+      }
+    }
+    if (set)
+    {
+      ann.graphMin = min;
+      ann.graphMax = max;
+    }
   }
 
   /**