From 6d2246e02a1232760ec873f9b6ee4a775c6b4b7d Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 20 Jul 2016 06:09:01 +0100
Subject: [PATCH] JAL-2068 AnnotationWorker create/update annotation, not
 delete / re-add

---
 src/jalview/workers/AlignCalcWorker.java     |   30 ++++++++++++++++++++++++++
 src/jalview/workers/AnnotationWorker.java    |   19 +++++++++++-----
 src/jalview/workers/ColumnCounterWorker.java |   29 -------------------------
 3 files changed, 44 insertions(+), 34 deletions(-)

diff --git a/src/jalview/workers/AlignCalcWorker.java b/src/jalview/workers/AlignCalcWorker.java
index 7719c88..771c492 100644
--- a/src/jalview/workers/AlignCalcWorker.java
+++ b/src/jalview/workers/AlignCalcWorker.java
@@ -26,6 +26,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 
 import java.util.List;
 
@@ -103,4 +104,33 @@ public abstract class AlignCalcWorker implements AlignCalcWorkerI
     return false;
   }
 
+  /**
+   * 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
+   */
+  protected 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;
+    }
+  }
+
 }
diff --git a/src/jalview/workers/AnnotationWorker.java b/src/jalview/workers/AnnotationWorker.java
index 65603d6..4d81307 100644
--- a/src/jalview/workers/AnnotationWorker.java
+++ b/src/jalview/workers/AnnotationWorker.java
@@ -79,7 +79,7 @@ class AnnotationWorker extends AlignCalcWorker
         return;
       }
 
-      removeAnnotation();
+      // removeAnnotation();
       AlignmentI alignment = alignViewport.getAlignment();
       if (alignment != null)
       {
@@ -89,10 +89,19 @@ class AnnotationWorker extends AlignCalcWorker
                   alignment, new FeatureRenderer(alignViewport));
           for (AlignmentAnnotation ann : anns)
           {
-            ann.showAllColLabels = true;
-            ann.graph = AlignmentAnnotation.BAR_GRAPH;
-            ourAnnots.add(ann);
-            alignment.addAnnotation(ann);
+            AlignmentAnnotation theAnn = alignment.findOrCreateAnnotation(
+                    ann.label, ann.description, false, null, null);
+            theAnn.showAllColLabels = true;
+            theAnn.graph = AlignmentAnnotation.BAR_GRAPH;
+            theAnn.scaleColLabel = true;
+            theAnn.annotations = ann.annotations;
+            setGraphMinMax(theAnn, theAnn.annotations);
+            theAnn.validateRangeAndDisplay();
+            if (!ourAnnots.contains(theAnn))
+            {
+              ourAnnots.add(theAnn);
+            }
+            // alignment.addAnnotation(ann);
           }
         } catch (IndexOutOfBoundsException x)
         {
diff --git a/src/jalview/workers/ColumnCounterWorker.java b/src/jalview/workers/ColumnCounterWorker.java
index 4e1a336..2f73cb5 100644
--- a/src/jalview/workers/ColumnCounterWorker.java
+++ b/src/jalview/workers/ColumnCounterWorker.java
@@ -184,35 +184,6 @@ class ColumnCounterWorker extends AlignCalcWorker
   }
 
   /**
-   * 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;
-    }
-  }
-
-  /**
    * Returns a count of any feature types present at the specified position of
    * the alignment
    * 
-- 
1.7.10.2