Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / appletgui / FeatureRenderer.java

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 194b18f..b35c079 100644 (file)
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -399,11 +399,14 @@ public class FeatureRenderer
     /*
      * only update default type and group if we used defaults
      */
-    String enteredType = name.getText().trim();
+    final String enteredType = name.getText().trim();
+    final String enteredGroup = group.getText().trim();
+    final String enteredDesc = description.getText().replace('\n', ' ');
+
     if (dialog.accept && useLastDefaults)
     {
       lastFeatureAdded = enteredType;
-      lastFeatureGroupAdded = group.getText().trim();
+      lastFeatureGroupAdded = enteredGroup;
     }
 
     if (!create)
@@ -411,29 +414,36 @@ public class FeatureRenderer
       SequenceFeature sf = features.get(featureIndex);
       if (dialog.accept)
       {
-        sf.type = enteredType;
-        sf.featureGroup = group.getText().trim();
-        if (sf.featureGroup != null && sf.featureGroup.length() < 1)
-        {
-          sf.featureGroup = null;
-        }
-        sf.description = description.getText().replace('\n', ' ');
         if (!colourPanel.isGcol)
         {
           // update colour - otherwise its already done.
-          setColour(sf.type,
+          setColour(enteredType,
                   new FeatureColour(colourPanel.getBackground()));
         }
+        int newBegin = sf.begin;
+        int newEnd = sf.end;
         try
         {
-          sf.begin = Integer.parseInt(start.getText());
-          sf.end = Integer.parseInt(end.getText());
+          newBegin = Integer.parseInt(start.getText());
+          newEnd = Integer.parseInt(end.getText());
         } catch (NumberFormatException ex)
         {
-          //
+          // 
         }
-        boolean typeOrGroupChanged = (!featureType.equals(sf.type)
-                || !featureGroup.equals(sf.featureGroup));
+
+        /*
+         * replace the feature by deleting it and adding a new one
+         * (to ensure integrity of SequenceFeatures data store)
+         */
+        sequences.get(0).deleteFeature(sf);
+        SequenceFeature newSf = new SequenceFeature(sf, enteredType,
+                newBegin, newEnd, enteredGroup, sf.getScore());
+        newSf.setDescription(enteredDesc);
+        ffile.parseDescriptionHTML(newSf, false);
+        // amend features dialog only updates one sequence at a time
+        sequences.get(0).addSequenceFeature(newSf);
+        boolean typeOrGroupChanged = (!featureType.equals(newSf.getType()) || !featureGroup
+                .equals(newSf.getFeatureGroup()));
 
         ffile.parseDescriptionHTML(sf, false);
         if (typeOrGroupChanged)
@@ -457,12 +467,11 @@ public class FeatureRenderer
       {
         for (int i = 0; i < sequences.size(); i++)
         {
-          features.get(i).type = enteredType;
-          features.get(i).featureGroup = group.getText().trim();
-          features.get(i).description = description.getText().replace('\n',
-                  ' ');
-          sequences.get(i).addSequenceFeature(features.get(i));
-          ffile.parseDescriptionHTML(features.get(i), false);
+          SequenceFeature sf = features.get(i);
+          SequenceFeature sf2 = new SequenceFeature(enteredType,
+                  enteredDesc, sf.getBegin(), sf.getEnd(), enteredGroup);
+          ffile.parseDescriptionHTML(sf2, false);
+          sequences.get(i).addSequenceFeature(sf2);
         }
 
         Color newColour = colourPanel.getBackground();