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

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

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index c0e3e73..ac56590 100644 (file)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -43,7 +43,6 @@ import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.util.Arrays;
 import java.util.Comparator;
-import java.util.HashMap;
 import java.util.List;
 
 import javax.swing.JColorChooser;
@@ -449,24 +448,11 @@ public class FeatureRenderer extends
          * (to ensure integrity of SequenceFeatures data store)
          */
         sequences.get(0).deleteFeature(sf);
-        SequenceFeature newSf = new SequenceFeature(enteredType,
-                enteredDescription, newBegin, newEnd, sf.getScore(),
-                enteredGroup);
-        // ensure any additional properties are copied
-        if (sf.otherDetails != null)
-        {
-          newSf.otherDetails = new HashMap<String, Object>(sf.otherDetails);
-        }
+        SequenceFeature newSf = new SequenceFeature(sf, newBegin, newEnd,
+                enteredGroup, sf.getScore());
+        sf.setDescription(enteredDescription);
         ffile.parseDescriptionHTML(newSf, false);
-        // add any additional links not parsed from description
-        if (sf.links != null)
-        {
-          for (String link : sf.links)
-          {
-            newSf.addLink(link);
-          }
-        }
-        // amend features only gets one sequence to act on
+        // amend features dialog only updates one sequence at a time
         sequences.get(0).addSequenceFeature(newSf);
 
         if (refreshSettings)
@@ -485,9 +471,9 @@ public class FeatureRenderer extends
           SequenceFeature sf = features.get(i);
           SequenceFeature sf2 = new SequenceFeature(enteredType,
                   enteredDescription, sf.getBegin(), sf.getEnd(),
-                  Float.NaN, enteredGroup);
-          sequences.get(i).addSequenceFeature(sf2);
+                  enteredGroup);
           ffile.parseDescriptionHTML(sf2, false);
+          sequences.get(i).addSequenceFeature(sf2);
         }
 
         setColour(enteredType, fcol);