JAL-2505 apply changed description to new, not deleted, feature!

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

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index c6610e1..d580eaf 100644 (file)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -41,6 +41,7 @@ import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Comparator;
 import java.util.List;
@@ -234,8 +235,9 @@ public class FeatureRenderer extends
     if (!create && features.size() > 1)
     {
       /*
-       * more than one feature at selected position - add a drop-down
-       * to choose the feature to amend
+       * more than one feature at selected position - 
+       * add a drop-down to choose the feature to amend
+       * space pad text if necessary to make entries distinct
        */
       gridPanel = new JPanel(new GridLayout(4, 1));
       JPanel choosePanel = new JPanel();
@@ -243,11 +245,17 @@ public class FeatureRenderer extends
               .getString("label.select_feature")
               + ":"));
       final JComboBox<String> overlaps = new JComboBox<String>();
+      List<String> added = new ArrayList<>();
       for (SequenceFeature sf : features)
       {
-        String text = sf.getType() + "/" + sf.getBegin() + "-"
-                + sf.getEnd() + " (" + sf.getFeatureGroup() + ")";
+        String text = String.format("%s/%d-%d (%s)", sf.getType(),
+                sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
+        while (added.contains(text))
+        {
+          text += " ";
+        }
         overlaps.addItem(text);
+        added.add(text);
       }
       choosePanel.add(overlaps);
 
@@ -271,7 +279,8 @@ public class FeatureRenderer extends
             highlight.addResult(sequences.get(0), sf.getBegin(),
                     sf.getEnd());
 
-            alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
+            alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(
+                    highlight, false);
 
           }
           FeatureColourI col = getFeatureStyle(name.getText());
@@ -448,9 +457,9 @@ public class FeatureRenderer extends
          * (to ensure integrity of SequenceFeatures data store)
          */
         sequences.get(0).deleteFeature(sf);
-        SequenceFeature newSf = new SequenceFeature(sf, newBegin, newEnd,
-                enteredGroup);
-        sf.setDescription(enteredDescription);
+        SequenceFeature newSf = new SequenceFeature(sf, enteredType,
+                newBegin, newEnd, enteredGroup, sf.getScore());
+        newSf.setDescription(enteredDescription);
         ffile.parseDescriptionHTML(newSf, false);
         // amend features dialog only updates one sequence at a time
         sequences.get(0).addSequenceFeature(newSf);
@@ -471,7 +480,7 @@ public class FeatureRenderer extends
           SequenceFeature sf = features.get(i);
           SequenceFeature sf2 = new SequenceFeature(enteredType,
                   enteredDescription, sf.getBegin(), sf.getEnd(),
-                  Float.NaN, enteredGroup);
+                  enteredGroup);
           ffile.parseDescriptionHTML(sf2, false);
           sequences.get(i).addSequenceFeature(sf2);
         }