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 358798d..17f5a71 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;
@@ -234,19 +235,26 @@ public class FeatureRenderer
     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();
       choosePanel.add(new JLabel(
               MessageManager.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);
 
@@ -270,9 +278,8 @@ public class FeatureRenderer
             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());
           if (col == null)
@@ -386,7 +393,10 @@ public class FeatureRenderer
 
     FeaturesFile ffile = new FeaturesFile();
 
-    String enteredType = name.getText().trim();
+    final String enteredType = name.getText().trim();
+    final String enteredGroup = group.getText().trim();
+    final String enteredDescription = description.getText().replaceAll("\n", " ");
+
     if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
     {
       /*
@@ -395,7 +405,7 @@ public class FeatureRenderer
       if (useLastDefaults)
       {
         lastFeatureAdded = enteredType;
-        lastFeatureGroupAdded = group.getText().trim();
+        lastFeatureGroupAdded = enteredGroup;
         // TODO: determine if the null feature group is valid
         if (lastFeatureGroupAdded.length() < 1)
         {
@@ -421,26 +431,37 @@ public class FeatureRenderer
       {
         /*
          * YES_OPTION corresponds to the Amend button
-         * need to refresh Feature Settings if type, group or colour changed
+         * need to refresh Feature Settings if type, group or colour changed;
+         * note we don't force the feature to be visible - the user has been
+         * warned if a hidden feature type or group was entered
          */
-        sf.type = enteredType;
-        sf.featureGroup = group.getText().trim();
-        sf.description = description.getText().replaceAll("\n", " ");
-        boolean refreshSettings = (!featureType.equals(sf.type)
-                || !featureGroup.equals(sf.featureGroup));
+        boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
+                .equals(enteredGroup));
         refreshSettings |= (fcol != oldcol);
-
-        setColour(sf.type, fcol);
-
+        setColour(enteredType, fcol);
+        int newBegin = sf.begin;
+        int newEnd = sf.end;
         try
         {
-          sf.begin = ((Integer) start.getValue()).intValue();
-          sf.end = ((Integer) end.getValue()).intValue();
+          newBegin = ((Integer) start.getValue()).intValue();
+          newEnd = ((Integer) end.getValue()).intValue();
         } catch (NumberFormatException ex)
         {
+          // JSpinner doesn't accept invalid format data :-)
         }
 
-        ffile.parseDescriptionHTML(sf, false);
+        /*
+         * 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(enteredDescription);
+        ffile.parseDescriptionHTML(newSf, false);
+        // amend features dialog only updates one sequence at a time
+        sequences.get(0).addSequenceFeature(newSf);
+
         if (refreshSettings)
         {
           featuresAdded();
@@ -455,12 +476,11 @@ public class FeatureRenderer
         for (int i = 0; i < sequences.size(); i++)
         {
           SequenceFeature sf = features.get(i);
-          sf.type = enteredType;
-          // fix for JAL-1538 - always set feature group here
-          sf.featureGroup = group.getText().trim();
-          sf.description = description.getText().replaceAll("\n", " ");
-          sequences.get(i).addSequenceFeature(sf);
-          ffile.parseDescriptionHTML(sf, false);
+          SequenceFeature sf2 = new SequenceFeature(enteredType,
+                  enteredDescription, sf.getBegin(), sf.getEnd(),
+                  enteredGroup);
+          ffile.parseDescriptionHTML(sf2, false);
+          sequences.get(i).addSequenceFeature(sf2);
         }
 
         setColour(enteredType, fcol);