JAL-2658 ensure features dropdown entries are unique

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

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 2f12eef..4d82d7e 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;
@@ -199,7 +200,7 @@ public class FeatureRenderer extends
           if (col != null)
           {
             fcol = new FeatureColour(col);
-            updateColourButton(mainPanel, colour, new FeatureColour(col));
+            updateColourButton(mainPanel, colour, fcol);
           }
         }
         else
@@ -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());
@@ -357,7 +366,7 @@ public class FeatureRenderer extends
     end.setValue(new Integer(firstFeature.getEnd()));
     description.setText(firstFeature.getDescription());
     updateColourButton(mainPanel, colour,
-            (oldcol = fcol = getFeatureStyle(name.getText())));
+            (oldcol = fcol = getFeatureStyle(featureType)));
     Object[] options;
     if (!create)
     {
@@ -386,15 +395,19 @@ public class FeatureRenderer extends
 
     FeaturesFile ffile = new FeaturesFile();
 
-    if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
+    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)
     {
       /*
        * update default values only if creating using default values
        */
       if (useLastDefaults)
       {
-        lastFeatureAdded = name.getText().trim();
-        lastFeatureGroupAdded = group.getText().trim();
+        lastFeatureAdded = enteredType;
+        lastFeatureGroupAdded = enteredGroup;
         // TODO: determine if the null feature group is valid
         if (lastFeatureGroupAdded.length() < 1)
         {
@@ -420,26 +433,37 @@ public class FeatureRenderer extends
       {
         /*
          * 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 = name.getText().trim();
-        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());
+        sf.setDescription(enteredDescription);
+        ffile.parseDescriptionHTML(newSf, false);
+        // amend features dialog only updates one sequence at a time
+        sequences.get(0).addSequenceFeature(newSf);
+
         if (refreshSettings)
         {
           featuresAdded();
@@ -449,20 +473,19 @@ public class FeatureRenderer extends
     else
     // NEW FEATURES ADDED
     {
-      if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
+      if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
       {
         for (int i = 0; i < sequences.size(); i++)
         {
           SequenceFeature sf = features.get(i);
-          sf.type = name.getText().trim();
-          // 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(lastFeatureAdded, fcol);
+        setColour(enteredType, fcol);
 
         featuresAdded();