JAL-3060 entry points for createFeatures, amendFeatures

diff --git a/src/jalview/gui/FeatureEditor.java b/src/jalview/gui/FeatureEditor.java
index a86725b..ad82612 100644 (file)
--- a/src/jalview/gui/FeatureEditor.java
+++ b/src/jalview/gui/FeatureEditor.java
@@ -75,6 +75,20 @@ public class FeatureEditor
     fr = alignPanel.getSeqPanel().seqCanvas.fr;
   }
 
+  public void amendFeatures(final List<SequenceI> sequences,
+          final List<SequenceFeature> features,
+          final Runnable responseHandler)
+  {
+    amendFeatures(sequences, features, false, responseHandler);
+  }
+
+  public void createFeatures(final List<SequenceI> sequences,
+          final List<SequenceFeature> features,
+          final Runnable responseHandler)
+  {
+    amendFeatures(sequences, features, true, responseHandler);
+  }
+
   /**
    * Presents a dialog allowing the user to add new features, or amend or delete
    * existing features. Currently this can be on
@@ -99,14 +113,14 @@ public class FeatureEditor
    * @param responseHandler
    *          boolean true RunResponse is run if features are created
    */
-  public boolean amendFeatures(final List<SequenceI> sequences,
+  private void amendFeatures(final List<SequenceI> sequences,
           final List<SequenceFeature> features, boolean create,
           final Runnable responseHandler)
   {
     featureIndex = 0;
-  
+
     final JPanel mainPanel = new JPanel(new BorderLayout());
-  
+
     final JTextField name = new JTextField(25);
     name.getDocument().addDocumentListener(new DocumentListener()
     {
@@ -115,20 +129,20 @@ public class FeatureEditor
       {
         warnIfTypeHidden(mainPanel, name.getText());
       }
-  
+
       @Override
       public void removeUpdate(DocumentEvent e)
       {
         warnIfTypeHidden(mainPanel, name.getText());
       }
-  
+
       @Override
       public void changedUpdate(DocumentEvent e)
       {
         warnIfTypeHidden(mainPanel, name.getText());
       }
     });
-  
+
     final JTextField group = new JTextField(25);
     group.getDocument().addDocumentListener(new DocumentListener()
     {
@@ -137,20 +151,20 @@ public class FeatureEditor
       {
         warnIfGroupHidden(mainPanel, group.getText());
       }
-  
+
       @Override
       public void removeUpdate(DocumentEvent e)
       {
         warnIfGroupHidden(mainPanel, group.getText());
       }
-  
+
       @Override
       public void changedUpdate(DocumentEvent e)
       {
         warnIfGroupHidden(mainPanel, group.getText());
       }
     });
-  
+
     final JTextArea description = new JTextArea(3, 25);
     final JSpinner start = new JSpinner();
     final JSpinner end = new JSpinner();
@@ -192,8 +206,7 @@ public class FeatureEditor
            */
           final String ft = features.get(featureIndex).getType();
           final String type = ft == null ? lastFeatureAdded : ft;
-          FeatureTypeSettings fcc = new FeatureTypeSettings(
-                  fr, type);
+          FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type);
           fcc.setRequestFocusEnabled(true);
           fcc.requestFocus();
           fcc.addActionListener(new ActionListener()
@@ -210,7 +223,7 @@ public class FeatureEditor
       }
     });
     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
-  
+
     if (!create && features.size() > 1)
     {
       /*
@@ -236,7 +249,7 @@ public class FeatureEditor
         added.add(text);
       }
       choosePanel.add(overlaps);
-  
+
       overlaps.addItemListener(new ItemListener()
       {
         @Override
@@ -252,13 +265,13 @@ public class FeatureEditor
             group.setText(sf.getFeatureGroup());
             start.setValue(new Integer(sf.getBegin()));
             end.setValue(new Integer(sf.getEnd()));
-  
+
             SearchResultsI highlight = new SearchResults();
             highlight.addResult(sequences.get(0), sf.getBegin(),
                     sf.getEnd());
-  
-            ap.getSeqPanel().seqCanvas
-                    .highlightSearchResults(highlight, false);
+
+            ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight,
+                    false);
           }
           FeatureColourI col = fr.getFeatureStyle(name.getText());
           if (col == null)
@@ -270,22 +283,22 @@ public class FeatureEditor
           updateColourButton(mainPanel, colour, col);
         }
       });
-  
+
       gridPanel.add(choosePanel);
     }
-  
+
     JPanel namePanel = new JPanel();
     gridPanel.add(namePanel);
     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
             JLabel.RIGHT));
     namePanel.add(name);
-  
+
     JPanel groupPanel = new JPanel();
     gridPanel.add(groupPanel);
     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
             JLabel.RIGHT));
     groupPanel.add(group);
-  
+
     JPanel colourPanel = new JPanel();
     gridPanel.add(colourPanel);
     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
@@ -299,18 +312,18 @@ public class FeatureEditor
     colour.setHorizontalTextPosition(SwingConstants.CENTER);
     colour.setVerticalTextPosition(SwingConstants.CENTER);
     mainPanel.add(gridPanel, BorderLayout.NORTH);
-  
+
     JPanel descriptionPanel = new JPanel();
     descriptionPanel.add(new JLabel(
             MessageManager.getString("label.description:"), JLabel.RIGHT));
     description.setFont(JvSwingUtils.getTextAreaFont());
     description.setLineWrap(true);
     descriptionPanel.add(new JScrollPane(description));
-  
+
     if (!create)
     {
       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
-  
+
       JPanel startEndPanel = new JPanel();
       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
               JLabel.RIGHT));
@@ -324,7 +337,7 @@ public class FeatureEditor
     {
       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
     }
-  
+
     /*
      * default feature type and group to that of the first feature supplied,
      * or to the last feature created if not supplied (null value) 
@@ -337,7 +350,7 @@ public class FeatureEditor
             : firstFeature.getFeatureGroup();
     name.setText(featureType);
     group.setText(featureGroup);
-  
+
     start.setValue(new Integer(firstFeature.getBegin()));
     end.setValue(new Integer(firstFeature.getEnd()));
     description.setText(firstFeature.getDescription());
@@ -356,18 +369,18 @@ public class FeatureEditor
       options = new Object[] { MessageManager.getString("action.ok"),
           MessageManager.getString("action.cancel") };
     }
-  
+
     String title = create
             ? MessageManager.getString("label.create_new_sequence_features")
             : MessageManager.formatMessage("label.amend_delete_features",
                     new String[]
                     { sequences.get(0).getName() });
-  
+
     /*
      * register responses and show the dialog
      */
     JvOptionPane.newOptionDialog(Desktop.desktop).response(
-  
+
             new RunResponse(JvOptionPane.OK_OPTION)
             {
               public void run()
@@ -377,7 +390,7 @@ public class FeatureEditor
                 final String enteredDescription = description.getText()
                         .replaceAll("\n", " ");
                 if (enteredType.length() > 0)
-  
+
                 {
                   /*
                    * update default values only if creating using default values
@@ -393,7 +406,7 @@ public class FeatureEditor
                     }
                   }
                 }
-  
+
                 if (create)
                 {
                   // NEW FEATURES ADDED
@@ -408,14 +421,16 @@ public class FeatureEditor
                       new FeaturesFile().parseDescriptionHTML(sf2, false);
                       sequences.get(i).addSequenceFeature(sf2);
                     }
-  
+
                     fr.setColour(enteredType, featureColour);
-  
+
                     fr.featuresAdded();
-  
+
                     responseHandler.run();
                   }
-                } else {
+                }
+                else
+                {
                   SequenceFeature sf = features.get(featureIndex);
                   /*
                    * Feature amended - YES_OPTION corresponds to the Amend button
@@ -423,7 +438,8 @@ public class FeatureEditor
                    * note we don't force the feature to be visible - the user has been
                    * warned if a hidden feature type or group was entered
                    */
-                  boolean refreshSettings = (!featureType.equals(enteredType)
+                  boolean refreshSettings = (!featureType
+                          .equals(enteredType)
                           || !featureGroup.equals(enteredGroup));
                   refreshSettings |= (featureColour != oldColour);
                   fr.setColour(enteredType, featureColour);
@@ -437,24 +453,26 @@ public class FeatureEditor
                   {
                     // JSpinner doesn't accept invalid format data :-)
                   }
-  
+
                   /*
                    * 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());
+                  SequenceFeature newSf = new SequenceFeature(sf,
+                          enteredType, newBegin, newEnd, enteredGroup,
+                          sf.getScore());
                   newSf.setDescription(enteredDescription);
                   new FeaturesFile().parseDescriptionHTML(newSf, false);
                   // amend features dialog only updates one sequence at a time
                   sequences.get(0).addSequenceFeature(newSf);
-  
+
                   if (refreshSettings)
                   {
                     fr.featuresAdded();
                   }
                 }
+
                 ap.getSeqPanel().seqCanvas.highlightSearchResults(null,
                         false);
                 ap.paintAlignment(true, true);
@@ -486,7 +504,6 @@ public class FeatureEditor
                     JvOptionPane.YES_NO_CANCEL_OPTION,
                     JvOptionPane.QUESTION_MESSAGE, null, options,
                     MessageManager.getString("action.ok"));
-    return true;
   }
 
   /**
@@ -503,7 +520,7 @@ public class FeatureEditor
     colour.setIcon(null);
     colour.setToolTipText(null);
     colour.setText("");
-  
+
     if (col.isSimpleColour())
     {
       colour.setBackground(col.getColour());

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 244e6df..ef69aa8 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -227,7 +227,7 @@ public class Finder extends GFinder
               match.getEnd(), desc));
     }
 
-    new FeatureEditor(ap).amendFeatures(seqs, features, true, new Runnable()
+    new FeatureEditor(ap).createFeatures(seqs, features, new Runnable()
     {
       @Override
               public void run()

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index cb94409..776fcd2 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -2038,15 +2038,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      */
     if (!seqs.isEmpty())
     {
-      new FeatureEditor(ap).amendFeatures(seqs, features, true,
-              new Runnable()
-              {
-                public void run()
-                {
-                  ap.alignFrame.setShowSeqFeatures(true);
-                  ap.av.setSearchResults(null); // clear highlighting
-                  ap.repaint(); // draw new/amended features
-      }});
+      new FeatureEditor(ap).createFeatures(seqs, features, new Runnable()
+      {
+        public void run()
+        {
+          ap.alignFrame.setShowSeqFeatures(true);
+          ap.av.setSearchResults(null); // clear highlighting
+          ap.repaint(); // draw new/amended features
+        }
+      });
     }
   }
 

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index db0d902..5ae4a0e 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1680,16 +1680,15 @@ public class SeqPanel extends JPanel
          * whether changes were made or not
          */
         List<SequenceI> seqs = Collections.singletonList(sequence);
-        new FeatureEditor(ap).amendFeatures(seqs, features, false,
-                new Runnable()
-                {
-                  @Override
-                  public void run()
-                  {
-                    av.setSearchResults(null); // clear highlighting
-                    seqCanvas.repaint(); // draw new/amended features
-                  }
-                });
+        new FeatureEditor(ap).amendFeatures(seqs, features, new Runnable()
+        {
+          @Override
+          public void run()
+          {
+            av.setSearchResults(null); // clear highlighting
+            seqCanvas.repaint(); // draw new/amended features
+          }
+        });
       }
     }
   }