X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=38ecf76428cf360d23b75cdd838c02fa515e3600;hb=3b239d86dc3a1bf3aa07c0ad3d38aeca57b54ada;hp=2db2cabba74768e496252f0c30990ff855a4bdab;hpb=19e044a2ce25aa395f9cf22f15c7378221636d21;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 2db2cab..38ecf76 100644
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -63,6 +63,13 @@ import java.util.Hashtable;
 public class FeatureRenderer extends
         jalview.renderer.seqfeatures.FeatureRenderer
 {
+  /*
+   * creating a new feature defaults to the type and group as
+   * the last one created
+   */
+  static String lastFeatureAdded = "feature_1";
+
+  static String lastFeatureGroupAdded = "Jalview";
 
   // Holds web links for feature groups and feature types
   // in the form label|link
@@ -79,12 +86,6 @@ public class FeatureRenderer extends
 
   }
 
-  static String lastFeatureAdded;
-
-  static String lastFeatureGroupAdded;
-
-  static String lastDescriptionAdded;
-
   int featureIndex = 0;
 
   boolean deleteFeature = false;
@@ -171,18 +172,19 @@ public class FeatureRenderer extends
 
   /**
    * Shows a dialog allowing the user to create, or amend or delete, sequence
-   * features.
+   * features. If null in the supplied feature(s), feature type and group
+   * default to those for the last feature created (with initial defaults of
+   * "feature_1" and "Jalview").
    * 
    * @param sequences
    * @param features
    * @param create
    * @param ap
-   * @param featureType
    * @return
    */
   boolean amendFeatures(final SequenceI[] sequences,
           final SequenceFeature[] features, boolean create,
-          final AlignmentPanel ap, String featureType)
+          final AlignmentPanel ap)
   {
     final Panel bigPanel = new Panel(new BorderLayout());
     final TextField name = new TextField(16);
@@ -321,36 +323,16 @@ public class FeatureRenderer extends
       bigPanel.add(panel, BorderLayout.CENTER);
     }
 
-    if (featureType != null)
-    {
-      lastFeatureAdded = featureType;
-    }
-    else
-    {
-      if (lastFeatureAdded == null)
-      {
-        if (features[0].type != null)
-        {
-          lastFeatureAdded = features[0].type;
-        }
-        else
-        {
-          lastFeatureAdded = "feature_1";
-        }
-      }
-    }
-
-    if (lastFeatureGroupAdded == null)
-    {
-      if (features[0].featureGroup != null)
-      {
-        lastFeatureGroupAdded = features[0].featureGroup;
-      }
-      else
-      {
-        lastFeatureAdded = "Jalview";
-      }
-    }
+    /*
+     * use defaults for type and group (and update them on Confirm) only
+     * if feature type has not been supplied by the caller
+     * (e.g. for Amend, or create features from Find) 
+     */
+    boolean useLastDefaults = features[0].getType() == null;
+    String featureType = useLastDefaults ? lastFeatureAdded : features[0]
+            .getType();
+    String featureGroup = useLastDefaults ? lastFeatureGroupAdded
+            : features[0].getFeatureGroup();
 
     String title = create ? MessageManager
             .getString("label.create_new_sequence_features")
@@ -362,12 +344,10 @@ public class FeatureRenderer extends
 
     dialog.setMainPanel(bigPanel);
 
-    if (create)
-    {
-      name.setText(lastFeatureAdded);
-      group.setText(lastFeatureGroupAdded);
-    }
-    else
+    name.setText(featureType);
+    group.setText(featureGroup);
+
+    if (!create)
     {
       dialog.ok.setLabel(MessageManager.getString("label.amend"));
       dialog.buttonPanel.add(deleteButton, 1);
@@ -380,8 +360,6 @@ public class FeatureRenderer extends
           dialog.setVisible(false);
         }
       });
-      name.setText(features[0].getType());
-      group.setText(features[0].getFeatureGroup());
     }
 
     start.setText(features[0].getBegin() + "");
@@ -413,29 +391,28 @@ public class FeatureRenderer extends
 
     FeaturesFile ffile = new FeaturesFile();
 
-    if (dialog.accept)
+    /*
+     * only update default type and group if we used defaults
+     */
+    String enteredType = name.getText().trim();
+    if (dialog.accept && useLastDefaults)
     {
-      lastFeatureAdded = name.getText().trim();
+      lastFeatureAdded = enteredType;
       lastFeatureGroupAdded = group.getText().trim();
-      lastDescriptionAdded = description.getText().replace('\n', ' ');
-    }
-
-    if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
-    {
-      lastFeatureGroupAdded = null;
     }
 
     if (!create)
     {
-
       SequenceFeature sf = features[featureIndex];
       if (dialog.accept)
       {
-        boolean typeOrGroupChanged = (!lastFeatureAdded.equals(sf.type) || !lastFeatureGroupAdded
-                .equals(sf.featureGroup));
-        sf.type = lastFeatureAdded;
-        sf.featureGroup = lastFeatureGroupAdded;
-        sf.description = lastDescriptionAdded;
+        sf.type = enteredType;
+        sf.featureGroup = group.getText().trim();
+        if (sf.featureGroup != null && sf.featureGroup.length() < 1)
+        {
+          sf.featureGroup = null;
+        }
+        sf.description = description.getText().replace('\n', ' ');
         if (!colourPanel.isGcol)
         {
           // update colour - otherwise its already done.
@@ -447,7 +424,10 @@ public class FeatureRenderer extends
           sf.end = Integer.parseInt(end.getText());
         } catch (NumberFormatException ex)
         {
+          //
         }
+        boolean typeOrGroupChanged = (!featureType.equals(sf.type) || !featureGroup
+                .equals(sf.featureGroup));
 
         ffile.parseDescriptionHTML(sf, false);
         if (typeOrGroupChanged)
@@ -461,7 +441,6 @@ public class FeatureRenderer extends
         // ensure Feature Settings reflects removal of feature / group
         featuresAdded();
       }
-
     }
     else
     {
@@ -472,9 +451,10 @@ public class FeatureRenderer extends
       {
         for (int i = 0; i < sequences.length; i++)
         {
-          features[i].type = lastFeatureAdded;
-          features[i].featureGroup = lastFeatureGroupAdded;
-          features[i].description = lastDescriptionAdded;
+          features[i].type = enteredType;
+          features[i].featureGroup = group.getText().trim();
+          features[i].description = description.getText()
+                  .replace('\n', ' ');
           sequences[i].addSequenceFeature(features[i]);
           ffile.parseDescriptionHTML(features[i], false);
         }
@@ -482,7 +462,7 @@ public class FeatureRenderer extends
         Color newColour = colourPanel.getBackground();
         // setColour(lastFeatureAdded, fcol);
 
-        setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol
+        setColour(enteredType, new FeatureColour(newColour)); // was fcol
         featuresAdded();
       }
       else