X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=ec9feb7786407694f87b0fc2384f0088767f0e3c;hb=19e044a2ce25aa395f9cf22f15c7378221636d21;hp=67eddcac4a21b8c0a0e25564c74374e12d70011b;hpb=20bb45279db7745e7d0062c1084f97644c60db19;p=jalview.git

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 67eddca..ec9feb7 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureRenderer;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
@@ -76,6 +77,10 @@ public class ChimeraViewFrame extends StructureViewerBase
 
   private Random random = new Random();
 
+  private int myWidth = 500;
+
+  private int myHeight = 150;
+
   /**
    * Initialise menu options.
    */
@@ -185,7 +190,9 @@ public class ChimeraViewFrame extends StructureViewerBase
    */
   protected void sendFeaturesToChimera()
   {
-    jmb.sendFeaturesToViewer(getAlignmentPanel());
+    int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
+    statusBar.setText(MessageManager.formatMessage("label.attributes_set",
+            count));
   }
 
   /**
@@ -254,7 +261,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       useAlignmentPanelForSuperposition(ap);
     }
     jmb.setColourBySequence(true);
-    setSize(400, 400); // probably should be a configurable/dynamic default here
+    setSize(myWidth, myHeight);
     initMenus();
 
     addingStructures = false;
@@ -607,6 +614,16 @@ public class ChimeraViewFrame extends StructureViewerBase
       jmb.setFinishedInit(true);
       jmb.setLoadingFromArchive(false);
 
+      /*
+       * ensure that any newly discovered features (e.g. RESNUM)
+       * are added to any open feature settings dialog
+       */
+      FeatureRenderer fr = getBinding().getFeatureRenderer(null);
+      if (fr != null)
+      {
+        fr.featuresAdded();
+      }
+
       // refresh the sequence colours for the new structure(s)
       for (AlignmentPanel ap : _colourwith)
       {
@@ -852,19 +869,18 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * Override superclass method to make the 'Chimera' menu always visible, but
-   * 'Superpose with...' only enabled if there is more than one structure shown
+   * Sends commands to align structures according to associated alignment(s).
+   * 
+   * @return
    */
   @Override
-  public void updateTitleAndMenus()
+  protected String alignStructs_withAllAlignPanels()
   {
-    super.updateTitleAndMenus();
-    viewerActionMenu.setVisible(true);
-    viewSelectionMenu.setEnabled(false);
-    if (getBinding().getPdbFile().length > 1
-            && getBinding().getSequence().length > 1)
+    String reply = super.alignStructs_withAllAlignPanels();
+    if (reply != null)
     {
-      viewSelectionMenu.setEnabled(true);
+      statusBar.setText("Superposition failed: " + reply);
     }
+    return reply;
   }
 }