X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=37e84c7044be1e727066f53ba2102bbfc47ec8c0;hb=207b06de28859536277608ad94897eaa526b1279;hp=9b0d85be02c6756f1b53888aa04531b4b6cb17c0;hpb=4762b29420ed4df01b55a8afe5ab05467aaf41a9;p=jalview.git

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 9b0d85b..37e84c7 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;
@@ -477,7 +484,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     StructureFile pdb = null;
     try
     {
-      String[] curfiles = jmb.getPdbFile(); // files currently in viewer
+      String[] curfiles = jmb.getStructureFiles(); // files currently in viewer
       // TODO: replace with reference fetching/transfer code (validate PDBentry
       // as a DBRef?)
       for (int pi = 0; pi < jmb.getPdbCount(); pi++)
@@ -585,7 +592,8 @@ public class ChimeraViewFrame extends StructureViewerBase
             }
             // Explicitly map to the filename used by Chimera ;
             pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
-                    jmb.getChains()[pos], pe.getFile(), protocol);
+                    jmb.getChains()[pos], pe.getFile(), protocol,
+                    progressBar);
             stashFoundChains(pdb, pe.getFile());
           } catch (OutOfMemoryError oomerror)
           {
@@ -607,6 +615,16 @@ 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)
       {
@@ -633,7 +651,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 
   /**
    * Fetch PDB data and save to a local file. Returns the full path to the file,
-   * or null if fetch fails.
+   * or null if fetch fails. TODO: refactor to common with Jmol ? duplication
    * 
    * @param processingEntry
    * @return
@@ -851,10 +869,31 @@ public class ChimeraViewFrame extends StructureViewerBase
     return "Chimera";
   }
 
+  /**
+   * Sends commands to align structures according to associated alignment(s).
+   * 
+   * @return
+   */
+  @Override
+  protected String alignStructs_withAllAlignPanels()
+  {
+    String reply = super.alignStructs_withAllAlignPanels();
+    if (reply != null)
+    {
+      statusBar.setText("Superposition failed: " + reply);
+    }
+    return reply;
+  }
+
   @Override
-  public void updateTitleAndMenus()
+  protected IProgressIndicator getIProgressIndicator()
   {
-    super.updateTitleAndMenus();
-    viewerActionMenu.setVisible(true);
+    return progressBar;
+  }
+
+  @Override
+  protected AAStructureBindingModel getBindingModel()
+  {
+    return jmb;
   }
 }