merge develop

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index fe4a000..37e84c7 100644 (file)
--- 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;
@@ -483,7 +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++)
@@ -591,7 +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)
           {
@@ -613,6 +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)
       {
@@ -639,7 +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
@@ -872,4 +884,16 @@ public class ChimeraViewFrame extends StructureViewerBase
     }
     return reply;
   }
+
+  @Override
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    return progressBar;
+  }
+
+  @Override
+  protected AAStructureBindingModel getBindingModel()
+  {
+    return jmb;
+  }
 }