X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=c595d9d290bdbc75b4b7abb8e56c39d5cf5510bb;hb=91d45e7c90753d8061883f351da796c50f467ef5;hp=ba360af3117fc953555dc98f06d739adc08e63ad;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index ba360af..c595d9d 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -202,7 +202,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * add a single PDB structure to a new or existing Chimera view
+   * open a single PDB structure in a new Chimera view
    * 
    * @param pdbentry
    * @param seq
@@ -213,30 +213,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           String[] chains, final AlignmentPanel ap)
   {
     this();
-    String pdbId = pdbentry.getId();
 
-    /*
-     * If the PDB file is already loaded, the user may just choose to add to an
-     * existing viewer (or cancel)
-     */
-    if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * Check if there are other Chimera views involving this alignment and give
-     * user the option to add and align this molecule to one of them (or cancel)
-     */
-    if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * If the options above are declined or do not apply, show the structure in
-     * a new viewer
-     */
     openNewChimera(ap, new PDBEntry[] { pdbentry },
             new SequenceI[][]
             { seq });
@@ -352,29 +329,6 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * Returns a list of any Chimera viewers in the desktop. The list is
-   * restricted to those linked to the given alignment panel if it is not null.
-   */
-  @Override
-  protected List<StructureViewerBase> getViewersFor(AlignmentPanel ap)
-  {
-    List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
-    JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
-    for (JInternalFrame frame : frames)
-    {
-      if (frame instanceof ChimeraViewFrame)
-      {
-        if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap))
-        {
-          result.add((StructureViewerBase) frame);
-        }
-      }
-    }
-    return result;
-  }
-
-  /**
    * Launch Chimera. If we have a chimera session file name, send Chimera the
    * command to open its saved session file.
    */
@@ -414,7 +368,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   @Override
   void showSelectedChains()
   {
-    List<String> toshow = new ArrayList<String>();
+    List<String> toshow = new ArrayList<>();
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
@@ -484,8 +438,8 @@ public class ChimeraViewFrame extends StructureViewerBase
     // todo - record which pdbids were successfully imported.
     StringBuilder errormsgs = new StringBuilder(128);
     StringBuilder files = new StringBuilder(128);
-    List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
-    List<Integer> filePDBpos = new ArrayList<Integer>();
+    List<PDBEntry> filePDB = new ArrayList<>();
+    List<Integer> filePDBpos = new ArrayList<>();
     PDBEntry thePdbEntry = null;
     StructureFile pdb = null;
     try
@@ -598,9 +552,12 @@ public class ChimeraViewFrame extends StructureViewerBase
               stopProgressBar("", startTime);
             }
             // 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)
           {
             new OOMWarning(
@@ -658,7 +615,7 @@ 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
@@ -891,4 +848,10 @@ public class ChimeraViewFrame extends StructureViewerBase
     }
     return reply;
   }
+
+  @Override
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    return progressBar;
+  }
 }