X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=c30a41835e4dd95b02d384f1ec06952a7f93e43c;hb=62cdf4a06bef088c02f81c66ab2fe0bc3264e321;hp=f1c509788da4d81d43409a9fd543819f3a85ed6e;hpb=3429e8b2a3fceff4350d5554853403e903b4fc68;p=jalview.git

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index f1c5097..c30a418 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -143,7 +143,6 @@ public class ChimeraViewFrame extends StructureViewerBase
             });
     viewMenu.add(seqColourBy);
     viewMenu.add(fitToWindow);
-    viewMenu.add(highlightSelection);
 
     final ItemListener handler;
     JMenu alpanels = new ViewSelectionMenu(
@@ -250,6 +249,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           SequenceI[][] seqs)
   {
     createProgressBar();
+    // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
     String[][] chains = extractChains(seqs);
     jmb = new JalviewChimeraBindingModel(this,
             ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
@@ -304,6 +304,9 @@ public class ChimeraViewFrame extends StructureViewerBase
                   .getAllPDBEntries();
           if (pdbrefs != null && pdbrefs.size() > 0)
           {
+            // FIXME: SequenceI.PDBEntry[0] chain mapping used for
+            // ChimeraViewFrame. Is this even used ???
+
             chain = pdbrefs.get(0).getChainCode();
           }
         }
@@ -657,7 +660,8 @@ public class ChimeraViewFrame extends StructureViewerBase
           {
             int pos = filePDBpos.get(num).intValue();
             long startTime = startProgressBar("Chimera "
-                    + MessageManager.getString("status.opening_file"));
+                    + MessageManager.getString("status.opening_file_for")
+                    + " " + pe.getId());
             jmb.openFile(pe);
             jmb.addSequence(pos, jmb.getSequence()[pos]);
             File fl = new File(pe.getFile());
@@ -729,6 +733,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    */
   private String fetchPdbFile(PDBEntry processingEntry) throws Exception
   {
+    // FIXME: this is duplicated code with Jmol frame ?
     String filePath = null;
     Pdb pdbclient = new Pdb();
     AlignmentI pdbseq = null;
@@ -1206,12 +1211,6 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   @Override
-  protected void highlightSelection_actionPerformed()
-  {
-    jmb.highlightSelection(getAlignmentPanel());
-  }
-
-  @Override
   public ViewerType getViewerType()
   {
     return ViewerType.CHIMERA;