JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 72c5054..c30a418 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -156,8 +156,8 @@ public class ChimeraViewFrame extends StructureViewerBase
                 alignStructs.setToolTipText(MessageManager
                         .formatMessage(
                                 "label.align_structures_using_linked_alignment_views",
-                                new Object[]
-                                { new Integer(_alignwith.size()).toString() }));
+                                new Object[] { new Integer(_alignwith
+                                        .size()).toString() }));
               }
             });
     handler.itemStateChanged(null);
@@ -249,6 +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,
@@ -270,6 +271,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
       {
         closeViewer(false);
@@ -298,9 +300,13 @@ public class ChimeraViewFrame extends StructureViewerBase
         String chain = null;
         if (seq.getDatasetSequence() != null)
         {
-          Vector<PDBEntry> pdbrefs = seq.getDatasetSequence().getAllPDBEntries();
+          Vector<PDBEntry> pdbrefs = seq.getDatasetSequence()
+                  .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();
           }
         }
@@ -323,8 +329,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    * @param newViewId
    */
   public ChimeraViewFrame(String chimeraSessionFile,
-          AlignmentPanel alignPanel,
-          PDBEntry[] pdbArray,
+          AlignmentPanel alignPanel, PDBEntry[] pdbArray,
           SequenceI[][] seqsArray, boolean colourByChimera,
           boolean colourBySequence, String newViewId)
   {
@@ -414,14 +419,13 @@ public class ChimeraViewFrame extends StructureViewerBase
   void initChimera()
   {
     jmb.setFinishedInit(false);
-    jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
-            getBounds().width, getBounds().height);
+    jalview.gui.Desktop.addInternalFrame(this,
+            jmb.getViewerTitle("Chimera", true), getBounds().width,
+            getBounds().height);
 
     if (!jmb.launchChimera())
     {
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
+      JOptionPane.showMessageDialog(Desktop.desktop,
               MessageManager.getString("label.chimera_failed"),
               MessageManager.getString("label.error_loading_file"),
               JOptionPane.ERROR_MESSAGE);
@@ -461,6 +465,7 @@ public class ChimeraViewFrame extends StructureViewerBase
             MessageManager.getString("label.all"));
     menuItem.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent evt)
       {
         allChainsSelected = true;
@@ -483,6 +488,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       menuItem = new JCheckBoxMenuItem(chainName, true);
       menuItem.addItemListener(new ItemListener()
       {
+        @Override
         public void itemStateChanged(ItemEvent evt)
         {
           if (!allChainsSelected)
@@ -524,6 +530,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    * @param closeChimera
    *          if true, close any linked Chimera process; if false, prompt first
    */
+  @Override
   public void closeViewer(boolean closeChimera)
   {
     if (jmb != null && jmb.isChimeraRunning())
@@ -531,8 +538,8 @@ public class ChimeraViewFrame extends StructureViewerBase
       if (!closeChimera)
       {
         String prompt = MessageManager.formatMessage(
-                "label.confirm_close_chimera", new Object[]
-                { jmb.getViewerTitle("Chimera", false) });
+                "label.confirm_close_chimera",
+                new Object[] { jmb.getViewerTitle("Chimera", false) });
         prompt = JvSwingUtils.wrapTooltip(true, prompt);
         int confirm = JOptionPane.showConfirmDialog(this, prompt,
                 MessageManager.getString("label.close_viewer"),
@@ -554,6 +561,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    * Open any newly added PDB structures in Chimera, having first fetched data
    * from PDB (if not already saved).
    */
+  @Override
   public void run()
   {
     _started = true;
@@ -625,9 +633,8 @@ public class ChimeraViewFrame extends StructureViewerBase
 
       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.pdb_entries_couldnt_be_retrieved",
-                      new Object[]
-                      { errormsgs.toString() }), MessageManager
-              .getString("label.couldnt_load_file"),
+                      new Object[] { errormsgs.toString() }),
+              MessageManager.getString("label.couldnt_load_file"),
               JOptionPane.ERROR_MESSAGE);
     }
 
@@ -653,7 +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());
@@ -672,9 +680,7 @@ public class ChimeraViewFrame extends StructureViewerBase
             }
             // Explicitly map to the filename used by Chimera ;
             jmb.getSsm().setMapping(jmb.getSequence()[pos],
-                    jmb.getChains()[pos],
-                    pe.getFile(),
-                    protocol);
+                    jmb.getChains()[pos], pe.getFile(), protocol);
           } catch (OutOfMemoryError oomerror)
           {
             new OOMWarning(
@@ -699,10 +705,11 @@ public class ChimeraViewFrame extends StructureViewerBase
         jmb.updateColours(ap);
       }
       // do superposition if asked to
-      if (alignAddedStructures)
+      if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
       {
         new Thread(new Runnable()
         {
+          @Override
           public void run()
           {
             alignStructs_withAllAlignPanels();
@@ -726,6 +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;
@@ -737,8 +745,7 @@ public class ChimeraViewFrame extends StructureViewerBase
      * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
      */
     String msg = MessageManager.formatMessage("status.fetching_pdb",
-            new Object[]
-            { pdbid });
+            new Object[] { pdbid });
     getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
     // long hdl = startProgressBar(MessageManager.formatMessage(
     // "status.fetching_pdb", new Object[]
@@ -751,8 +758,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
     } finally
     {
-      msg = pdbid + " "
-              + MessageManager.getString("label.state_completed");
+      msg = pdbid + " " + MessageManager.getString("label.state_completed");
       getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
       // stopProgressBar(msg, hdl);
     }
@@ -1097,6 +1103,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     }
   }
 
+  @Override
   public void setJalviewColourScheme(ColourSchemeI ucs)
   {
     jmb.setJalviewColourScheme(ucs);