Merge branch 'develop' into features/JAL-2295setChimeraAttributes

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index f2244d5..ae3ff9e 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -59,9 +59,7 @@ import java.io.InputStream;
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Map;
 import java.util.Random;
-import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -183,6 +181,31 @@ public class ChimeraViewFrame extends StructureViewerBase
         // TODO Auto-generated method stub
       }
     });
+    JMenuItem writeFeatures = new JMenuItem(
+            MessageManager.getString("label.create_chimera_attributes"));
+    writeFeatures.setToolTipText(MessageManager
+            .getString("label.create_chimera_attributes_tip"));
+    writeFeatures.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sendFeaturesToChimera();
+      }
+    });
+    viewerActionMenu.add(writeFeatures);
+  }
+
+  /**
+   * Send a command to Chimera to create residue attributes for Jalview features
+   * <p>
+   * The syntax is: setattr r <attName> <attValue> <atomSpec>
+   * <p>
+   * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A
+   */
+  protected void sendFeaturesToChimera()
+  {
+    jmb.sendFeaturesToChimera(getAlignmentPanel());
   }
 
   /**
@@ -196,7 +219,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
           String[] chains, final AlignmentPanel ap)
   {
-    super();
+    this();
     String pdbId = pdbentry.getId();
 
     /*
@@ -249,6 +272,7 @@ 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,
@@ -303,6 +327,9 @@ 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();
           }
         }
@@ -329,7 +356,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           SequenceI[][] seqsArray, boolean colourByChimera,
           boolean colourBySequence, String newViewId)
   {
-    super();
+    this();
     setViewId(newViewId);
     this.chimeraSessionFile = chimeraSessionFile;
     openNewChimera(alignPanel, pdbArray, seqsArray);
@@ -358,31 +385,22 @@ public class ChimeraViewFrame extends StructureViewerBase
   public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
           AlignmentPanel ap)
   {
-    super();
+    this();
     openNewChimera(ap, pe, seqs);
   }
 
-  public ChimeraViewFrame(Map<PDBEntry, List<SequenceI>> toView,
-          AlignmentPanel alignPanel)
+  /**
+   * Default constructor
+   */
+  public ChimeraViewFrame()
   {
     super();
 
     /*
-     * Convert the map of sequences per pdb entry into the tied arrays expected
-     * by openNewChimera
-     * 
-     * TODO pass the Map down to openNewChimera and its callees instead
+     * closeViewer will decide whether or not to close this frame
+     * depending on whether user chooses to Cancel or not
      */
-    final Set<PDBEntry> pdbEntries = toView.keySet();
-    PDBEntry[] pdbs = pdbEntries.toArray(new PDBEntry[pdbEntries.size()]);
-    SequenceI[][] seqsForPdbs = new SequenceI[pdbEntries.size()][];
-    for (int i = 0; i < pdbs.length; i++)
-    {
-      final List<SequenceI> seqsForPdb = toView.get(pdbs[i]);
-      seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]);
-    }
-
-    openNewChimera(alignPanel, pdbs, seqsForPdbs);
+    setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
   }
 
   /**
@@ -539,7 +557,15 @@ public class ChimeraViewFrame extends StructureViewerBase
         prompt = JvSwingUtils.wrapTooltip(true, prompt);
         int confirm = JOptionPane.showConfirmDialog(this, prompt,
                 MessageManager.getString("label.close_viewer"),
-                JOptionPane.YES_NO_OPTION);
+                JOptionPane.YES_NO_CANCEL_OPTION);
+        /*
+         * abort closure if user hits escape or Cancel
+         */
+        if (confirm == JOptionPane.CANCEL_OPTION
+                || confirm == JOptionPane.CLOSED_OPTION)
+        {
+          return;
+        }
         closeChimera = confirm == JOptionPane.YES_OPTION;
       }
       jmb.closeViewer(closeChimera);
@@ -551,6 +577,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     // TODO: check for memory leaks where instance isn't finalised because jmb
     // holds a reference to the window
     jmb = null;
+    dispose();
   }
 
   /**
@@ -656,7 +683,8 @@ 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());
@@ -728,6 +756,7 @@ 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;
@@ -1036,10 +1065,10 @@ public class ChimeraViewFrame extends StructureViewerBase
     setChainMenuItems(jmb.getChainNames());
 
     this.setTitle(jmb.getViewerTitle("Chimera", true));
-    if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
-    {
+    // if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
+    // {
       viewerActionMenu.setVisible(true);
-    }
+    // }
     if (!jmb.isLoadingFromArchive())
     {
       seqColour_actionPerformed(null);