X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=ab23e62b67bfea8c089f62c72aac6ee908584002;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=bccbda87ab1aabe83ac697394765b20f1f877354;hpb=e4114b3b614b3fd7a83e7706e4a6f0e8a3a7228e;p=jalview.git

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index bccbda8..ab23e62 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -28,9 +28,10 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
 import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
+import jalview.io.StructureFile;
 import jalview.schemes.BuriedColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.HelixColourScheme;
@@ -46,7 +47,6 @@ import jalview.util.Platform;
 import jalview.ws.dbsources.Pdb;
 
 import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.io.BufferedReader;
@@ -59,16 +59,13 @@ 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;
 import javax.swing.JColorChooser;
 import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
-import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
@@ -250,10 +247,8 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     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,
-            null);
+            ap.getStructureSelectionManager(), pdbentrys, seqs, null);
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
     if (pdbentrys.length > 1)
@@ -280,41 +275,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 
   }
 
-  /**
-   * Retrieve chains for sequences by inspecting their PDB refs. The hope is
-   * that the first will be to the sequence's own chain. Really need a more
-   * managed way of doing this.
-   * 
-   * @param seqs
-   * @return
-   */
-  protected String[][] extractChains(SequenceI[][] seqs)
-  {
-    String[][] chains = new String[seqs.length][];
-    for (int i = 0; i < seqs.length; i++)
-    {
-      chains[i] = new String[seqs[i].length];
-      int seqno = 0;
-      for (SequenceI seq : seqs[i])
-      {
-        String chain = null;
-        if (seq.getDatasetSequence() != null)
-        {
-          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();
-          }
-        }
-        chains[i][seqno++] = chain;
-      }
-    }
-    return chains;
-  }
 
   /**
    * Create a new viewer from saved session state data including Chimera session
@@ -439,63 +400,11 @@ public class ChimeraViewFrame extends StructureViewerBase
     jmb.startChimeraListener();
   }
 
-  /**
-   * If the list is not empty, add menu items for 'All' and each individual
-   * chain to the "View | Show Chain" sub-menu. Multiple selections are allowed.
-   * 
-   * @param chainNames
-   */
-  void setChainMenuItems(List<String> chainNames)
-  {
-    chainMenu.removeAll();
-    if (chainNames == null || chainNames.isEmpty())
-    {
-      return;
-    }
-    JMenuItem menuItem = new JMenuItem(
-            MessageManager.getString("label.all"));
-    menuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent evt)
-      {
-        allChainsSelected = true;
-        for (int i = 0; i < chainMenu.getItemCount(); i++)
-        {
-          if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
-          {
-            ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
-          }
-        }
-        showSelectedChains();
-        allChainsSelected = false;
-      }
-    });
-
-    chainMenu.add(menuItem);
-
-    for (String chainName : chainNames)
-    {
-      menuItem = new JCheckBoxMenuItem(chainName, true);
-      menuItem.addItemListener(new ItemListener()
-      {
-        @Override
-        public void itemStateChanged(ItemEvent evt)
-        {
-          if (!allChainsSelected)
-          {
-            showSelectedChains();
-          }
-        }
-      });
-
-      chainMenu.add(menuItem);
-    }
-  }
 
   /**
    * Show only the selected chain(s) in the viewer
    */
+  @Override
   void showSelectedChains()
   {
     List<String> toshow = new ArrayList<String>();
@@ -535,7 +444,11 @@ public class ChimeraViewFrame extends StructureViewerBase
         int confirm = JOptionPane.showConfirmDialog(this, prompt,
                 MessageManager.getString("label.close_viewer"),
                 JOptionPane.YES_NO_CANCEL_OPTION);
-        if (confirm == JOptionPane.CANCEL_OPTION)
+        /*
+         * abort closure if user hits escape or Cancel
+         */
+        if (confirm == JOptionPane.CANCEL_OPTION
+                || confirm == JOptionPane.CLOSED_OPTION)
         {
           return;
         }
@@ -567,6 +480,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
     List<Integer> filePDBpos = new ArrayList<Integer>();
     PDBEntry thePdbEntry = null;
+    StructureFile pdb = null;
     try
     {
       String[] curfiles = jmb.getPdbFile(); // files currently in viewer
@@ -661,12 +575,12 @@ public class ChimeraViewFrame extends StructureViewerBase
             jmb.openFile(pe);
             jmb.addSequence(pos, jmb.getSequence()[pos]);
             File fl = new File(pe.getFile());
-            String protocol = AppletFormatAdapter.URL;
+            DataSourceType protocol = DataSourceType.URL;
             try
             {
               if (fl.exists())
               {
-                protocol = AppletFormatAdapter.FILE;
+                protocol = DataSourceType.FILE;
               }
             } catch (Throwable e)
             {
@@ -675,8 +589,9 @@ public class ChimeraViewFrame extends StructureViewerBase
               stopProgressBar("", startTime);
             }
             // Explicitly map to the filename used by Chimera ;
-            jmb.getSsm().setMapping(jmb.getSequence()[pos],
+            pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
                     jmb.getChains()[pos], pe.getFile(), protocol);
+            stashFoundChains(pdb, pe.getFile());
           } catch (OutOfMemoryError oomerror)
           {
             new OOMWarning(
@@ -692,6 +607,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           }
         }
       }
+      jmb.refreshGUI();
       jmb.setFinishedInit(true);
       jmb.setLoadingFromArchive(false);
 
@@ -727,6 +643,17 @@ public class ChimeraViewFrame extends StructureViewerBase
    * @return
    * @throws Exception
    */
+
+  private void stashFoundChains(StructureFile pdb, String file)
+  {
+    for (int i = 0; i < pdb.getChains().size(); i++)
+    {
+      String chid = new String(pdb.getId() + ":"
+              + pdb.getChains().elementAt(i).id);
+      jmb.getChainNames().add(chid);
+      jmb.getChainFile().put(chid, file);
+    }
+  }
   private String fetchPdbFile(PDBEntry processingEntry) throws Exception
   {
     // FIXME: this is duplicated code with Jmol frame ?