Merge branch 'features/JAL-2295setChimeraAttributes' into

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 530f4fe..9b0d85b 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -24,6 +24,7 @@ import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.ChimeraCommands;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
@@ -35,16 +36,22 @@ import jalview.util.Platform;
 import jalview.ws.dbsources.Pdb;
 
 import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.Random;
 
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
@@ -58,8 +65,6 @@ public class ChimeraViewFrame extends StructureViewerBase
 {
   private JalviewChimeraBinding jmb;
 
-  private boolean allChainsSelected = false;
-
   private IProgressIndicator progressBar = null;
 
   /*
@@ -89,6 +94,98 @@ public class ChimeraViewFrame extends StructureViewerBase
     helpItem.setText(MessageManager.getString("label.chimera_help"));
     savemenu.setVisible(false); // not yet implemented
     viewMenu.add(fitToWindow);
+
+    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);
+
+    final JMenu fetchAttributes = new JMenu(
+            MessageManager.getString("label.fetch_chimera_attributes"));
+    fetchAttributes.setToolTipText(MessageManager
+            .getString("label.fetch_chimera_attributes_tip"));
+    fetchAttributes.addMouseListener(new MouseAdapter()
+    {
+
+      @Override
+      public void mouseEntered(MouseEvent e)
+      {
+        buildAttributesMenu(fetchAttributes);
+      }
+    });
+    viewerActionMenu.add(fetchAttributes);
+
+  }
+
+  /**
+   * Query Chimera for its residue attribute names and add them as items off the
+   * attributes menu
+   * 
+   * @param attributesMenu
+   */
+  protected void buildAttributesMenu(JMenu attributesMenu)
+  {
+    List<String> atts = jmb.sendChimeraCommand("list resattr", true);
+    if (atts == null)
+    {
+      return;
+    }
+    attributesMenu.removeAll();
+    Collections.sort(atts);
+    for (String att : atts)
+    {
+      final String attName = att.split(" ")[1];
+
+      /*
+       * ignore 'jv_*' attributes, as these are Jalview features that have
+       * been transferred to residue attributes in Chimera!
+       */
+      if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
+      {
+        JMenuItem menuItem = new JMenuItem(attName);
+        menuItem.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            getChimeraAttributes(attName);
+          }
+        });
+        attributesMenu.add(menuItem);
+      }
+    }
+  }
+
+  /**
+   * Read residues in Chimera with the given attribute name, and set as features
+   * on the corresponding sequence positions (if any)
+   * 
+   * @param attName
+   */
+  protected void getChimeraAttributes(String attName)
+  {
+    jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel());
+  }
+
+  /**
+   * 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.sendFeaturesToViewer(getAlignmentPanel());
   }
 
   /**
@@ -146,7 +243,6 @@ public class ChimeraViewFrame extends StructureViewerBase
           SequenceI[][] seqs)
   {
     createProgressBar();
-    // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
     jmb = new JalviewChimeraBindingModel(this,
             ap.getStructureSelectionManager(), pdbentrys, seqs, null);
     addAlignmentPanel(ap);
@@ -270,7 +366,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   void initChimera()
   {
     jmb.setFinishedInit(false);
-    jalview.gui.Desktop.addInternalFrame(this,
+    Desktop.addInternalFrame(this,
             jmb.getViewerTitle(getViewerName(), true), getBounds().width,
             getBounds().height);
 
@@ -294,12 +390,10 @@ public class ChimeraViewFrame extends StructureViewerBase
                         + chimeraSessionFile);
       }
     }
-    jmb.setFinishedInit(true);
 
     jmb.startChimeraListener();
   }
 
-
   /**
    * Show only the selected chain(s) in the viewer
    */
@@ -450,6 +544,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 
     if (files.length() > 0)
     {
+      jmb.setFinishedInit(false);
       if (!addingStructures)
       {
         try
@@ -507,6 +602,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           }
         }
       }
+
       jmb.refreshGUI();
       jmb.setFinishedInit(true);
       jmb.setLoadingFromArchive(false);
@@ -656,7 +752,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     {
       BrowserLauncher
               .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
-    } catch (Exception ex)
+    } catch (IOException ex)
     {
     }
   }
@@ -754,4 +850,11 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     return "Chimera";
   }
+
+  @Override
+  public void updateTitleAndMenus()
+  {
+    super.updateTitleAndMenus();
+    viewerActionMenu.setVisible(true);
+  }
 }