JAL-2295 JAL-2296 skeleton 'attributes to features'; renamed methods

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index d68cce8..d43702c 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -26,6 +26,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 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.AppletFormatAdapter;
@@ -49,6 +50,8 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
@@ -58,6 +61,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.PrintWriter;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.Random;
 import java.util.Vector;
@@ -181,6 +185,7 @@ public class ChimeraViewFrame extends StructureViewerBase
         // TODO Auto-generated method stub
       }
     });
+
     JMenuItem writeFeatures = new JMenuItem(
             MessageManager.getString("label.create_chimera_attributes"));
     writeFeatures.setToolTipText(MessageManager
@@ -194,6 +199,71 @@ public class ChimeraViewFrame extends StructureViewerBase
       }
     });
     viewerActionMenu.add(writeFeatures);
+
+    final JMenu fetchAttributes = new JMenu("Fetch Chimera attributes");
+    fetchAttributes
+            .setToolTipText("Copy Chimera attribute to Jalview feature");
+    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());
   }
 
   /**
@@ -205,7 +275,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    */
   protected void sendFeaturesToChimera()
   {
-    jmb.sendFeaturesToChimera(getAlignmentPanel());
+    jmb.sendFeaturesToViewer(getAlignmentPanel());
   }
 
   /**