new ajax api methods for linking existing jmol viewers with sequences in an alignframe

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0aefe9b..ccf7c06 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -24,7 +24,10 @@ import java.util.*;
 import java.awt.*;
 import java.awt.event.*;
 
+import org.jmol.api.JmolViewer;
+
 import jalview.analysis.*;
+import jalview.api.SequenceStructureBinding;
 import jalview.bin.JalviewLite;
 import jalview.commands.*;
 import jalview.datamodel.*;
@@ -3180,4 +3183,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               DEFAULT_HEIGHT);
     }
   }
+
+  public SequenceStructureBinding addJmolInstance(JmolViewer viewer, String[] sequenceIds)
+  {
+    SequenceI[] seqs=null;
+    if (sequenceIds==null || sequenceIds.length==0)
+    {
+      seqs = viewport.getAlignment().getSequencesArray();
+    } else {
+      // resolve seqs for sequenceIds.
+    }
+    if (// viewer is not mapped)
+            true){
+      AppletJmol jmv = new AppletJmol(viewer, alignPanel, seqs);
+      return jmv;
+    }
+    return null;
+    
+  }
 }

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 153d4df..338b319 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -25,6 +25,7 @@ import java.io.BufferedReader;
 import java.io.InputStreamReader;
 import java.util.*;
 
+import jalview.api.SequenceStructureBinding;
 import jalview.appletgui.*;
 import jalview.datamodel.*;
 import jalview.io.*;
@@ -1310,30 +1311,34 @@ public class JalviewLite extends Applet
    * @param alFrame
    * @param pdbFile - pdbFile URI as given via applet's parameters or by addPdb 
    * @param viewer
-   * @return true if instance was bound corectly. 
+   * @return binding for viewer 
    * TODO: consider making an exception structure for indicating when binding fails
    */
-  public boolean addJmolInstance(AlignFrame alFrame, String pdbFile, org.jmol.api.JmolViewer viewer) 
+  public SequenceStructureBinding addJmolInstance(AlignFrame alFrame, String pdbFile, org.jmol.api.JmolViewer viewer) 
   {
     System.err.println("addJmolInstance not yet implemented.");
     /**
      */
+    return null;
+  }
+  /**
+   * bind structures in a viewer to any matching sequences in an alignFrame (use seuqenceIds to limit scope of search to specific sequences)
+   * @param alFrame
+   * @param viewer
+   * @param sequenceIds
+   * @return
+   */
+  public SequenceStructureBinding addJmolInstance(AlignFrame alFrame, org.jmol.api.JmolViewer viewer, String sequenceIds) 
+  {
     if (viewer!=null)
     {
-/*      viewer.getFrameCount
-    }
-      String alreadyMapped = StructureSelectionManager
-      .getStructureSelectionManager().alreadyMappedToFile(
-              pdbentry.getId());
-MCview.PDBfile reader = null;
-if (alreadyMapped != null)
-{
-reader = StructureSelectionManager.getStructureSelectionManager()
-        .setMapping(seq, chains, pdbentry.getFile(), protocol);
-
-    } */
+      if (sequenceIds!=null && sequenceIds.length()>0)
+      {
+        return alFrame.addJmolInstance(viewer, separatorListToArray(sequenceIds));
+      } else {
+        return alFrame.addJmolInstance(viewer, null);
+      }
     }
-    return false;
+    return null;
   }
-
 }