From 43b40c25679ed9beee4c488f36a0c2d50d9016c6 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 18 Jun 2010 08:15:04 +0000
Subject: [PATCH] new jmol/pdb relates api calls

---
 src/jalview/bin/JalviewLite.java |   45 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index a904d7c..153d4df 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1291,4 +1291,49 @@ public class JalviewLite extends Applet
     }
     return false;
   }
+  /**
+   * bind a pdb file to a sequence in the given alignFrame.  
+   * @param alFrame - null or specific alignFrame. This specifies the dataset that will be searched for a seuqence called sequenceId
+   * @param sequenceId - sequenceId within the dataset.
+   * @param pdbEntryString - the short name for the PDB file
+   * @param pdbFile - pdb file - either a URL or a valid PDB file.
+   * @return true if binding was as success
+   * TODO: consider making an exception structure for indicating when PDB parsing or seqeunceId location fails.
+   */
+  public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile)
+  {
+    System.err.println("addPdbFile not yet implemented.");
+      return true;
+  }
+  /**
+   * bind the viewer instance to the pdbFile associated with sequences in the given alFrame.
+   * @param alFrame
+   * @param pdbFile - pdbFile URI as given via applet's parameters or by addPdb 
+   * @param viewer
+   * @return true if instance was bound corectly. 
+   * TODO: consider making an exception structure for indicating when binding fails
+   */
+  public boolean addJmolInstance(AlignFrame alFrame, String pdbFile, org.jmol.api.JmolViewer viewer) 
+  {
+    System.err.println("addJmolInstance not yet implemented.");
+    /**
+     */
+    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);
+
+    } */
+    }
+    return false;
+  }
+
 }
-- 
1.7.10.2