From 03b4b7c1b8be6a6fb4410e87192870a3ef0c3faf Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 28 Aug 2008 11:12:25 +0000
Subject: [PATCH] bugfix for applet examples with 1gaq where new classloader
 jmol connection is used

---
 src/jalview/appletgui/AppletJmol.java |   66 +++++++++++++++++++++++++++------
 1 file changed, 55 insertions(+), 11 deletions(-)

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 1533530..aa81764 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -75,7 +75,10 @@ public class AppletJmol extends EmbmenuFrame
   PDBEntry pdbentry;
   boolean colourBySequence = true;
   Vector atomsPicked = new Vector();
-
+  /**
+   * datasource protocol for access to PDBEntry
+   */
+  String protocol=null;
   public AppletJmol(PDBEntry pdbentry,
                     SequenceI[] seq,
                     String[] chains,
@@ -86,14 +89,32 @@ public class AppletJmol extends EmbmenuFrame
     this.sequence = seq;
     this.chains = chains;
     this.pdbentry = pdbentry;
-
-   String alreadyMapped = StructureSelectionManager
+    this.protocol = protocol; 
+    if (pdbentry.getId()==null || pdbentry.getId().length()<1)
+    {
+      if (jalview.bin.JalviewLite.debug)
+      {
+        System.err.println("Setting PDB id for file "+pdbentry.getFile());
+        if (protocol.equals(AppletFormatAdapter.PASTE))
+        {
+          pdbentry.setId("PASTED PDB"+(chains==null ? "_" : chains.toString()));
+        } else {
+          pdbentry.setId(pdbentry.getFile());
+        }
+      }
+    } 
+    if (jalview.bin.JalviewLite.debug)
+    {
+        System.err.println("AppletJmol: PDB ID is '"+pdbentry.getId()+"'");
+    }
+    
+    String alreadyMapped = StructureSelectionManager
         .getStructureSelectionManager()
         .alreadyMappedToFile(pdbentry.getId());
-
+   MCview.PDBfile reader = null; 
     if (alreadyMapped != null)
     {
-       StructureSelectionManager.getStructureSelectionManager()
+       reader = StructureSelectionManager.getStructureSelectionManager()
             .setMapping(seq, chains, pdbentry.getFile(), protocol);
        //PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
        //FOR NOW, LETS JUST OPEN A NEW WINDOW
@@ -175,12 +196,35 @@ public class AppletJmol extends EmbmenuFrame
         // probably CLASSLOADER based datasource..
         // Try and get a reader on the datasource, and pass that to Jmol
         try {
-          FileParse fparser = new jalview.io.FileParse(protocol, pdbentry.getFile());
-          if (!fparser.isValid())
-          {
-            throw new Exception("Invalid datasource. "+fparser.getWarningMessage());
+          java.io.Reader freader = null;
+          if (reader!=null) {
+            if  (jalview.bin.JalviewLite.debug)
+            {
+              System.err.println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
+            }
+            // re-use the one we opened earlier
+            freader = reader.getReader();
+          } 
+          if (freader==null) {
+            if  (jalview.bin.JalviewLite.debug)
+            {
+              System.err.println("AppletJmol:Creating new PDBfile IO parser.");
+            }
+            FileParse fp = new FileParse(pdbentry.getFile(), protocol);
+            fp.mark();
+            // reader = new MCview.PDBfile(fp);
+            // could set ID, etc.
+            //if (!reader.isValid())
+            //{
+            //  throw new Exception("Invalid datasource. "+reader.getWarningMessage());
+            //}
+            //fp.reset();
+            freader = fp.getReader();
+          }
+          if (freader==null) {
+            throw new Exception("Invalid datasource. Could not obtain Reader.");
           }
-          viewer.openReader(pdbentry.getFile(), pdbentry.getId(), fparser.getReader());
+          viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader);
         } catch (Exception e)
         {
           // give up!
@@ -659,7 +703,7 @@ public class AppletJmol extends EmbmenuFrame
       {
          pdb = ssm.setMapping(sequence,chains,
                               pdbentry.getFile(),
-                              AppletFormatAdapter.URL);
+                              protocol);
       }
 
       pdbentry.setId(pdb.id);
-- 
1.7.10.2