From 11a49ff3022aff104f294e3365659ef388b38015 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 12 Feb 2012 14:49:42 +0000
Subject: [PATCH] JAL-1025 JAL-1022 use File based equivalence to map between
 jalview string pdb handles and Jmol filenames

---
 src/jalview/ext/jmol/JalviewJmolBinding.java |   12 +++++++-----
 src/jalview/gui/AppJmol.java                 |    9 +++++----
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 0640b8c..38e58d8 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -871,6 +871,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
         // recover PDB filename for the model hovered over.
         pdbfilename = viewer
                 .getModelFileName(new Integer(mdlId).intValue() - 1);
+        
       } catch (Exception e)
       {
       }
@@ -1130,7 +1131,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
           }
           else
           {
-            if (matches = pdbentry[pe].getFile().equals(fileName))
+            File fl;
+            if (matches = (fl=new File(pdbentry[pe].getFile())).equals(new File(fileName)))
             {
               foundEntry = true;
               // TODO: Jmol can in principle retrieve from CLASSLOADER but
@@ -1141,7 +1143,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
               String protocol = AppletFormatAdapter.URL;
               try
               {
-                File fl = new java.io.File(pdbentry[pe].getFile());
                 if (fl.exists())
                 {
                   protocol = AppletFormatAdapter.FILE;
@@ -1151,9 +1152,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
               } catch (Error e)
               {
               }
-              ;
+              //Explicitly map to the filename used by Jmol ;
               pdb = ssm.setMapping(sequence[pe], chains[pe],
-                      pdbentry[pe].getFile(), protocol);
+                      fileName, protocol);
+                      //pdbentry[pe].getFile(), protocol);
 
             }
           }
@@ -1164,7 +1166,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
             {
               String chid = new String(pdb.id + ":"
                       + ((MCview.PDBChain) pdb.chains.elementAt(i)).id);
-              chainFile.put(chid, pdbentry[pe].getFile());
+              chainFile.put(chid, fileName);
               chainNames.addElement(chid);
             }
             notifyLoaded = true;
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 8d9d9f0..bd86275 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -722,10 +722,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
           {
             // just transfer the file name from the first sequence's first
             // PDBEntry
-            jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq
-                    .getSequenceAt(0).getPDBId().elementAt(0)).getFile());
+            file = new File(((PDBEntry) pdbseq
+                    .getSequenceAt(0).getPDBId().elementAt(0)).getFile()).toURI().getPath().substring(1);
+            jmb.pdbentry[pi].setFile(file);
             
-            files.append(" \"" + jalview.util.Platform.escapeString(file) + "\"");
+            files.append(" \"" + file + "\"");
           }
           else
           {
@@ -748,7 +749,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
           }
           if (file != null)
           {
-            files.append(" \"" + jalview.util.Platform.escapeString(file) + "\"");
+            files.append(" \"" + file + "\"");
           }
         }
       }
-- 
1.7.10.2