From 0a55a33506f2a76f7e557462257ec7918c764a2f Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 12 Feb 2012 15:08:16 +0000
Subject: [PATCH] (JAL-1025 JAL-1022) File based equivalence used to match
 Jmol and jalview paths. Use Jmol style '/' paths for local
 PDB file strings

---
 src/jalview/gui/Jalview2XML.java |   20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index e259309..3c5259e 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1823,9 +1823,9 @@ public class Jalview2XML
         }
         ;
         out.close();
-
-        alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
-        return outFile.getAbsolutePath();
+        String t=outFile.toURI().getPath().substring(1);
+        alreadyLoadedPDB.put(pdbId, t);
+        return t;
       }
       else
       {
@@ -2627,12 +2627,13 @@ public class Jalview2XML
               }
               if (ids[p].getFile() != null)
               {
+                File mapkey=new File(ids[p].getFile());
                 Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
-                        .get(ids[p].getFile());
+                        .get(mapkey);
                 if (seqstrmaps == null)
                 {
                   ((Hashtable) jmoldat[2]).put(
-                          new File(ids[p].getFile()).toString(),
+                          mapkey,
                           seqstrmaps = new Object[]
                           { pdbFile, ids[p].getId(), new Vector(),
                               new Vector() });
@@ -2665,7 +2666,7 @@ public class Jalview2XML
           Object[] svattrib = entry.getValue();
           int[] geom = (int[]) svattrib[0];
           String state = (String) svattrib[1];
-          Hashtable<String, Object[]> oldFiles = (Hashtable<String, Object[]>) svattrib[2];
+          Hashtable<File, Object[]> oldFiles = (Hashtable<File, Object[]>) svattrib[2];
           final boolean useinJmolsuperpos = ((boolean[]) svattrib[3])[0], usetoColourbyseq = ((boolean[]) svattrib[3])[1], jmolColouring = ((boolean[]) svattrib[3])[2];
           int x = geom[0], y = geom[1], width = geom[2], height = geom[3];
           // collate the pdbfile -> sequence mappings from this view
@@ -2736,8 +2737,7 @@ public class Jalview2XML
               // recover the new mapping data for this old filename
               // have to normalize filename - since Jmol and jalview do filename
               // translation differently.
-              Object[] filedat = oldFiles.get(new File(oldfilenam)
-                      .toString());
+              Object[] filedat = oldFiles.get(new File(oldfilenam));
               newFileLoc.append(((String) filedat[0]));
               pdbfilenames.addElement((String) filedat[0]);
               pdbids.addElement((String) filedat[1]);
@@ -2758,7 +2758,7 @@ public class Jalview2XML
                       .print("Ignoring incomplete Jmol state for PDB ids: ");
               newFileLoc = new StringBuffer(state);
               newFileLoc.append("; load append ");
-              for (String id : oldFiles.keySet())
+              for (File id : oldFiles.keySet())
               {
                 // add this and any other pdb files that should be present in
                 // the viewer
@@ -2856,7 +2856,7 @@ public class Jalview2XML
 
             // add mapping for sequences in this view to an already open Jmol
             // instance
-            for (String id : oldFiles.keySet())
+            for (File id : oldFiles.keySet())
             {
               // add this and any other pdb files that should be present in the
               // viewer
-- 
1.7.10.2