(JAL-1050) ensure all filenames passed in to the load command are updated and their...

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index b899ae9..c8466b1 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -612,7 +612,8 @@ public class Jalview2XML
 
                 for (int smap = 0; smap < jmol.jmb.sequence[peid].length; smap++)
                 {
-                  if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
+//                  if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
+                  if (jds==jmol.jmb.sequence[peid][smap])
                   {
                     StructureState state = new StructureState();
                     state.setVisible(true);
@@ -1822,9 +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
       {
@@ -2626,12 +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() });
@@ -2648,7 +2650,7 @@ public class Jalview2XML
               }
               else
               {
-                errorMessage = ("The Jmol views in the Jalview 2 project may\nnot be correctly bound to sequences in the alignment.\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
+                errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
                 warn(errorMessage);
               }
             }
@@ -2664,7 +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
@@ -2728,6 +2730,8 @@ public class Jalview2XML
               {
                 newFileLoc = new StringBuffer();
               }
+              do {
+                // look for next filename in load statement
               newFileLoc.append(state.substring(cp,
                       ncp = (state.indexOf("\"", ncp + 1) + 1)));
               String oldfilenam = state.substring(ncp,
@@ -2735,8 +2739,7 @@ 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]);
@@ -2745,6 +2748,7 @@ public class Jalview2XML
               newFileLoc.append("\"");
               cp = ecp + 1; // advance beyond last \" and set cursor so we can
                             // look for next file statement.
+              } while ((ncp=state.indexOf("/*file*/",cp))>-1);
             }
             if (cp > 0)
             {
@@ -2757,7 +2761,7 @@ 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
@@ -2855,7 +2859,7 @@ 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