X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=7f949c78c97048588bab395d73697bb6d6da7bfd;hb=6909336c10f55ddf2813b983b0eb0fe79488c971;hp=90c28c736f44f961b1af882029156db708cf34f3;hpb=88ba474b631ee8844b2212cf0ef1bff6a97ec7e1;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 90c28c7..7f949c7 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -357,7 +357,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
       for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
       {
         StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
+        // RACE CONDITION - getMapping only returns Jmol loaded filenames once Jmol callback has completed. 
         if (mapping == null || mapping.length < 1)
           continue;
 
@@ -690,10 +690,17 @@ public abstract class JalviewJmolBinding implements StructureListener,
       String mset[] = new String[viewer.getModelCount()];
       _modelFileNameMap = new int[mset.length];
       int j = 1;
-      mset[0] = viewer.getModelFileName(0);
+      String m=viewer.getModelFileName(0);
+      if (m!=null)
+      {
+        mset[0] = new File(m).getAbsolutePath();
+      }
       for (int i = 1; i < mset.length; i++)
       {
-        mset[j] = viewer.getModelFileName(i);
+        m=viewer.getModelFileName(i);
+        if (m!=null) {
+          mset[j] = new File(m).getAbsolutePath();
+        }
         _modelFileNameMap[j] = i; // record the model index for the filename
         // skip any additional models in the same file (NMR structures)
         if ((mset[j] == null ? mset[j] != mset[j - 1]
@@ -869,8 +876,17 @@ public abstract class JalviewJmolBinding implements StructureListener,
       try
       {
         // recover PDB filename for the model hovered over.
-        pdbfilename = viewer
-                .getModelFileName(new Integer(mdlId).intValue() - 1);
+        int _mp=_modelFileNameMap.length-1,
+                mnumber=new Integer(mdlId).intValue() - 1;
+        while(mnumber<_modelFileNameMap[_mp])
+        {
+          _mp--;
+        }
+        pdbfilename = modelFileNames[_mp];
+        if (pdbfilename==null) {pdbfilename=new File(viewer
+                .getModelFileName(mnumber)).getAbsolutePath();
+        }
+        
       } catch (Exception e)
       {
       }
@@ -1130,7 +1146,8 @@ 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 +1158,6 @@ 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 +1167,10 @@ 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 +1181,7 @@ 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;