Merge branch 'test_paolo_JAL-1065' into Tcoffee_JAL-1065

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 0640b8c..a625fd7 100644 (file)
--- 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++)\r
       {\r
         StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);\r
-\r
+        // RACE CONDITION - getMapping only returns Jmol loaded filenames once Jmol callback has completed. \r
         if (mapping == null || mapping.length < 1)\r
           continue;\r
 \r
@@ -690,10 +690,17 @@ public abstract class JalviewJmolBinding implements StructureListener,
       String mset[] = new String[viewer.getModelCount()];\r
       _modelFileNameMap = new int[mset.length];\r
       int j = 1;\r
-      mset[0] = viewer.getModelFileName(0);\r
+      String m=viewer.getModelFileName(0);\r
+      if (m!=null)\r
+      {\r
+        mset[0] = new File(m).getAbsolutePath();\r
+      }\r
       for (int i = 1; i < mset.length; i++)\r
       {\r
-        mset[j] = viewer.getModelFileName(i);\r
+        m=viewer.getModelFileName(i);\r
+        if (m!=null) {\r
+          mset[j] = new File(m).getAbsolutePath();\r
+        }\r
         _modelFileNameMap[j] = i; // record the model index for the filename\r
         // skip any additional models in the same file (NMR structures)\r
         if ((mset[j] == null ? mset[j] != mset[j - 1]\r
@@ -869,8 +876,17 @@ public abstract class JalviewJmolBinding implements StructureListener,
       try\r
       {\r
         // recover PDB filename for the model hovered over.\r
-        pdbfilename = viewer\r
-                .getModelFileName(new Integer(mdlId).intValue() - 1);\r
+        int _mp=_modelFileNameMap.length-1,\r
+                mnumber=new Integer(mdlId).intValue() - 1;\r
+        while(mnumber<_modelFileNameMap[_mp])\r
+        {\r
+          _mp--;\r
+        }\r
+        pdbfilename = modelFileNames[_mp];\r
+        if (pdbfilename==null) {pdbfilename=new File(viewer\r
+                .getModelFileName(mnumber)).getAbsolutePath();\r
+        }\r
+        \r
       } catch (Exception e)\r
       {\r
       }\r
@@ -1130,7 +1146,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
           }\r
           else\r
           {\r
-            if (matches = pdbentry[pe].getFile().equals(fileName))\r
+            File fl;\r
+            if (matches = (fl=new File(pdbentry[pe].getFile())).equals(new File(fileName)))\r
             {\r
               foundEntry = true;\r
               // TODO: Jmol can in principle retrieve from CLASSLOADER but\r
@@ -1141,7 +1158,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
               String protocol = AppletFormatAdapter.URL;\r
               try\r
               {\r
-                File fl = new java.io.File(pdbentry[pe].getFile());\r
                 if (fl.exists())\r
                 {\r
                   protocol = AppletFormatAdapter.FILE;\r
@@ -1151,9 +1167,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
               } catch (Error e)\r
               {\r
               }\r
-              ;\r
+              //Explicitly map to the filename used by Jmol ;\r
               pdb = ssm.setMapping(sequence[pe], chains[pe],\r
-                      pdbentry[pe].getFile(), protocol);\r
+                      fileName, protocol);\r
+                      //pdbentry[pe].getFile(), protocol);\r
 \r
             }\r
           }\r
@@ -1164,7 +1181,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
             {\r
               String chid = new String(pdb.id + ":"\r
                       + ((MCview.PDBChain) pdb.chains.elementAt(i)).id);\r
-              chainFile.put(chid, pdbentry[pe].getFile());\r
+              chainFile.put(chid, fileName);\r
               chainNames.addElement(chid);\r
             }\r
             notifyLoaded = true;\r