(JAL-1022) ensure all Jmol model filenames are normalised with File().getAbsolutePath...

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 38e58d8..4a1efe6 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -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 +876,16 @@ 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