From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 12 Feb 2012 17:04:00 +0000 (+0000)
Subject: (JAL-1022) ensure all Jmol model filenames are normalised with File().getAbsolutePath... 
X-Git-Tag: Archived_Release_2_7~6
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=6fb2cd8a74354ef16d9bb2a6e596f30ab5aa7d1d

(JAL-1022) ensure all Jmol model filenames are normalised with File().getAbsolutePath() before binding to associated sequences in the structure manager.
---

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