JAL-1025 JAL-1022 use File based equivalence to map between jalview

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 0e00de4..bd86275 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -722,8 +722,10 @@ public class AppJmol extends GStructureViewer implements Runnable,
           {
             // just transfer the file name from the first sequence's first
             // PDBEntry
-            jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq
-                    .getSequenceAt(0).getPDBId().elementAt(0)).getFile());
+            file = new File(((PDBEntry) pdbseq
+                    .getSequenceAt(0).getPDBId().elementAt(0)).getFile()).toURI().getPath().substring(1);
+            jmb.pdbentry[pi].setFile(file);
+            
             files.append(" \"" + file + "\"");
           }
           else