Merge branch 'test_paolo_JAL-1065' into Tcoffee_JAL-1065

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 2c0d7d6..93a2994 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -35,6 +35,7 @@ import jalview.structure.*;
 import jalview.datamodel.PDBEntry;
 import jalview.io.*;
 import jalview.schemes.*;
+import jalview.util.Platform;
 
 public class AppJmol extends GStructureViewer implements Runnable,
         SequenceStructureBinding, ViewSetProvider
@@ -321,7 +322,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
     openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
   }
   private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) {
-    boolean promptUser=pdbentrys.length==1;
     progressBar = ap.alignFrame;
     jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
     addAlignmentPanel(ap);
@@ -335,24 +335,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
     worker=null;
-    String filelist="";
-//    for (PDBEntry pe: pdbentrys)
-//    {
-//      if (pe.getFile()==null)
       {
         addingStructures = false;
         worker = new Thread(this);
         worker.start();
-//        break;
       }
-//      filelist+=" \""+pe.getFile()+"\"";
-              
-/*    }
-    if (worker==null)
-    {
-      initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist);
-    }
-*/
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
@@ -736,9 +723,11 @@ 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());
-            files.append(" \"" + file + "\"");
+            file = new File(((PDBEntry) pdbseq
+                    .getSequenceAt(0).getPDBId().elementAt(0)).getFile()).getAbsolutePath();
+            jmb.pdbentry[pi].setFile(file);
+            
+            files.append(" \"" + Platform.escapeString(file) + "\"");
           }
           else
           {
@@ -761,7 +750,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
           }
           if (file != null)
           {
-            files.append(" \"" + file + "\"");
+            files.append(" \"" + Platform.escapeString(file) + "\"");
           }
         }
       }