JAL-3390 pull-up refactoring towards functional changes...

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 6c934c8..b28b81c 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
@@ -326,7 +327,7 @@ public class AppJmol extends StructureViewerBase
     for (String s : files)
     {
       fileList.append(SPACE).append(QUOTE)
-              .append(Platform.escapeString(s)).append(QUOTE);
+              .append(Platform.escapeBackslashes(s)).append(QUOTE);
     }
     String filesString = fileList.toString();
 
@@ -396,9 +397,9 @@ public class AppJmol extends StructureViewerBase
     }
 
     // refresh the sequence colours for the new structure(s)
-    for (AlignmentPanel ap : _colourwith)
+    for (AlignmentViewPanel avp : _colourwith)
     {
-      jmb.updateColours(ap);
+      jmb.updateColours(avp);
     }
     // do superposition if asked to
     if (alignAddedStructures)
@@ -515,7 +516,7 @@ public class AppJmol extends StructureViewerBase
             addingStructures = true; // already files loaded.
             for (int c = 0; c < filesInViewer.length; c++)
             {
-              if (filesInViewer[c].equals(file))
+              if (Platform.pathEquals(filesInViewer[c], file))
               {
                 file = null;
                 break;