JAL-1641 Further refactoring of JSON export option, introduction of Viewport to the...

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index bd4a393..2180d07 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -147,9 +147,9 @@ public class AppJmol extends StructureViewerBase
     PDBEntry[] pdbentrys = new PDBEntry[files.length];
     for (int i = 0; i < pdbentrys.length; i++)
     {
-      PDBEntry pdbentry = new PDBEntry();
-      pdbentry.setFile(files[i]);
-      pdbentry.setId(ids[i]);
+      // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
+      PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB,
+              files[i]);
       pdbentrys[i] = pdbentry;
     }
     // / TODO: check if protocol is needed to be set, and if chains are
@@ -169,7 +169,7 @@ public class AppJmol extends StructureViewerBase
       seqColour.setSelected(false);
       viewerColour.setSelected(true);
     }
-    if (usetoColour)
+    else if (usetoColour)
     {
       useAlignmentPanelForColourbyseq(ap);
       jmb.setColourBySequence(true);
@@ -186,7 +186,7 @@ public class AppJmol extends StructureViewerBase
     {
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
       {
-        closeViewer();
+        closeViewer(false);
       }
     });
     initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
@@ -408,7 +408,7 @@ public class AppJmol extends StructureViewerBase
     {
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
       {
-        closeViewer();
+        closeViewer(false);
       }
     });
 
@@ -604,8 +604,9 @@ public class AppJmol extends StructureViewerBase
     jmb.centerViewer(toshow);
   }
 
-  public void closeViewer()
+  public void closeViewer(boolean closeExternalViewer)
   {
+    // JMol does not use an external viewer
     jmb.closeViewer();
     setAlignmentPanel(null);
     _aps.clear();
@@ -667,8 +668,8 @@ public class AppJmol extends StructureViewerBase
           {
             // just transfer the file name from the first sequence's first
             // PDBEntry
-            file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
-                    .elementAt(0)).getFile()).getAbsolutePath();
+            file = new File(pdbseq.getSequenceAt(0).getPDBId()
+                    .elementAt(0).getFile()).getAbsolutePath();
             jmb.getPdbEntry(pi).setFile(file);
 
             files.append(" \"" + Platform.escapeString(file) + "\"");
@@ -940,7 +941,7 @@ public class AppJmol extends StructureViewerBase
       // Set the colour using the current view for the associated alignframe
       for (AlignmentPanel ap : _colourwith)
       {
-        jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+        jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
       }
     }
   }