JAL-1717 updated the PDBEntry model and updated the method use for its equality test...

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 04235be..2180d07 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -20,6 +20,28 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -51,28 +73,6 @@ import javax.swing.event.InternalFrameEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 public class AppJmol extends StructureViewerBase
 {
   AppJmolBinding jmb;
@@ -147,7 +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(files[i], 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
@@ -666,8 +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) + "\"");