Merge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 90fef07..105209f 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
@@ -30,6 +32,7 @@ import javax.swing.*;
 
 import org.exolab.castor.xml.*;
 
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -37,6 +40,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.schemabinding.version2.*;
 import jalview.schemes.*;
+import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.jarInputStreamProvider;
 import jalview.viewmodel.AlignmentViewport;
@@ -434,7 +438,7 @@ public class Jalview2XML
     for (String dssids : dsses.keySet())
     {
       AlignFrame _af = dsses.get(dssids);
-      String jfileName = fileName + " Dataset for " + _af.getTitle();
+      String jfileName = MessageManager.formatMessage("label.dataset_for", new String[]{fileName,_af.getTitle()});
       if (!jfileName.endsWith(".xml"))
       {
         jfileName = jfileName + ".xml";
@@ -1499,8 +1503,7 @@ public class Jalview2XML
         return false;
       }
     }
-    throw new Error("Unsupported Version for calcIdparam "
-            + calcIdParam.toString());
+    throw new Error(MessageManager.formatMessage("error.unsupported_version_calcIdparam", new String[]{calcIdParam.toString()}));
   }
 
   /**
@@ -1793,7 +1796,7 @@ public class Jalview2XML
     try
     {
       // create list to store references for any new Jmol viewers created
-      newStructureViewers = new Vector<AppJmol>();
+      newStructureViewers = new Vector<JalviewStructureDisplayI>();
       // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
       // Workaround is to make sure caller implements the JarInputStreamProvider
       // interface
@@ -3130,10 +3133,11 @@ public class Jalview2XML
                   @Override
                   public void run()
                   {
-                    AppJmol sview = null;
+                    JalviewStructureDisplayI sview = null;
                     try
                     {
-                      sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
+                      // JAL-1333 note - we probably can't migrate Jmol views to UCSF Chimera!
+                      sview = new StructureViewer(alf.alignPanel.getStructureSelectionManager()).createView(StructureViewer.Viewer.JMOL, pdbf, id, sq, alf.alignPanel,
                               useinJmolsuperpos, usetoColourbyseq,
                               jmolColouring, fileloc, rect, vid);
                       addNewStructureViewer(sview);
@@ -3209,15 +3213,18 @@ public class Jalview2XML
 
   /**
    * 
-   * @param supported - minimum version we are comparing against
-   * @param version - version of data being processsed.
+   * @param supported
+   *          - minimum version we are comparing against
+   * @param version
+   *          - version of data being processsed.
    * @return true if version is development/null or evaluates to the same or
    *         later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
    */
   private boolean isVersionStringLaterThan(String supported, String version)
   {
     if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
-            || version.equalsIgnoreCase("Test"))
+            || version.equalsIgnoreCase("Test")
+            || version.equalsIgnoreCase("AUTOMATED BUILD"))
     {
       System.err.println("Assuming project file with "
               + (version == null ? "null" : version)
@@ -3260,13 +3267,13 @@ public class Jalview2XML
     return true;
   }
 
-  Vector<AppJmol> newStructureViewers = null;
+  Vector<JalviewStructureDisplayI> newStructureViewers = null;
 
-  protected void addNewStructureViewer(AppJmol sview)
+  protected void addNewStructureViewer(JalviewStructureDisplayI sview)
   {
     if (newStructureViewers != null)
     {
-      sview.jmb.setFinishedLoadingFromArchive(false);
+      sview.getBinding().setFinishedLoadingFromArchive(false);
       newStructureViewers.add(sview);
     }
   }
@@ -3275,9 +3282,9 @@ public class Jalview2XML
   {
     if (newStructureViewers != null)
     {
-      for (AppJmol sview : newStructureViewers)
+      for (JalviewStructureDisplayI sview : newStructureViewers)
       {
-        sview.jmb.setFinishedLoadingFromArchive(true);
+        sview.getBinding().setFinishedLoadingFromArchive(true);
       }
       newStructureViewers.clear();
       newStructureViewers = null;