JAL-1769 fixed output to jalview (.jpv) file in headless mode. Initial cause of failu...

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 0ebc804..e4ec30b 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -20,45 +20,6 @@
  */
 package jalview.gui;
 
-import java.awt.Rectangle;
-import java.io.BufferedReader;
-import java.io.DataInputStream;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.lang.reflect.InvocationTargetException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.StringTokenizer;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
-import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
-
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
@@ -128,6 +89,45 @@ import jalview.ws.params.ArgumentI;
 import jalview.ws.params.AutoCalcSetting;
 import jalview.ws.params.WsParamSetI;
 
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.StringTokenizer;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
 /**
  * Write out the current jalview desktop state as a Jalview XML stream.
  * 
@@ -1372,6 +1372,10 @@ public class Jalview2XML
           final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
           boolean storeDataset)
   {
+    if (Desktop.desktop == null)
+    {
+      return;
+    }
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
     for (int f = frames.length - 1; f > -1; f--)
     {
@@ -2172,7 +2176,7 @@ public class Jalview2XML
         });
       } catch (Exception x)
       {
-
+        System.err.println("Error loading alignment: " + x.getMessage());
       }
     }
     return af;
@@ -3344,11 +3348,10 @@ public class Jalview2XML
           String sessionState = ss.getViewerState();
           String tempStateFile = copyJarEntry(jprovider, sessionState,
                   "varna");
-          RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped,
-                  tempStateFile);
-          appVarna.addModel(rna, rnaTitle);
+          RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
+          appVarna.addModelSession(rna, rnaTitle, tempStateFile);
         }
-        appVarna.setSelectedIndex(viewer.getSelectedRna());
+        appVarna.setInitialSelection(viewer.getSelectedRna());
       }
     }
   }