JAL-892 1 second delay for correct initial rendering; code tidy up

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8dfe839..be56292 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.
  * 
@@ -868,7 +868,7 @@ public class Jalview2XML
         }
       }
 
-      saveRnaViewers(jout, jseq, jds, viewIds, storeDS);
+      saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
 
       jms.addJSeq(jseq);
     }
@@ -1365,10 +1365,12 @@ public class Jalview2XML
    * @param jseq
    * @param jds
    * @param viewIds
+   * @param ap
    * @param storeDataset
    */
   protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
-          final SequenceI jds, List<String> viewIds, boolean storeDataset)
+          final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
+          boolean storeDataset)
   {
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
     for (int f = frames.length - 1; f > -1; f--)
@@ -1376,11 +1378,12 @@ public class Jalview2XML
       if (frames[f] instanceof AppVarna)
       {
         AppVarna varna = (AppVarna) frames[f];
-        if (varna.isListeningFor(jds))
+        /*
+         * link the sequence to every viewer that is showing it and is linked to
+         * its alignment panel
+         */
+        if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
         {
-          /*
-           * link the sequence to every viewer that is showing it
-           */
           String viewId = varna.getViewId();
           RnaViewer rna = new RnaViewer();
           rna.setViewId(viewId);
@@ -2169,7 +2172,7 @@ public class Jalview2XML
         });
       } catch (Exception x)
       {
-
+        System.err.println("Error loading alignment: " + x.getMessage());
       }
     }
     return af;
@@ -3341,11 +3344,10 @@ 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());
       }
     }
   }