X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=dcb2a7ddea8ca0519fadc574e3e07400c0df4d55;hb=528dcd143968fc270232e4cec64a79b447aa5ec6;hp=beb4980cd87f4a582e910410056e8f7007b9658f;hpb=c54581c9ab50f031fe6400fa4f578a44f1f55798;p=jalview.git

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index beb4980..dcb2a7d 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -20,9 +20,24 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.ext.varna.RnaModel;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.ShiftList;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
-import java.lang.reflect.InvocationTargetException;
 import java.util.Collection;
 import java.util.Hashtable;
 import java.util.LinkedHashMap;
@@ -47,22 +62,6 @@ import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
 import fr.orsay.lri.varna.models.rna.ModeleBase;
 import fr.orsay.lri.varna.models.rna.RNA;
 
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.RnaViewerModel;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.ext.varna.RnaModel;
-import jalview.structure.SecondaryStructureListener;
-import jalview.structure.SelectionListener;
-import jalview.structure.SelectionSource;
-import jalview.structure.StructureSelectionManager;
-import jalview.structure.VamsasSource;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.ShiftList;
-
 public class AppVarna extends JInternalFrame implements SelectionListener,
         SecondaryStructureListener, InterfaceVARNASelectionListener,
         VamsasSource
@@ -189,17 +188,16 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     setTitle(theTitle);
 
     String gappedTitle = sname + " (with gaps)";
-    RnaModel gappedModel = new RnaModel(gappedTitle, aa, seq, null, true,
-            null);
+    RnaModel gappedModel = new RnaModel(gappedTitle, aa, seq, null, true);
     addModel(gappedModel, gappedTitle);
 
     String trimmedTitle = "trimmed " + sname;
-    RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null,
-            false, null);
+    RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null, false);
     addModel(trimmedModel, trimmedTitle);
     vab.setSelectedIndex(0);
   }
 
+
   /**
    * Constructor that links the viewer to a parent panel (but has no structures
    * yet - use addModel to add them)
@@ -405,14 +403,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     if (rnaModel.seq == sequence)
     {
       int highlightPos = rnaModel.gapped ? index : position - 1;
-      // int highlightPos = index;
-      // ShiftList shift = offsets.get(rna);
-      // if (shift != null)
-      // {
-      // System.err.print("Orig pos:" + index);
-      // highlightPos = shift.shift(index);
-      // System.err.println("\nFinal pos:" + index);
-      // }
       mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos);
       vab.updateSelectedRNA(rna);
     }
@@ -600,34 +590,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     }
 
     /*
-     * loaded from project file with Varna session data
-     */
-    if (model.varnaSession != null)
-    {
-      try
-      {
-        FullBackup fromSession = vab.vp.loadSession(model.varnaSession);
-        vab.addStructure(fromSession.rna, fromSession.config);
-        RNA rna = fromSession.rna;
-        // copy the model, but now including the RNA object
-        RnaModel newModel = new RnaModel(model.title, model.ann, model.seq,
-                rna, model.gapped, model.varnaSession);
-        if (!model.gapped)
-        {
-          registerOffset(rna, buildOffset(model.seq));
-        }
-        models.put(rna, newModel);
-        // capture rna selection state when saved
-        selectionHighlighter = new VarnaHighlighter(rna);
-        return fromSession.rna;
-      } catch (ExceptionLoadingFailed e)
-      {
-        e.printStackTrace();
-        return null;
-      }
-    }
-
-    /*
      * opened on request in Jalview session
      */
     RNA rna = new RNA(modelName);
@@ -651,7 +613,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
       rna = trimRNA(rna, modelName);
     }
     models.put(rna, new RnaModel(modelName, model.ann, model.seq, rna,
-            model.gapped, null));
+            model.gapped));
     vab.addStructure(rna);
     return rna;
   }
@@ -701,10 +663,64 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
   /**
    * Set the selected index in the model selection list
    * 
-   * @param selectedR
+   * @param selectedIndex
    */
   public void setInitialSelection(final int selectedIndex)
   {
+    /*
+     * empirically it needs a second for Varna/AWT to finish loading/drawing
+     * models for this to work; SwingUtilities.invokeLater _not_ a solution;
+     * explanation and/or better solution welcome!
+     */
+    synchronized (this)
+    {
+      try
+      {
+        wait(1000);
+      } catch (InterruptedException e)
+      {
+        // meh
+      }
+    }
     vab.setSelectedIndex(selectedIndex);
   }
+
+
+  /**
+   * Add a model with associated Varna session file
+   * 
+   * @param rna
+   * @param modelName
+   */
+  public RNA addModelSession(RnaModel model, String modelName,
+          String sessionFile)
+  {
+    if (!model.ann.isValidStruc())
+    {
+      throw new IllegalArgumentException("Invalid RNA structure annotation");
+    }
+
+    try
+    {
+      FullBackup fromSession = vab.vp.loadSession(sessionFile);
+      vab.addStructure(fromSession.rna, fromSession.config);
+      RNA rna = fromSession.rna;
+      // copy the model, but now including the RNA object
+      RnaModel newModel = new RnaModel(model.title, model.ann, model.seq,
+              rna, model.gapped);
+      if (!model.gapped)
+      {
+        registerOffset(rna, buildOffset(model.seq));
+      }
+      models.put(rna, newModel);
+      // capture rna selection state when saved
+      selectionHighlighter = new VarnaHighlighter(rna);
+      return fromSession.rna;
+    } catch (ExceptionLoadingFailed e)
+    {
+      System.err
+              .println("Error restoring Varna session: " + e.getMessage());
+      return null;
+    }
+  }
 }