X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=a2336a0e1283da95811d6c3703be97bc7b193c76;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=a27b495c213dc47689d6662f9f5839d2205283ee;hpb=1f4a20a53b80b7ea459bbecb59ac2c83beb68a60;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a27b495..a2336a0 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -81,6 +81,7 @@ import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
 import jalview.io.ScoreMatrixFile;
 import jalview.io.TCoffeeScoreFile;
+import jalview.io.vcf.VCFLoader;
 import jalview.jbgui.GAlignFrame;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
@@ -732,9 +733,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     int aSize = alignPanels.size();
 
-    tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+    tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 
-    if (aSize == 1 && ap.av.viewName == null)
+    if (aSize == 1 && ap.av.getViewName() == null)
     {
       this.getContentPane().add(ap, BorderLayout.CENTER);
     }
@@ -747,7 +748,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       expandViews.setEnabled(true);
       gatherViews.setEnabled(true);
-      tabbedPane.addTab(ap.av.viewName, ap);
+      tabbedPane.addTab(ap.av.getViewName(), ap);
 
       ap.setVisible(false);
     }
@@ -770,7 +771,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     gatherViews.setEnabled(true);
     tabbedPane.setVisible(true);
     AlignmentPanel first = alignPanels.get(0);
-    tabbedPane.addTab(first.av.viewName, first);
+    tabbedPane.addTab(first.av.getViewName(), first);
     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
   }
 
@@ -839,6 +840,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignmentI al = getViewport().getAlignment();
     boolean nucleotide = al.isNucleotide();
 
+    loadVcf.setVisible(nucleotide);
     showTranslation.setVisible(nucleotide);
     showReverse.setVisible(nucleotide);
     showReverseComplement.setVisible(nucleotide);
@@ -870,7 +872,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param av
    *          AlignViewport
    */
-  void setMenusFromViewport(AlignViewport av)
+  public void setMenusFromViewport(AlignViewport av)
   {
     padGapsMenuitem.setSelected(av.isPadGaps());
     colourTextMenuItem.setSelected(av.isShowColourText());
@@ -1390,13 +1392,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void exportFeatures_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportFeatures(alignPanel);
+    new AnnotationExporter(alignPanel).exportFeatures();
   }
 
   @Override
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportAnnotations(alignPanel);
+    new AnnotationExporter(alignPanel).exportAnnotations();
   }
 
   @Override
@@ -1826,7 +1828,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void copy_actionPerformed(ActionEvent e)
   {
-    System.gc();
     if (viewport.getSelectionGroup() == null)
     {
       return;
@@ -2712,10 +2713,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     newap.av.setGatherViewsHere(false);
 
-    if (viewport.viewName == null)
+    if (viewport.getViewName() == null)
     {
-      viewport.viewName = MessageManager
-              .getString("label.view_name_original");
+      viewport.setViewName(MessageManager
+              .getString("label.view_name_original"));
     }
 
     /*
@@ -2739,7 +2740,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       newap.refresh(true); // adjust layout of annotations
     }
 
-    newap.av.viewName = getNewViewName(viewTitle);
+    newap.av.setViewName(getNewViewName(viewTitle));
 
     addAlignmentPanel(newap, true);
     newap.alignmentChanged();
@@ -2802,9 +2803,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (comp instanceof AlignmentPanel)
       {
         AlignmentPanel ap = (AlignmentPanel) comp;
-        if (!existingNames.contains(ap.av.viewName))
+        if (!existingNames.contains(ap.av.getViewName()))
         {
-          existingNames.add(ap.av.viewName);
+          existingNames.add(ap.av.getViewName());
         }
       }
     }
@@ -3596,9 +3597,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     frameTitle += " from ";
 
-    if (viewport.viewName != null)
+    if (viewport.getViewName() != null)
     {
-      frameTitle += viewport.viewName + " of ";
+      frameTitle += viewport.getViewName() + " of ";
     }
 
     frameTitle += this.title;
@@ -4250,7 +4251,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
           final String source)
   {
-    new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+    new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
             .start();
   }
 
@@ -4766,7 +4767,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (reply != null)
       {
-        viewport.viewName = reply;
+        viewport.setViewName(reply);
         // TODO warn if reply is in getExistingViewNames()?
         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
       }
@@ -5304,6 +5305,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (avc.createGroup())
     {
+      if (applyAutoAnnotationSettings.isSelected())
+      {
+        alignPanel.updateAnnotation(true, false);
+      }
       alignPanel.alignmentChanged();
     }
   }
@@ -5588,6 +5593,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       new CalculationChooser(AlignFrame.this);
     }
   }
+
+  @Override
+  protected void loadVcf_actionPerformed()
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            Cache.getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
+    chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", choice);
+      SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+      new VCFLoader(choice).loadVCF(seqs, this);
+    }
+
+  }
 }
 
 class PrintThread extends Thread