Merge branch 'develop' into features/JAL-1793VCF

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 298688b..5b812c2 100644 (file)
--- 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;
@@ -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);
@@ -4258,7 +4260,7 @@ 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();
   }
 
@@ -5585,6 +5587,26 @@ 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);
+      new VCFLoader(viewport.getAlignment()).loadVCF(choice, this);
+    }
+
+  }
 }
 
 class PrintThread extends Thread