X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=9c6231a2e066a9e0d8892f493cb06389082669e7;hb=1a802c6cf08e703f6b722a91b1e7f58f76356476;hp=de6aaa09bb059dcc54c3ea93920940e827fef3ae;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index de6aaa0..9c6231a 100755
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -18,6 +18,7 @@
 package jalview.gui;
 
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 import java.awt.event.*;
@@ -44,7 +45,7 @@ public class AnnotationExporter extends JPanel
 
   AlignmentAnnotation[] annotations;
 
-  Vector sequenceGroups;
+  List<SequenceGroup> sequenceGroups;
 
   Hashtable alignmentProperties;
 
@@ -61,7 +62,7 @@ public class AnnotationExporter extends JPanel
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "", 260, 125);
+    Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width, frame.getPreferredSize().height);
   }
 
   public void exportFeatures(AlignmentPanel ap)
@@ -73,7 +74,7 @@ public class AnnotationExporter extends JPanel
   }
 
   public void exportAnnotations(AlignmentPanel ap,
-          AlignmentAnnotation[] annotations, Vector sequenceGroups,
+          AlignmentAnnotation[] annotations, List<SequenceGroup> list,
           Hashtable alProperties)
   {
     this.ap = ap;
@@ -81,7 +82,7 @@ public class AnnotationExporter extends JPanel
     GFFFormat.setVisible(false);
     CSVFormat.setVisible(true);
     this.annotations = annotations;
-    this.sequenceGroups = sequenceGroups;
+    this.sequenceGroups = list;
     this.alignmentProperties = alProperties;
     frame.setTitle("Export Annotations");
   }
@@ -105,13 +106,13 @@ public class AnnotationExporter extends JPanel
       {
         if (GFFFormat.isSelected())
         {
-          text = new FeaturesFile().printGFFFormat(ap.av.alignment
+          text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
                   .getDataset().getSequencesArray(),
                   getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
         }
         else
         {
-          text = new FeaturesFile().printJalviewFormat(ap.av.alignment
+          text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
                   .getDataset().getSequencesArray(),
                   getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
         }
@@ -152,13 +153,13 @@ public class AnnotationExporter extends JPanel
     {
       if (GFFFormat.isSelected())
       {
-        text = new FeaturesFile().printGFFFormat(ap.av.alignment
+        text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
                 .getDataset().getSequencesArray(),
                 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
       }
       else
       {
-        text = new FeaturesFile().printJalviewFormat(ap.av.alignment
+        text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
                 .getDataset().getSequencesArray(),
                 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
       }
@@ -196,7 +197,7 @@ public class AnnotationExporter extends JPanel
   private Hashtable getDisplayedFeatureCols()
   {
     Hashtable fcols = new Hashtable();
-    if (ap.av.featuresDisplayed==null)
+    if (ap.av.featuresDisplayed == null)
     {
       return fcols;
     }
@@ -225,7 +226,8 @@ public class AnnotationExporter extends JPanel
 
   private void jbInit() throws Exception
   {
-    this.setLayout(flowLayout1);
+    this.setLayout(new BorderLayout());
+    
     toFile.setText("to File");
     toFile.addActionListener(new ActionListener()
     {
@@ -273,8 +275,8 @@ public class AnnotationExporter extends JPanel
     buttonGroup.add(jalviewFormat);
     buttonGroup.add(GFFFormat);
     buttonGroup.add(CSVFormat);
-    this.add(jPanel3, null);
-    this.add(jPanel1, null);
+    this.add(jPanel3, BorderLayout.CENTER);
+    this.add(jPanel1, BorderLayout.SOUTH);
   }
 
   JPanel jPanel1 = new JPanel();