X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=9c6231a2e066a9e0d8892f493cb06389082669e7;hb=49bb27409f71165b4d2daa6c38142a6466bb3946;hp=a6ccc7b05fa51d92501903005adcd5ddfa0fab36;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index a6ccc7b..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 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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;
 
@@ -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());
       }