Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

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

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 1efd100..a23496d 100644 (file)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -20,24 +20,13 @@
  */
 package jalview.gui;
 
-import java.util.Locale;
-
-import jalview.api.FeatureRenderer;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.SequenceI;
-import jalview.io.AnnotationFile;
-import jalview.io.FeaturesFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.util.MessageManager;
-
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.io.FileWriter;
 import java.io.PrintWriter;
+import java.util.Locale;
 
 import javax.swing.BoxLayout;
 import javax.swing.ButtonGroup;
@@ -50,6 +39,16 @@ import javax.swing.JPanel;
 import javax.swing.JRadioButton;
 import javax.swing.SwingConstants;
 
+import jalview.api.FeatureRenderer;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.FeaturesFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.util.MessageManager;
+
 /**
  * 
  * GUI dialog for exporting features or alignment annotations depending upon
@@ -108,6 +107,7 @@ public class AnnotationExporter extends JPanel
     }
 
     frame = new JInternalFrame();
+    frame.setFrameIcon(null);
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     Dimension preferredSize = frame.getPreferredSize();
@@ -163,6 +163,14 @@ public class AnnotationExporter extends JPanel
     frame.setTitle(MessageManager.getString("label.export_annotations"));
   }
 
+  public void setExportAsCSV()
+  {
+    if (CSVFormat != null)
+    {
+      CSVFormat.setSelected(true);
+    }
+  }
+
   private void toFile_actionPerformed()
   {
     // TODO: JAL-3048 JalviewFileChooser - Save option
@@ -202,7 +210,7 @@ public class AnnotationExporter extends JPanel
    * 
    * @return
    */
-  private String getText()
+  public String getText()
   {
     return exportFeatures ? getFeaturesText() : getAnnotationsText();
   }
@@ -213,12 +221,14 @@ public class AnnotationExporter extends JPanel
    * 
    * @return
    */
-  private String getAnnotationsText()
+  public String getAnnotationsText()
   {
     String text;
     if (CSVFormat.isSelected())
     {
-      text = new AnnotationFile().printCSVAnnotations(annotations);
+      text = new AnnotationFile().printCSVAnnotations(
+              wholeView ? ap.av.getAlignment().getAlignmentAnnotation()
+                      : annotations);
     }
     else
     {
@@ -241,7 +251,7 @@ public class AnnotationExporter extends JPanel
    * 
    * @return
    */
-  private String getFeaturesText()
+  public String getFeaturesText()
   {
     String text;
     SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();