develop merge

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

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 643d8a0..d688ddd 100644 (file)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
 import jalview.io.FeaturesFile;
 import jalview.io.JalviewFileChooser;
@@ -32,6 +33,7 @@ import java.awt.Color;
 import java.awt.FlowLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.Map;
 
 import javax.swing.BorderFactory;
 import javax.swing.ButtonGroup;
@@ -153,17 +155,20 @@ public class AnnotationExporter extends JPanel
             .getString("label.no_features_on_alignment");
     if (features)
     {
+      FeaturesFile formatter = new FeaturesFile();
+      SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
+      Map<String, Object> featureColours = ap.getFeatureRenderer()
+              .getDisplayedFeatureCols();
+      boolean includeNonPositional = ap.av.isShowNPFeats();
       if (GFFFormat.isSelected())
       {
-        text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
-                .getDataset().getSequencesArray(), ap.getFeatureRenderer()
-                .getDisplayedFeatureCols(), true, ap.av.isShowNPFeats());// ap.av.featuresDisplayed//);
+        text = formatter.printGffFormat(sequences, featureColours, true,
+                includeNonPositional);
       }
       else
       {
-        text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
-                .getDataset().getSequencesArray(), ap.getFeatureRenderer()
-                .getDisplayedFeatureCols(), true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
+        text = formatter.printJalviewFormat(sequences, featureColours,
+                true, includeNonPositional);
       }
     }
     else
@@ -236,6 +241,7 @@ public class AnnotationExporter extends JPanel
     toFile.setText(MessageManager.getString("label.to_file"));
     toFile.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         toFile_actionPerformed(e);
@@ -244,6 +250,7 @@ public class AnnotationExporter extends JPanel
     toTextbox.setText(MessageManager.getString("label.to_textbox"));
     toTextbox.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         toTextbox_actionPerformed(e);
@@ -252,6 +259,7 @@ public class AnnotationExporter extends JPanel
     close.setText(MessageManager.getString("action.close"));
     close.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         close_actionPerformed(e);