X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=beb77ca14b8e7e0f692d77368473db4a1893c9bc;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=eacf152512de72a65769fbd6501f3802117ea1c8;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index eacf152..beb77ca 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,7 +20,9 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
 import jalview.io.FeaturesFile;
 import jalview.io.JalviewFileChooser;
@@ -32,6 +34,7 @@ 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;
@@ -91,8 +94,8 @@ public class AnnotationExporter extends JPanel
   public void exportAnnotations(AlignmentPanel ap)
   {
     this.ap = ap;
-    annotations = ap.av.isShowAnnotation() ? null : ap.av.getAlignment()
-            .getAlignmentAnnotation();
+    annotations = ap.av.isShowAnnotation() ? null
+            : ap.av.getAlignment().getAlignmentAnnotation();
     wholeView = true;
     startExportAnnotation();
   }
@@ -120,9 +123,9 @@ public class AnnotationExporter extends JPanel
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(features ? MessageManager
-            .getString("label.save_features_to_file") : MessageManager
-            .getString("label.save_annotation_to_file"));
+    chooser.setDialogTitle(features
+            ? MessageManager.getString("label.save_features_to_file")
+            : MessageManager.getString("label.save_annotation_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -153,17 +156,28 @@ public class AnnotationExporter extends JPanel
             .getString("label.no_features_on_alignment");
     if (features)
     {
+      Map<String, FeatureColourI> displayedFeatureColours = ap
+              .getFeatureRenderer().getDisplayedFeatureCols();
+      FeaturesFile formatter = new FeaturesFile();
+      SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
+      Map<String, FeatureColourI> 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 = new FeaturesFile().printGffFormat(
+                ap.av.getAlignment().getDataset().getSequencesArray(),
+                displayedFeatureColours, true, ap.av.isShowNPFeats());
+        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 = new FeaturesFile().printJalviewFormat(
+                ap.av.getAlignment().getDataset().getSequencesArray(),
+                displayedFeatureColours, true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
+        text = formatter.printJalviewFormat(sequences, featureColours, true,
+                includeNonPositional);
       }
     }
     else
@@ -196,23 +210,23 @@ public class AnnotationExporter extends JPanel
     {
       String text = getFileContents();
       cap.setText(text);
-      Desktop.addInternalFrame(
-              cap,
-              (features ? MessageManager.formatMessage(
-                      "label.features_for_params",
-                      new String[] { ap.alignFrame.getTitle() })
-                      : MessageManager.formatMessage(
-                              "label.annotations_for_params",
-                              new String[] { ap.alignFrame.getTitle() })),
+      Desktop.addInternalFrame(cap, (features ? MessageManager
+              .formatMessage("label.features_for_params", new String[]
+              { ap.alignFrame.getTitle() })
+              : MessageManager.formatMessage("label.annotations_for_params",
+                      new String[]
+                      { ap.alignFrame.getTitle() })),
               600, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning((features ? MessageManager.formatMessage(
-              "label.generating_features_for_params",
-              new String[] { ap.alignFrame.getTitle() })
+              "label.generating_features_for_params", new String[]
+              { ap.alignFrame.getTitle() })
               : MessageManager.formatMessage(
                       "label.generating_annotations_for_params",
-                      new String[] { ap.alignFrame.getTitle() })), oom);
+                      new String[]
+                      { ap.alignFrame.getTitle() })),
+              oom);
       cap.dispose();
     }
 
@@ -236,6 +250,7 @@ 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 +259,7 @@ 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 +268,7 @@ public class AnnotationExporter extends JPanel
     close.setText(MessageManager.getString("action.close"));
     close.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         close_actionPerformed(e);