X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=a23496d3b38fb25e70fc163418e650c18fade4f4;hb=0ebbad305e982eeda562a1842362dc415c36cc8d;hp=0b0916d1ec753e5e1d7264117944b94fb32b0bb9;hpb=3595f261bc6f18dd8a4780976716bea81bd4fae4;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 0b0916d..a23496d 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -20,22 +20,13 @@
  */
 package jalview.gui;
 
-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;
@@ -48,6 +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
@@ -106,6 +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();
@@ -114,9 +116,9 @@ public class AnnotationExporter extends JPanel
   }
 
   /**
-   * Configures the dialog for options to export visible features. If from a split
-   * frame panel showing linked features, make the option to include these in the
-   * export visible.
+   * Configures the dialog for options to export visible features. If from a
+   * split frame panel showing linked features, make the option to include these
+   * in the export visible.
    */
   public void exportFeatures()
   {
@@ -161,8 +163,17 @@ 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
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty("LAST_DIRECTORY"));
 
@@ -194,28 +205,30 @@ public class AnnotationExporter extends JPanel
   }
 
   /**
-   * Answers the text to output for either Features (in GFF or Jalview format) or
-   * Annotations (in CSV or Jalview format)
+   * Answers the text to output for either Features (in GFF or Jalview format)
+   * or Annotations (in CSV or Jalview format)
    * 
    * @return
    */
-  private String getText()
+  public String getText()
   {
     return exportFeatures ? getFeaturesText() : getAnnotationsText();
   }
 
   /**
-   * Returns the text contents for output of annotations in either CSV or Jalview
-   * format
+   * Returns the text contents for output of annotations in either CSV or
+   * Jalview format
    * 
    * @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
     {
@@ -238,7 +251,7 @@ public class AnnotationExporter extends JPanel
    * 
    * @return
    */
-  private String getFeaturesText()
+  public String getFeaturesText()
   {
     String text;
     SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
@@ -322,10 +335,10 @@ public class AnnotationExporter extends JPanel
   }
 
   /**
-   * Builds a panel with a checkbox for the option to export linked (CDS/peptide)
-   * features. This is hidden by default, and only made visible if exporting
-   * features from a split frame panel which is configured to show linked
-   * features.
+   * Builds a panel with a checkbox for the option to export linked
+   * (CDS/peptide) features. This is hidden by default, and only made visible if
+   * exporting features from a split frame panel which is configured to show
+   * linked features.
    * 
    * @return
    */
@@ -335,17 +348,14 @@ public class AnnotationExporter extends JPanel
     linkedFeaturesPanel.setOpaque(false);
 
     boolean nucleotide = ap.av.isNucleotide();
-    String complement = nucleotide
-            ? MessageManager.getString("label.protein").toLowerCase()
-            : "CDS";
-    JLabel label = new JLabel(
-            MessageManager.formatMessage("label.include_linked_features",
-                    complement));
+    String complement = nucleotide ? MessageManager
+            .getString("label.protein").toLowerCase(Locale.ROOT) : "CDS";
+    JLabel label = new JLabel(MessageManager
+            .formatMessage("label.include_linked_features", complement));
     label.setHorizontalAlignment(SwingConstants.TRAILING);
     String tooltip = MessageManager
             .formatMessage("label.include_linked_tooltip", complement);
-    label.setToolTipText(
-            JvSwingUtils.wrapTooltip(true, tooltip));
+    label.setToolTipText(JvSwingUtils.wrapTooltip(true, tooltip));
 
     includeLinkedFeatures = new JCheckBox();
     linkedFeaturesPanel.add(label);
@@ -402,8 +412,8 @@ public class AnnotationExporter extends JPanel
   }
 
   /**
-   * Builds the panel with options to output in Jalview, GFF or CSV format. GFF is
-   * only made visible when exporting features, CSV only when exporting
+   * Builds the panel with options to output in Jalview, GFF or CSV format. GFF
+   * is only made visible when exporting features, CSV only when exporting
    * annotation.
    * 
    * @return