X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=41689c566a8004d98c270efe34489e887f90c764;hb=29f633ca27df2db2790b81b1ca346d6692d4936c;hp=d4975a6c6196b44a9f8e6eacb1a99c2b21caa3b7;hpb=9922c9eec14599f6b141a8db8a3859cab7227ce0;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index d4975a6..41689c5 100755
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -19,17 +19,14 @@
 
 package jalview.gui;
 
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
 import javax.swing.*;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
 
+import jalview.datamodel.*;
 import jalview.io.*;
-import jalview.datamodel.AlignmentAnnotation;
-
-import java.awt.Color;
-import java.awt.FlowLayout;
-import javax.swing.BorderFactory;
-
 
 public class AnnotationExporter
     extends JPanel
@@ -37,7 +34,9 @@ public class AnnotationExporter
   JInternalFrame frame;
   AlignmentPanel ap;
   boolean features = true;
-  AlignmentAnnotation [] annotations;
+  AlignmentAnnotation[] annotations;
+  Vector sequenceGroups;
+  Hashtable alignmentProperties;
 
   public AnnotationExporter()
   {
@@ -66,102 +65,122 @@ public class AnnotationExporter
   }
 
   public void exportAnnotations(AlignmentPanel ap,
-                                AlignmentAnnotation [] annotations)
+                                AlignmentAnnotation[] annotations,
+                                Vector sequenceGroups,
+                                Hashtable alProperties)
   {
     this.ap = ap;
     features = false;
     GFFFormat.setVisible(false);
     this.annotations = annotations;
+    this.sequenceGroups = sequenceGroups;
+    this.alignmentProperties = alProperties;
     frame.setTitle("Export Annotations");
   }
 
   public void toFile_actionPerformed(ActionEvent e)
   {
-      JalviewFileChooser chooser = new JalviewFileChooser(
-      jalview.bin.Cache.getProperty( "LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(
+        jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 
-      chooser.setFileView(new JalviewFileView());
-      chooser.setDialogTitle(
-          features ? "Save Features to File" : "Save Annotation to File");
-      chooser.setToolTipText("Save");
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle(
+        features ? "Save Features to File" : "Save Annotation to File");
+    chooser.setToolTipText("Save");
 
-      int value = chooser.showSaveDialog(this);
+    int value = chooser.showSaveDialog(this);
 
-      if (value == JalviewFileChooser.APPROVE_OPTION)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String text = "No features found on alignment";
+      if (features)
       {
-        String text = "No features found on alignment";
-        if (features)
+        if (GFFFormat.isSelected())
         {
-          if (GFFFormat.isSelected())
-            text = new FeaturesFile().printGFFFormat(
-                ap.av.alignment.getDataset().getSequencesArray(),
-                ap.av.featuresDisplayed);
-          else
-            text = new FeaturesFile().printJalviewFormat(
-                ap.av.alignment.getDataset().getSequencesArray(),
-                ap.av.featuresDisplayed);
+          text = new FeaturesFile().printGFFFormat(
+              ap.av.alignment.getDataset().getSequencesArray(),
+              ap.av.featuresDisplayed);
         }
         else
         {
-           text = new AnnotationFile().printAnnotations( annotations );
+          text = new FeaturesFile().printJalviewFormat(
+              ap.av.alignment.getDataset().getSequencesArray(),
+              ap.av.featuresDisplayed);
         }
+      }
+      else
+      {
+        text = new AnnotationFile().printAnnotations(
+            annotations,
+            sequenceGroups,
+            alignmentProperties);
+      }
 
-        try
-        {
-          java.io.PrintWriter out = new java.io.PrintWriter(
-              new java.io.FileWriter(chooser.getSelectedFile()));
+      try
+      {
+        java.io.PrintWriter out = new java.io.PrintWriter(
+            new java.io.FileWriter(chooser.getSelectedFile()));
 
-          out.print(text);
-          out.close();
-        }
-        catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
+        out.print(text);
+        out.close();
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
       }
+    }
+
+    close_actionPerformed(null);
   }
 
   public void toTextbox_actionPerformed(ActionEvent e)
   {
     String text = "No features found on alignment";
-    if(features)
+    if (features)
     {
       if (GFFFormat.isSelected())
+      {
         text = new FeaturesFile().printGFFFormat(
             ap.av.alignment.getDataset().getSequencesArray(),
             ap.av.featuresDisplayed);
+      }
       else
+      {
         text = new FeaturesFile().printJalviewFormat(
             ap.av.alignment.getDataset().getSequencesArray(),
-                ap.av.featuresDisplayed);
+            ap.av.featuresDisplayed);
+      }
     }
-    else if(!features)
+    else if (!features)
     {
-      text = new AnnotationFile().printAnnotations( annotations );
+      text = new AnnotationFile().printAnnotations(
+          annotations,
+          sequenceGroups,
+          alignmentProperties);
     }
 
-
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setText(text);
     Desktop.addInternalFrame(cap,
-                             (features ?  "Features for - " : "Annotations for - ")
+                             (features ? "Features for - " :
+                              "Annotations for - ")
                              + ap.alignFrame.getTitle(),
                              600,
                              500);
 
-
+    close_actionPerformed(null);
   }
 
   public void close_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
       frame.setClosed(true);
-    }catch(java.beans.PropertyVetoException ex)
+    }
+    catch (java.beans.PropertyVetoException ex)
     {}
   }
 
-
-
   private void jbInit()
       throws Exception
   {