X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=676611c1d818e897e122c19df1cb6fae5f9f402e;hb=a878db688154da91ca7cc75a90c75d39bd193b3c;hp=522622d7ba7b814cf8dd683afc6ffe1e848451d0;hpb=5d455c2d0b8b1ac94d82584e2885654693abb39f;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 522622d..676611c 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
@@ -19,18 +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 java.util.Vector;
-import javax.swing.BorderFactory;
-
 
 public class AnnotationExporter
     extends JPanel
@@ -38,7 +34,7 @@ public class AnnotationExporter
   JInternalFrame frame;
   AlignmentPanel ap;
   boolean features = true;
-  AlignmentAnnotation [] annotations;
+  AlignmentAnnotation[] annotations;
   Vector sequenceGroups;
 
   public AnnotationExporter()
@@ -68,7 +64,7 @@ public class AnnotationExporter
   }
 
   public void exportAnnotations(AlignmentPanel ap,
-                                AlignmentAnnotation [] annotations,
+                                AlignmentAnnotation[] annotations,
                                 Vector sequenceGroups)
   {
     this.ap = ap;
@@ -81,95 +77,102 @@ public class AnnotationExporter
 
   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,
-              sequenceGroups );
+          text = new FeaturesFile().printJalviewFormat(
+              ap.av.alignment.getDataset().getSequencesArray(),
+              ap.av.featuresDisplayed);
         }
+      }
+      else
+      {
+        text = new AnnotationFile().printAnnotations(
+            annotations,
+            sequenceGroups);
+      }
 
-        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();
       }
+    }
   }
 
   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,
-          sequenceGroups );
+          sequenceGroups);
     }
 
-
     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);
 
-
   }
 
   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
   {