X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=be0ef742a5b5fd8a59b9b812209834b6e6f7a19b;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=ab3f0d1006903cc74bc1024c64ff6e2bf55970cf;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index ab3f0d1..be0ef74 100755
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.gui;
 
 import java.util.*;
@@ -30,19 +29,24 @@ import jalview.io.*;
 
 /**
  * 
- * GUI dialog for exporting features or alignment annotations depending upon which method is called.
+ * GUI dialog for exporting features or alignment annotations depending upon
+ * which method is called.
  * 
  * @author AMW
- *
+ * 
  */
-public class AnnotationExporter
-    extends JPanel
+public class AnnotationExporter extends JPanel
 {
   JInternalFrame frame;
+
   AlignmentPanel ap;
+
   boolean features = true;
+
   AlignmentAnnotation[] annotations;
+
   Vector sequenceGroups;
+
   Hashtable alignmentProperties;
 
   public AnnotationExporter()
@@ -50,8 +54,7 @@ public class AnnotationExporter
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -59,9 +62,7 @@ public class AnnotationExporter
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame,
-                             "",
-                             260, 125);
+    Desktop.addInternalFrame(frame, "", 260, 125);
   }
 
   public void exportFeatures(AlignmentPanel ap)
@@ -73,9 +74,8 @@ public class AnnotationExporter
   }
 
   public void exportAnnotations(AlignmentPanel ap,
-                                AlignmentAnnotation[] annotations,
-                                Vector sequenceGroups,
-                                Hashtable alProperties)
+          AlignmentAnnotation[] annotations, Vector sequenceGroups,
+          Hashtable alProperties)
   {
     this.ap = ap;
     features = false;
@@ -89,12 +89,12 @@ 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.setDialogTitle(features ? "Save Features to File"
+            : "Save Annotation to File");
     chooser.setToolTipText("Save");
 
     int value = chooser.showSaveDialog(this);
@@ -106,15 +106,15 @@ public class AnnotationExporter
       {
         if (GFFFormat.isSelected())
         {
-          text = new FeaturesFile().printGFFFormat(
-              ap.av.alignment.getDataset().getSequencesArray(),
-              ap.av.featuresDisplayed);
+          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().printJalviewFormat(ap.av.alignment
+                  .getDataset().getSequencesArray(),
+                  ap.av.featuresDisplayed);
         }
       }
       else
@@ -122,23 +122,22 @@ public class AnnotationExporter
         if (CSVFormat.isSelected())
         {
           text = new AnnotationFile().printCSVAnnotations(annotations);
-        } else {
-          text = new AnnotationFile().printAnnotations(
-            annotations,
-            sequenceGroups,
-            alignmentProperties);
+        }
+        else
+        {
+          text = new AnnotationFile().printAnnotations(annotations,
+                  sequenceGroups, alignmentProperties);
         }
       }
 
       try
       {
         java.io.PrintWriter out = new java.io.PrintWriter(
-            new java.io.FileWriter(chooser.getSelectedFile()));
+                new java.io.FileWriter(chooser.getSelectedFile()));
 
         out.print(text);
         out.close();
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
@@ -154,15 +153,13 @@ public class AnnotationExporter
     {
       if (GFFFormat.isSelected())
       {
-        text = new FeaturesFile().printGFFFormat(
-            ap.av.alignment.getDataset().getSequencesArray(),
-            ap.av.featuresDisplayed);
+        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().printJalviewFormat(ap.av.alignment
+                .getDataset().getSequencesArray(), ap.av.featuresDisplayed);
       }
     }
     else if (!features)
@@ -170,22 +167,19 @@ public class AnnotationExporter
       if (CSVFormat.isSelected())
       {
         text = new AnnotationFile().printCSVAnnotations(annotations);
-      } else {
-        text = new AnnotationFile().printAnnotations(
-          annotations,
-          sequenceGroups,
-          alignmentProperties);
+      }
+      else
+      {
+        text = new AnnotationFile().printAnnotations(annotations,
+                sequenceGroups, alignmentProperties);
       }
     }
 
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setText(text);
-    Desktop.addInternalFrame(cap,
-                             (features ? "Features for - " :
-                              "Annotations for - ")
-                             + ap.alignFrame.getTitle(),
-                             600,
-                             500);
+    Desktop.addInternalFrame(cap, (features ? "Features for - "
+            : "Annotations for - ")
+            + ap.alignFrame.getTitle(), 600, 500);
 
     close_actionPerformed(null);
   }
@@ -195,13 +189,12 @@ public class AnnotationExporter
     try
     {
       frame.setClosed(true);
+    } catch (java.beans.PropertyVetoException ex)
+    {
     }
-    catch (java.beans.PropertyVetoException ex)
-    {}
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     this.setLayout(flowLayout1);
     toFile.setText("to File");
@@ -256,15 +249,25 @@ public class AnnotationExporter
   }
 
   JPanel jPanel1 = new JPanel();
+
   JButton toFile = new JButton();
+
   JButton toTextbox = new JButton();
+
   JButton close = new JButton();
+
   ButtonGroup buttonGroup = new ButtonGroup();
+
   JRadioButton jalviewFormat = new JRadioButton();
+
   JRadioButton GFFFormat = new JRadioButton();
+
   JRadioButton CSVFormat = new JRadioButton();
+
   JLabel jLabel1 = new JLabel();
+
   JPanel jPanel3 = new JPanel();
+
   FlowLayout flowLayout1 = new FlowLayout();
 
 }