X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=ab3f0d1006903cc74bc1024c64ff6e2bf55970cf;hb=50ea78c7b98de7614cd386956e9aa0ee73dd7936;hp=676611c1d818e897e122c19df1cb6fae5f9f402e;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 676611c..ab3f0d1 100755
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -28,6 +28,13 @@ import javax.swing.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 
+/**
+ * 
+ * GUI dialog for exporting features or alignment annotations depending upon which method is called.
+ * 
+ * @author AMW
+ *
+ */
 public class AnnotationExporter
     extends JPanel
 {
@@ -36,6 +43,7 @@ public class AnnotationExporter
   boolean features = true;
   AlignmentAnnotation[] annotations;
   Vector sequenceGroups;
+  Hashtable alignmentProperties;
 
   public AnnotationExporter()
   {
@@ -60,18 +68,22 @@ public class AnnotationExporter
   {
     this.ap = ap;
     features = true;
+    CSVFormat.setVisible(false);
     frame.setTitle("Export Features");
   }
 
   public void exportAnnotations(AlignmentPanel ap,
                                 AlignmentAnnotation[] annotations,
-                                Vector sequenceGroups)
+                                Vector sequenceGroups,
+                                Hashtable alProperties)
   {
     this.ap = ap;
     features = false;
     GFFFormat.setVisible(false);
+    CSVFormat.setVisible(true);
     this.annotations = annotations;
     this.sequenceGroups = sequenceGroups;
+    this.alignmentProperties = alProperties;
     frame.setTitle("Export Annotations");
   }
 
@@ -107,9 +119,15 @@ public class AnnotationExporter
       }
       else
       {
-        text = new AnnotationFile().printAnnotations(
+        if (CSVFormat.isSelected())
+        {
+          text = new AnnotationFile().printCSVAnnotations(annotations);
+        } else {
+          text = new AnnotationFile().printAnnotations(
             annotations,
-            sequenceGroups);
+            sequenceGroups,
+            alignmentProperties);
+        }
       }
 
       try
@@ -125,6 +143,8 @@ public class AnnotationExporter
         ex.printStackTrace();
       }
     }
+
+    close_actionPerformed(null);
   }
 
   public void toTextbox_actionPerformed(ActionEvent e)
@@ -147,9 +167,15 @@ public class AnnotationExporter
     }
     else if (!features)
     {
-      text = new AnnotationFile().printAnnotations(
+      if (CSVFormat.isSelected())
+      {
+        text = new AnnotationFile().printCSVAnnotations(annotations);
+      } else {
+        text = new AnnotationFile().printAnnotations(
           annotations,
-          sequenceGroups);
+          sequenceGroups,
+          alignmentProperties);
+      }
     }
 
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
@@ -161,6 +187,7 @@ public class AnnotationExporter
                              600,
                              500);
 
+    close_actionPerformed(null);
   }
 
   public void close_actionPerformed(ActionEvent e)
@@ -206,6 +233,8 @@ public class AnnotationExporter
     jalviewFormat.setText("Jalview");
     GFFFormat.setOpaque(false);
     GFFFormat.setText("GFF");
+    CSVFormat.setOpaque(false);
+    CSVFormat.setText("CSV(Spreadsheet)");
     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
     jLabel1.setText("Format: ");
     this.setBackground(Color.white);
@@ -218,8 +247,10 @@ public class AnnotationExporter
     jPanel3.add(jLabel1);
     jPanel3.add(jalviewFormat);
     jPanel3.add(GFFFormat);
+    jPanel3.add(CSVFormat);
     buttonGroup.add(jalviewFormat);
     buttonGroup.add(GFFFormat);
+    buttonGroup.add(CSVFormat);
     this.add(jPanel3, null);
     this.add(jPanel1, null);
   }
@@ -231,6 +262,7 @@ public class AnnotationExporter
   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();