Output groups in annotation file

[jalview.git] / src / jalview / gui / AnnotationExporter.java

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index d4975a6..522622d 100755 (executable)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -28,6 +28,7 @@ import jalview.datamodel.AlignmentAnnotation;
 \r
 import java.awt.Color;\r
 import java.awt.FlowLayout;\r
+import java.util.Vector;\r
 import javax.swing.BorderFactory;\r
 \r
 \r
@@ -38,6 +39,7 @@ public class AnnotationExporter
   AlignmentPanel ap;\r
   boolean features = true;\r
   AlignmentAnnotation [] annotations;\r
+  Vector sequenceGroups;\r
 \r
   public AnnotationExporter()\r
   {\r
@@ -66,12 +68,14 @@ public class AnnotationExporter
   }\r
 \r
   public void exportAnnotations(AlignmentPanel ap,\r
-                                AlignmentAnnotation [] annotations)\r
+                                AlignmentAnnotation [] annotations,\r
+                                Vector sequenceGroups)\r
   {\r
     this.ap = ap;\r
     features = false;\r
     GFFFormat.setVisible(false);\r
     this.annotations = annotations;\r
+    this.sequenceGroups = sequenceGroups;\r
     frame.setTitle("Export Annotations");\r
   }\r
 \r
@@ -103,7 +107,9 @@ public class AnnotationExporter
         }\r
         else\r
         {\r
-           text = new AnnotationFile().printAnnotations( annotations );\r
+           text = new AnnotationFile().printAnnotations(\r
+              annotations,\r
+              sequenceGroups );\r
         }\r
 \r
         try\r
@@ -137,7 +143,9 @@ public class AnnotationExporter
     }\r
     else if(!features)\r
     {\r
-      text = new AnnotationFile().printAnnotations( annotations );\r
+      text = new AnnotationFile().printAnnotations(\r
+          annotations,\r
+          sequenceGroups );\r
     }\r
 \r
 \r