From 6cfc81d62c929df5f7dd70b3048e5e5dced1429a Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 25 Apr 2007 14:07:10 +0000
Subject: [PATCH] Export annotations with properties

---
 src/jalview/appletgui/AlignFrame.java   |    3 ++-
 src/jalview/gui/AnnotationExporter.java |   11 ++++++++---
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 4ee6e27..57a09ef 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -868,7 +868,8 @@ public class AlignFrame
   {
     String annotation = new AnnotationFile().printAnnotations(
         viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
-        viewport.alignment.getGroups());
+        viewport.alignment.getGroups(),
+         ((Alignment)viewport.alignment).alignmentProperties);
 
     if (displayTextbox)
     {
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 676611c..1307483 100755
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -36,6 +36,7 @@ public class AnnotationExporter
   boolean features = true;
   AlignmentAnnotation[] annotations;
   Vector sequenceGroups;
+  Hashtable alignmentProperties;
 
   public AnnotationExporter()
   {
@@ -65,13 +66,15 @@ public class AnnotationExporter
 
   public void exportAnnotations(AlignmentPanel ap,
                                 AlignmentAnnotation[] annotations,
-                                Vector sequenceGroups)
+                                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");
   }
 
@@ -109,7 +112,8 @@ public class AnnotationExporter
       {
         text = new AnnotationFile().printAnnotations(
             annotations,
-            sequenceGroups);
+            sequenceGroups,
+            alignmentProperties);
       }
 
       try
@@ -149,7 +153,8 @@ public class AnnotationExporter
     {
       text = new AnnotationFile().printAnnotations(
           annotations,
-          sequenceGroups);
+          sequenceGroups,
+          alignmentProperties);
     }
 
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-- 
1.7.10.2