Export annotations with properties

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 4ee6e27..57a09ef 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -868,7 +868,8 @@ public class AlignFrame
   {\r
     String annotation = new AnnotationFile().printAnnotations(\r
         viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,\r
-        viewport.alignment.getGroups());\r
+        viewport.alignment.getGroups(),\r
+         ((Alignment)viewport.alignment).alignmentProperties);\r
 \r
     if (displayTextbox)\r
     {\r

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 676611c..1307483 100755 (executable)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -36,6 +36,7 @@ public class AnnotationExporter
   boolean features = true;\r
   AlignmentAnnotation[] annotations;\r
   Vector sequenceGroups;\r
+  Hashtable alignmentProperties;\r
 \r
   public AnnotationExporter()\r
   {\r
@@ -65,13 +66,15 @@ public class AnnotationExporter
 \r
   public void exportAnnotations(AlignmentPanel ap,\r
                                 AlignmentAnnotation[] annotations,\r
-                                Vector sequenceGroups)\r
+                                Vector sequenceGroups,\r
+                                Hashtable alProperties)\r
   {\r
     this.ap = ap;\r
     features = false;\r
     GFFFormat.setVisible(false);\r
     this.annotations = annotations;\r
     this.sequenceGroups = sequenceGroups;\r
+    this.alignmentProperties = alProperties;\r
     frame.setTitle("Export Annotations");\r
   }\r
 \r
@@ -109,7 +112,8 @@ public class AnnotationExporter
       {\r
         text = new AnnotationFile().printAnnotations(\r
             annotations,\r
-            sequenceGroups);\r
+            sequenceGroups,\r
+            alignmentProperties);\r
       }\r
 \r
       try\r
@@ -149,7 +153,8 @@ public class AnnotationExporter
     {\r
       text = new AnnotationFile().printAnnotations(\r
           annotations,\r
-          sequenceGroups);\r
+          sequenceGroups,\r
+          alignmentProperties);\r
     }\r
 \r
     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r