From 18f3cccd416493708352f425317f5861b6ee190d Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 20 Sep 2006 07:46:25 +0000
Subject: [PATCH] jalview alignment titles are preserved.

---
 src/jalview/gui/VamsasClient.java   |    2 +-
 src/jalview/io/VamsasDatastore.java |   12 ++++++++++--
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/jalview/gui/VamsasClient.java b/src/jalview/gui/VamsasClient.java
index 250fdde..cefa928 100755
--- a/src/jalview/gui/VamsasClient.java
+++ b/src/jalview/gui/VamsasClient.java
@@ -171,7 +171,7 @@ public class VamsasClient extends ArchiveClient {
                 	AlignFrame af = (AlignFrame) frames[i];
                 	
                 	// update alignment and root from frame.
-                	vds.storeVAMSAS(af.getViewport());
+                	vds.storeVAMSAS(af.getViewport(), af.getTitle());
                 }
             }
         }
diff --git a/src/jalview/io/VamsasDatastore.java b/src/jalview/io/VamsasDatastore.java
index 63a3e52..c9d5994 100755
--- a/src/jalview/io/VamsasDatastore.java
+++ b/src/jalview/io/VamsasDatastore.java
@@ -145,9 +145,10 @@ public class VamsasDatastore {
   /**
    * put the alignment viewed by AlignViewport into cdoc.
    * 
-   * @param av
+   * @param av alignViewport to be stored
+   * @param aFtitle title for alignment
    */
-  public void storeVAMSAS(AlignViewport av) {
+  public void storeVAMSAS(AlignViewport av, String aFtitle) {
     try
     {
       jalview.datamodel.AlignmentI jal = av.getAlignment();
@@ -292,6 +293,13 @@ public class VamsasDatastore {
         // sensible source
         // here
         dataset.addAlignment(alignment);
+        {
+          Property title = new Property();
+          title.setName("jalview:AlTitle");
+          title.setType("string");
+          title.setContent(aFtitle);
+          alignment.addProperty(title);
+        }
         alignment.setGapChar(String.valueOf(av.getGapCharacter()));
         AlignmentSequence alseq = null;
         for (int i = 0; i < jal.getHeight(); i++)
-- 
1.7.10.2