From 89176d88cd000522d92623d6cb6bacf154c4c9e7 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 1 Nov 2005 16:01:03 +0000
Subject: [PATCH] stores reference to dataset sequence if present

---
 src/jalview/analysis/SeqsetUtils.java |    7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 11a31be..06a8192 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -52,7 +52,7 @@ public class SeqsetUtils
     sqinfo.put("SeqFeatures", (seq.getSequenceFeatures() !=null) ? seq.getSequenceFeatures() : new Vector());
     sqinfo.put("PdbId",
                (seq.getPDBId() != null) ? seq.getPDBId() : new String(""));
-
+    sqinfo.put("datasetSequence", (seq.getDatasetSequence() !=null) ? seq.getDatasetSequence() : new Sequence("THISISAPLACEHOLDER",""));
     return sqinfo;
   }
 
@@ -72,7 +72,7 @@ public class SeqsetUtils
     java.util.Vector sfeatures = (java.util.Vector) sqinfo.get(
         "SeqFeatures");
     String pdbid = (String) sqinfo.get("PdbId");
-
+    Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
     if (oldname == null)
     {
       namePresent = false;
@@ -97,6 +97,9 @@ public class SeqsetUtils
     {
       sq.setSequenceFeatures(sfeatures);
     }
+    if ((seqds!=null) && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds.getLength()==0)) {
+      sq.setDatasetSequence(seqds);
+    }
 
     return namePresent;
   }
-- 
1.7.10.2