From 58025959cd65fd79736adb061f2f381867b87738 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 23 Jun 2008 07:45:38 +0000
Subject: [PATCH] local sequence properties are preserved in SeqCigar
 representation of sequence using SeqHash/SeqUnhash in
 jalview.analysis.SeqsetUtils. Ensures input data and
 alignment results from webservice have same visible names
 as original sequences input.

---
 src/jalview/datamodel/SeqCigar.java |   21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index c896555..9ed0388 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -18,6 +18,8 @@
  */
 package jalview.datamodel;
 
+import java.util.Hashtable;
+
 import jalview.analysis.*;
 import jalview.util.*;
 
@@ -29,6 +31,7 @@ public class SeqCigar
    */
   private int start, end;
   private SequenceI refseq = null;
+  private Hashtable seqProps;
   /**
    * Reference dataset sequence for the cigar string
    * @return SequenceI
@@ -91,9 +94,20 @@ public class SeqCigar
                        refseq.getStart() + start + bounds[0],
                        refseq.getStart() + start +
                        ( (bounds[2] == 0) ? -1 : bounds[2]));
+    seq.setDescription(refseq.getDescription());
+    int sstart = seq.getStart(),
+      send = seq.getEnd();
     // seq.checkValidRange(); probably not needed
+    // recover local properties if present 
+    if (seqProps!=null)
+    {
+      // this recovers dataset sequence reference as well as local features, names, start/end settings.
+      SeqsetUtils.SeqCharacterUnhash(seq, seqProps);
+    }
+    // ensure dataset sequence is up to date from local reference 
     seq.setDatasetSequence(refseq);
-    seq.setDescription(refseq.getDescription());
+    seq.setStart(sstart);
+    seq.setEnd(send);
     return seq;
   }
 
@@ -182,8 +196,9 @@ public class SeqCigar
       hasgaps = true;
     }
 
-    this.refseq = ds;
-
+    refseq = ds;
+    // copy over local properties for the sequence instance of the refseq
+    seqProps = SeqsetUtils.SeqCharacterHash(seq);
     // Check  offsets
     if (end > ds.getLength())
     {
-- 
1.7.10.2