From 173a7ca81c8d8c00f889fd4e3583cc8733d3d179 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 1 Mar 2006 16:23:15 +0000
Subject: [PATCH] fixed after refactoring of SequenceFeature[]
 seq.getSequenceFeatures

---
 src/jalview/analysis/SeqsetUtils.java |   18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 61f10b5..691b905 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -49,7 +49,13 @@ public class SeqsetUtils
     sqinfo.put("Name", seq.getName());
     sqinfo.put("Start", new Integer(seq.getStart()));
     sqinfo.put("End", new Integer(seq.getEnd()));
-    sqinfo.put("SeqFeatures", (seq.getSequenceFeatures() !=null) ? seq.getSequenceFeatures() : null);
+    Vector sfeat = new Vector();
+    jalview.datamodel.SequenceFeature[] sfarray=seq.getSequenceFeatures();
+    if (sfarray!=null && sfarray.length>0) {
+      for (int i=0;i<sfarray.length;i++)
+        sfeat.add(sfarray[i]);
+    }
+    sqinfo.put("SeqFeatures", sfeat);
     sqinfo.put("PdbId",
                (seq.getPDBId() != null) ? seq.getPDBId() : new Vector());
     sqinfo.put("datasetSequence", (seq.getDatasetSequence() !=null) ? seq.getDatasetSequence() : new Sequence("THISISAPLACEHOLDER",""));
@@ -61,7 +67,7 @@ public class SeqsetUtils
    * TODO: replace these methods with something more elegant.
    * @param sq SequenceI
    * @param sqinfo Hashtable
-   * @return boolean
+   * @return boolean true if name was not updated from sqinfo Name entry
    */
   public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
   {
@@ -71,7 +77,7 @@ public class SeqsetUtils
     String oldname = (String) sqinfo.get("Name");
     Integer start = (Integer) sqinfo.get("Start");
     Integer end = (Integer) sqinfo.get("End");
-    SequenceFeature [] sfeatures = (SequenceFeature[]) sqinfo.get(
+    Vector sfeatures = (Vector) sqinfo.get(
         "SeqFeatures");
     Vector pdbid = (Vector) sqinfo.get("PdbId");
     Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
@@ -94,10 +100,12 @@ public class SeqsetUtils
       sq.setEnd(end.intValue());
     }
 
-    if ((sfeatures != null) && (sfeatures.length>0))
+    if ((sfeatures != null) && (sfeatures.size()>0))
     {
-      sq.setSequenceFeatures(sfeatures);
+      SequenceFeature[] sfarray = (SequenceFeature[]) sfeatures.toArray();
+      sq.setSequenceFeatures(sfarray);
     }
+
     if ((seqds!=null) && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds.getLength()==0)) {
       sq.setDatasetSequence(seqds);
     }
-- 
1.7.10.2