X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=fabd0c69d178e483ab7c651245d888c183976d26;hb=refs%2Fheads%2Ffeatures%2FJAL-2446NCList;hp=2b21e5eb589bf1f2cb94563834923f26102bfdcf;hpb=e327ac5df98f528afeb347ac9a79085ad0d0975b;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 2b21e5e..fabd0c6 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -27,6 +27,7 @@ import jalview.datamodel.SequenceI;
 
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 public class SeqsetUtils
@@ -50,15 +51,11 @@ public class SeqsetUtils
     {
       sqinfo.put("Description", seq.getDescription());
     }
-    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.addElement(sfarray[i]);
-      }
-    }
+
+    Vector<SequenceFeature> sfeat = new Vector<SequenceFeature>();
+    List<SequenceFeature> sfs = seq.getFeatures().getAllFeatures();
+    sfeat.addAll(sfs);
+
     if (seq.getDatasetSequence() == null)
     {
       sqinfo.put("SeqFeatures", sfeat);
@@ -95,7 +92,8 @@ public class SeqsetUtils
     String oldname = (String) sqinfo.get("Name");
     Integer start = (Integer) sqinfo.get("Start");
     Integer end = (Integer) sqinfo.get("End");
-    Vector sfeatures = (Vector) sqinfo.get("SeqFeatures");
+    Vector<SequenceFeature> sfeatures = (Vector<SequenceFeature>) sqinfo
+            .get("SeqFeatures");
     Vector<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
     String description = (String) sqinfo.get("Description");
     Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
@@ -118,14 +116,9 @@ public class SeqsetUtils
       sq.setEnd(end.intValue());
     }
 
-    if ((sfeatures != null) && (sfeatures.size() > 0))
+    if (sfeatures != null && !sfeatures.isEmpty())
     {
-      SequenceFeature[] sfarray = new SequenceFeature[sfeatures.size()];
-      for (int is = 0, isize = sfeatures.size(); is < isize; is++)
-      {
-        sfarray[is] = (SequenceFeature) sfeatures.elementAt(is);
-      }
-      sq.setSequenceFeatures(sfarray);
+      sq.setSequenceFeatures(sfeatures);
     }
     if (description != null)
     {