X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FModellerDescription.java;h=13431c17c0433c4f9c9490515a20dde762e1d99f;hb=e760a92aa57282a2ea3892656e12f03d45e60cf6;hp=13e48b4e05981d1f48d29fd3b19c1988874387a3;hpb=74333501ca7e85ea8f5d6f6d7c6787cf9d5e7c0e;p=jalview.git

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 13e48b4..13431c1 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -1,8 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io;
 
 import jalview.datamodel.SequenceI;
 import java.util.Vector;
-import com.stevesoft.pat.Regex;
 public class ModellerDescription
 {
     /**
@@ -70,7 +87,7 @@ public class ModellerDescription
   private resCode validResidueCode(String field)
   {
     Integer val = null;
-    com.stevesoft.pat.Regex r = new Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
+    com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
 
     if (!r.search(field))
     {
@@ -225,19 +242,17 @@ public class ModellerDescription
       if (seq.getDatasetSequence() != null &&
           seq.getDatasetSequence().getDBRef() != null)
       {
-        Vector dbr = seq.getDatasetSequence().getDBRef();
+        jalview.datamodel.DBRefEntry [] dbr = seq.getDatasetSequence().getDBRef();
         int i, j;
-        for (i = 0, j = dbr.size(); i < j; i++)
+        for (i = 0, j = dbr.length; i < j; i++)
         {
-          jalview.datamodel.DBRefEntry dref = (jalview.datamodel.DBRefEntry)
-              dbr.elementAt(i);
-          if (dref != null)
+          if (dbr[i] != null)
           {
             // JBPNote PDB dbRefEntry needs properties to propagate onto ModellerField
             // JBPNote Need to get info from the user about whether the sequence is the one being modelled, or if it is a template.
-            if (dref.getSource().equals("PDB"))
+            if (dbr[i].getSource().equals(jalview.datamodel.DBRefSource.PDB))
             {
-              fields.put(Fields[LOCALID], dref.getAccessionId());
+              fields.put(Fields[LOCALID], dbr[i].getAccessionId());
               t = 2;
               break;
             }