X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FModellerDescription.java;h=7e05b15482d6828fbfa191a734ab91344f8edfd9;hb=3ca62ac09227ae36e2197050e8910382ea30f3fe;hp=a7a1efac04870066a37975a6b7cda801b7df17ec;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index a7a1efa..7e05b15 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,8 +20,11 @@
  */
 package jalview.io;
 
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 
+import java.util.List;
+
 public class ModellerDescription
 {
   /**
@@ -61,7 +64,8 @@ public class ModellerDescription
    */
   final int Types[] = { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
 
-  final char Padding[] = { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.' };
+  final char Padding[] = { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.',
+      '.' };
 
   java.util.Hashtable fields = new java.util.Hashtable();
 
@@ -244,15 +248,15 @@ public class ModellerDescription
     {
       // Set start and end before we update the type (in the case of a
       // synthesized field set)
-      if (getStartCode() == null
-              || (getStartNum() != seq.getStart() && getStartCode().val != null))
+      if (getStartCode() == null || (getStartNum() != seq.getStart()
+              && getStartCode().val != null))
       {
         // unset or user updated sequence start position
         setStartCode(seq.getStart());
       }
 
-      if (getEndCode() == null
-              || (getEndNum() != seq.getEnd() && getStartCode() != null && getStartCode().val != null))
+      if (getEndCode() == null || (getEndNum() != seq.getEnd()
+              && getStartCode() != null && getStartCode().val != null))
       {
         setEndCode(seq.getEnd());
       }
@@ -268,23 +272,22 @@ public class ModellerDescription
       // sets the local reference field
       int t = 0; // sequence
       if (seq.getDatasetSequence() != null
-              && seq.getDatasetSequence().getDBRef() != null)
+              && seq.getDatasetSequence().getDBRefs() != null)
       {
-        jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
-                .getDBRef();
-        int i, j;
-        for (i = 0, j = dbr.length; i < j; i++)
+        List<DBRefEntry> dbr = seq.getDatasetSequence().getDBRefs();
+        for (int i = 0, ni = dbr.size(); i < ni; i++)
         {
-          if (dbr[i] != null)
+        	DBRefEntry dbri = dbr.get(i);
+          if (dbri != 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 (dbr[i].getSource()
+            if (dbri.getSource()
                     .equals(jalview.datamodel.DBRefSource.PDB))
             {
-              fields.put(Fields[LOCALID], dbr[i].getAccessionId());
+              fields.put(Fields[LOCALID], dbri.getAccessionId());
               t = 2;
               break;
             }