X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FModellerDescription.java;h=f7c94c38a8f4701e959f0f7e59b02eb7fd4a0c95;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=fd28956d3c9e8b22e961fa196410c29c0496de6a;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index fd28956..f7c94c3 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -1,24 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview 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 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceI;
 
 public class ModellerDescription
 {
@@ -27,13 +29,12 @@ public class ModellerDescription
    * single line, and sequence start/end and other properties. See PIRFile IO
    * for its use.
    */
-  final String[] seqTypes =
-  { "sequence", "structure", "structureX", "structureN" };
+  final String[] seqTypes = { "sequence", "structure", "structureX",
+      "structureN" };
 
-  final String[] Fields =
-  { "objectType", "objectId", "startField", "startCode", "endField",
-      "endCode", "description1", "description2", "resolutionField",
-      "tailField" };
+  final String[] Fields = { "objectType", "objectId", "startField",
+      "startCode", "endField", "endCode", "description1", "description2",
+      "resolutionField", "tailField" };
 
   final int TYPE = 0;
 
@@ -58,11 +59,9 @@ public class ModellerDescription
   /**
    * 0 is free text or empty 1 is something that parses to an integer, or \@
    */
-  final int Types[] =
-  { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
+  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();
 
@@ -269,10 +268,10 @@ 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();
+                .getDBRefs();
         int i, j;
         for (i = 0, j = dbr.length; i < j; i++)
         {