X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FModellerDescription.java;h=a56f2af0b1165c911f9f89eaff30e0b8b0ccc688;hb=9c127c47a7bf73c3e538815635f525fe59f7faba;hp=cc9b966feec9a46bbe5e3face354a6bcdfd38da6;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index cc9b966..a56f2af 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 2.8.2b1)
- * Copyright (C) 2014 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.
  * 
@@ -20,7 +20,12 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
+
+import com.stevesoft.pat.Regex;
 
 public class ModellerDescription
 {
@@ -29,13 +34,12 @@ 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;
 
@@ -60,11 +64,10 @@ 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();
 
@@ -87,7 +90,7 @@ public class ModellerDescription
 
     resCode(int v)
     {
-      val = new Integer(v);
+      val = Integer.valueOf(v);
       field = val.toString();
     }
   };
@@ -95,7 +98,7 @@ public class ModellerDescription
   private resCode validResidueCode(String field)
   {
     Integer val = null;
-    com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
+    Regex r = new Regex(
             "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
 
     if (!r.search(field))
@@ -247,15 +250,15 @@ 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());
       }
@@ -271,23 +274,22 @@ 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;
             }