X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FModellerDescription.java;h=d66fe6c5be246bb21fb8a18b0274e345c3b35433;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=1ab95451a2be99a890c622dce470cfe0dfc0789b;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 1ab9545..d66fe6c 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -20,8 +20,14 @@
  */
 package jalview.io;
 
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 
+import java.util.List;
+
+import com.stevesoft.pat.Regex;
+
 public class ModellerDescription
 {
   /**
@@ -61,7 +67,8 @@ 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();
 
@@ -84,7 +91,7 @@ public class ModellerDescription
 
     resCode(int v)
     {
-      val = new Integer(v);
+      val = Integer.valueOf(v);
       field = val.toString();
     }
   };
@@ -92,7 +99,7 @@ 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))
@@ -104,7 +111,7 @@ public class ModellerDescription
     {
       value = r.stringMatched(1);
     }
-    // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
+    // Cache.debug("from '" + field + "' matched '" + value +
     // "'");
     try
     {
@@ -159,7 +166,7 @@ public class ModellerDescription
                 }
                 else
                 {
-                  // jalview.bin.Cache.log.debug(
+                  // Cache.debug(
                   // "Ignoring non-Modeller description: invalid integer-like
                   // field '" + field + "'");
                   type = -1; /* invalid field! - throw the FieldSet away */
@@ -244,15 +251,15 @@ 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());
       }
@@ -270,21 +277,20 @@ public class ModellerDescription
       if (seq.getDatasetSequence() != null
               && seq.getDatasetSequence().getDBRefs() != null)
       {
-        jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
-                .getDBRefs();
-        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;
             }