X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FModellerDescription.java;h=48a69034ee8eb9bf7cc54ba426b9a6242b46fd96;hb=2d87a86ac0dbbcb50622156ccd4292545121ca2c;hp=c1849fc3d5e5a06422ff20001f577524aa958f2f;hpb=3027bfb4b1b13af8686abcd419888e03141bd672;p=jalview.git

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index c1849fc..48a6903 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -20,7 +20,13 @@
  */
 package jalview.io;
 
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
+import jalview.util.Platform;
+
+import java.util.List;
+
+import com.stevesoft.pat.Regex;
 
 public class ModellerDescription
 {
@@ -90,12 +96,20 @@ public class ModellerDescription
     }
   };
 
+  private static Regex VALIDATION_REGEX;
+
+  private static Regex getRegex()
+  {
+    return (VALIDATION_REGEX == null
+            ? VALIDATION_REGEX = Platform
+                    .newRegex("\\s*((([-0-9]+).?)|FIRST|LAST|@)", null)
+            : VALIDATION_REGEX);
+  }
+
   private resCode validResidueCode(String field)
   {
     Integer val = null;
-    com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
-            "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
-
+    Regex r = getRegex();
     if (!r.search(field))
     {
       return null; // invalid
@@ -271,21 +285,20 @@ 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;
             }