JAL-3541 selectively merged build.gradle and gradle.properties

[jalview.git] / src / jalview / io / ModellerDescription.java

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index c1849fc..a56f2af 100755 (executable)
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -20,8 +20,13 @@
  */
 package jalview.io;
 
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 
+import java.util.List;
+
+import com.stevesoft.pat.Regex;
+
 public class ModellerDescription
 {
   /**
@@ -93,7 +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))
@@ -271,21 +276,20 @@ 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;
             }