X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2FModellerDescription.java;fp=src%2Fjalview%2Fio%2FModellerDescription.java;h=9a3453ffcc17a453ea3a05988d01b1fabee2ae52;hp=30f46bf64e1f256a0838f55bac5371ea97b61d49;hb=67b3acb8df1438ef37a756c04e14f5a3b8406808;hpb=aa91e8c4561c2dd0f18760e18fb0052979733bf8

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 30f46bf..9a3453f 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -20,7 +20,11 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+
+import com.stevesoft.pat.Regex;
 
 public class ModellerDescription
 {
@@ -95,8 +99,7 @@ public class ModellerDescription
   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 = new Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
 
     if (!r.search(field))
     {
@@ -107,7 +110,7 @@ public class ModellerDescription
     {
       value = r.stringMatched(1);
     }
-    // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
+    // Cache.log.debug("from '" + field + "' matched '" + value +
     // "'");
     try
     {
@@ -162,7 +165,7 @@ public class ModellerDescription
                 }
                 else
                 {
-                  // jalview.bin.Cache.log.debug(
+                  // Cache.log.debug(
                   // "Ignoring non-Modeller description: invalid integer-like
                   // field '" + field + "'");
                   type = -1; /* invalid field! - throw the FieldSet away */
@@ -273,8 +276,7 @@ public class ModellerDescription
       if (seq.getDatasetSequence() != null
               && seq.getDatasetSequence().getDBRef() != null)
       {
-        jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
-                .getDBRef();
+        DBRefEntry[] dbr = seq.getDatasetSequence().getDBRef();
         int i, j;
         for (i = 0, j = dbr.length; i < j; i++)
         {
@@ -284,8 +286,7 @@ public class ModellerDescription
             // 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()
-                    .equals(jalview.datamodel.DBRefSource.PDB))
+            if (dbr[i].getSource().equals(DBRefSource.PDB))
             {
               fields.put(Fields[LOCALID], dbr[i].getAccessionId());
               t = 2;