JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 7e05b15..e184d74 100755 (executable)
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -20,11 +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
 {
   /**
@@ -88,7 +91,7 @@ public class ModellerDescription
 
     resCode(int v)
     {
-      val = new Integer(v);
+      val = Integer.valueOf(v);
       field = val.toString();
     }
   };
@@ -96,8 +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))
     {
@@ -108,7 +110,7 @@ public class ModellerDescription
     {
       value = r.stringMatched(1);
     }
-    // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
+    // Cache.debug("from '" + field + "' matched '" + value +
     // "'");
     try
     {
@@ -163,7 +165,7 @@ 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 */
@@ -277,15 +279,14 @@ public class ModellerDescription
         List<DBRefEntry> dbr = seq.getDatasetSequence().getDBRefs();
         for (int i = 0, ni = dbr.size(); i < ni; i++)
         {
-               DBRefEntry dbri = dbr.get(i);
+          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 (dbri.getSource()
-                    .equals(jalview.datamodel.DBRefSource.PDB))
+            if (dbri.getSource().equals(jalview.datamodel.DBRefSource.PDB))
             {
               fields.put(Fields[LOCALID], dbri.getAccessionId());
               t = 2;