X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=671142b3fa8013828ec2118bcd284a5968734f24;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=fb54bbabaad9e6585e5cee0eb3e20f8a91e8c3a2;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index fb54bba..671142b 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -20,11 +20,7 @@
  */
 package jalview.util;
 
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.Mapping;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
+import java.util.Locale;
 
 import java.util.ArrayList;
 import java.util.BitSet;
@@ -32,10 +28,15 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 
 import com.stevesoft.pat.Regex;
 
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+
 /**
  * Utilities for handling DBRef objects and their collections.
  */
@@ -74,7 +75,7 @@ public class DBRefUtils
 	    // guarantee we always have lowercase entries for canonical string lookups
 	    for (String k : canonicalSourceNameLookup.keySet())
 	    {
-	      canonicalSourceNameLookup.put(k.toLowerCase(),
+	      canonicalSourceNameLookup.put(k.toLowerCase(Locale.ROOT),
 	              canonicalSourceNameLookup.get(k));
 	    }
    }
@@ -99,7 +100,7 @@ public class DBRefUtils
 	HashSet<String> srcs = new HashSet<String>();
 	for (String src : sources) 
 	{
-	  srcs.add(src.toUpperCase());
+	  srcs.add(src.toUpperCase(Locale.ROOT));
 	}
 
 	int nrefs = dbrefs.size();
@@ -108,7 +109,7 @@ public class DBRefUtils
 	{
 	  DBRefEntry dbr = dbrefs.get(ib);
 	  String source = getCanonicalName(dbr.getSource());
-	  if (srcs.contains(source.toUpperCase())) 
+	  if (srcs.contains(source.toUpperCase(Locale.ROOT))) 
 	  {
 	    res.add(dbr);
 	  }
@@ -182,7 +183,7 @@ public class DBRefUtils
 	  {
 		return null;
 	  }
-	  String canonical = canonicalSourceNameLookup.get(source.toLowerCase());
+	  String canonical = canonicalSourceNameLookup.get(source.toLowerCase(Locale.ROOT));
 	  return canonical == null ? source : canonical;
 	}
 
@@ -308,6 +309,83 @@ public class DBRefUtils
 
 	};
 
+  private static Regex PARSE_REGEX;
+
+  private static Regex getParseRegex()
+  {
+    return (PARSE_REGEX == null ? PARSE_REGEX = Platform.newRegex(
+            "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)")
+            : PARSE_REGEX);
+  }
+
+  /**
+   * Parses a DBRefEntry and adds it to the sequence, also a PDBEntry if the
+   * database is PDB.
+   * <p>
+   * Used by file parsers to generate DBRefs from annotation within file (eg
+   * Stockholm)
+   * 
+   * @param dbname
+   * @param version
+   * @param acn
+   * @param seq
+   *          where to annotate with reference
+   * @return parsed version of entry that was added to seq (if any)
+   */
+  public static DBRefEntry parseToDbRef(SequenceI seq, String dbname,
+          String version, String acn)
+  {
+    DBRefEntry ref = null;
+    if (dbname != null)
+    {
+      String locsrc = DBRefUtils.getCanonicalName(dbname);
+      if (locsrc.equals(DBRefSource.PDB))
+      {
+        /*
+         * Check for PFAM style stockhom PDB accession id citation e.g.
+         * "1WRI A; 7-80;"
+         */
+        Regex r = getParseRegex();
+        if (r.search(acn.trim()))
+        {
+          String pdbid = r.stringMatched(1);
+          String chaincode = r.stringMatched(2);
+          if (chaincode == null)
+          {
+            chaincode = " ";
+          }
+          // String mapstart = r.stringMatched(3);
+          // String mapend = r.stringMatched(4);
+          if (chaincode.equals(" "))
+          {
+            chaincode = "_";
+          }
+          // construct pdb ref.
+          ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
+          PDBEntry pdbr = new PDBEntry();
+          pdbr.setId(pdbid);
+          pdbr.setType(PDBEntry.Type.PDB);
+          pdbr.setChainCode(chaincode);
+          seq.addPDBId(pdbr);
+        }
+        else
+        {
+          System.err.println("Malformed PDB DR line:" + acn);
+        }
+      }
+      else
+      {
+        // default:
+        ref = new DBRefEntry(locsrc, version, acn.trim());
+      }
+    }
+    if (ref != null)
+    {
+      seq.addDBRef(ref);
+    }
+    return ref;
+  }
+
 	/**
 	 * accession ID and DB must be identical. Version is ignored. Map is either not
 	 * defined or is a match (or is compatible?)
@@ -451,60 +529,6 @@ public class DBRefUtils
   }
 
 	/**
-	 * Parses a DBRefEntry and adds it to the sequence, also a PDBEntry if the
-	 * database is PDB.
-	 * <p>
-	 * Used by file parsers to generate DBRefs from annotation within file (eg
-	 * Stockholm)
-	 * 
-	 * @param dbname
-	 * @param version
-	 * @param acn
-	 * @param seq     where to annotate with reference
-	 * @return parsed version of entry that was added to seq (if any)
-	 */
-	public static DBRefEntry parseToDbRef(SequenceI seq, String dbname, String version, String acn) {
-		DBRefEntry ref = null;
-		if (dbname != null) {
-			String locsrc = DBRefUtils.getCanonicalName(dbname);
-			if (locsrc.equals(DBRefSource.PDB)) {
-				/*
-				 * Check for PFAM style stockhom PDB accession id citation e.g. "1WRI A; 7-80;"
-				 */
-				Regex r = new com.stevesoft.pat.Regex("([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
-				if (r.search(acn.trim())) {
-					String pdbid = r.stringMatched(1);
-					String chaincode = r.stringMatched(2);
-					if (chaincode == null) {
-						chaincode = " ";
-					}
-					// String mapstart = r.stringMatched(3);
-					// String mapend = r.stringMatched(4);
-					if (chaincode.equals(" ")) {
-						chaincode = "_";
-					}
-					// construct pdb ref.
-					ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
-					PDBEntry pdbr = new PDBEntry();
-					pdbr.setId(pdbid);
-					pdbr.setType(PDBEntry.Type.PDB);
-					pdbr.setChainCode(chaincode);
-					seq.addPDBId(pdbr);
-				} else {
-					System.err.println("Malformed PDB DR line:" + acn);
-				}
-			} else {
-				// default:
-				ref = new DBRefEntry(locsrc, version, acn);
-			}
-		}
-		if (ref != null) {
-			seq.addDBRef(ref);
-		}
-		return ref;
-	}
-
-	/**
 	 * Returns true if either object is null, or they are equal
 	 * 
 	 * @param o1