X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=123a4e104759d438d43433d65cca3425d5545fe9;hb=6e79eb7f3978f7e4ab11b7e2aa334a6e9b739996;hp=49f04cb960ba417e2f263f215de4920a16ff2c30;hpb=33fec402191308cc21b8b91c473a2fa68abe8962;p=jalview.git

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 49f04cb..123a4e1 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,39 +1,71 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.util;
 
-import java.util.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
+import com.stevesoft.pat.Regex;
 
 public class DBRefUtils
 {
+  private static Map<String, String> canonicalSourceNameLookup = new HashMap<String, String>();
+
+  private static Map<String, String> dasCoordinateSystemsLookup = new HashMap<String, String>();
+
+  static
+  {
+    // TODO load these from a resource file?
+    canonicalSourceNameLookup.put("uniprotkb/swiss-prot",
+            DBRefSource.UNIPROT);
+    canonicalSourceNameLookup.put("uniprotkb/trembl", DBRefSource.UNIPROT);
+    canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
+
+    dasCoordinateSystemsLookup.put("pdbresnum", DBRefSource.PDB);
+    dasCoordinateSystemsLookup.put("uniprot", DBRefSource.UNIPROT);
+    dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBL);
+    // dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBLCDS);
+  }
+
   /**
    * Utilities for handling DBRef objects and their collections.
    */
   /**
-   *
-   * @param dbrefs Vector of DBRef objects to search
-   * @param sources String[] array of source DBRef IDs to retrieve
+   * 
+   * @param dbrefs
+   *          Vector of DBRef objects to search
+   * @param sources
+   *          String[] array of source DBRef IDs to retrieve
    * @return Vector
    */
-  public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs, String[] sources)
+  public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs,
+          String[] sources)
   {
     if (dbrefs == null)
     {
@@ -43,8 +75,8 @@ public class DBRefUtils
     {
       return dbrefs;
     }
-    Hashtable srcs = new Hashtable();
-    Vector res = new Vector();
+    Map<String, Integer> srcs = new HashMap<String, Integer>();
+    ArrayList<DBRefEntry> res = new ArrayList<DBRefEntry>();
 
     for (int i = 0; i < sources.length; i++)
     {
@@ -54,339 +86,390 @@ public class DBRefUtils
     {
       if (srcs.containsKey(dbrefs[i].getSource()))
       {
-        res.addElement(dbrefs[i]);
+        res.add(dbrefs[i]);
       }
     }
 
     if (res.size() > 0)
     {
       DBRefEntry[] reply = new DBRefEntry[res.size()];
-      for (int i = 0; i < res.size(); i++)
-      {
-        reply[i] = (DBRefEntry) res.elementAt(i);
-      }
-      return reply;
+      return res.toArray(reply);
     }
     res = null;
-    // there are probable  memory leaks in the hashtable!
+    // there are probable memory leaks in the hashtable!
     return null;
   }
 
   /**
    * isDasCoordinateSystem
-   *
-   * @param string String
-   * @param dBRefEntry DBRefEntry
-   * @return boolean true if Source DBRefEntry is compatible with DAS CoordinateSystem name
+   * 
+   * @param string
+   *          String
+   * @param dBRefEntry
+   *          DBRefEntry
+   * @return boolean true if Source DBRefEntry is compatible with DAS
+   *         CoordinateSystem name
    */
-  public static Hashtable DasCoordinateSystemsLookup = null;
+
   public static boolean isDasCoordinateSystem(String string,
-                                              DBRefEntry dBRefEntry)
+          DBRefEntry dBRefEntry)
   {
-    if (DasCoordinateSystemsLookup == null)
-    { // Initialise
-      DasCoordinateSystemsLookup = new Hashtable();
-      DasCoordinateSystemsLookup.put("pdbresnum",
-                                     jalview.datamodel.DBRefSource.PDB);
-      DasCoordinateSystemsLookup.put("uniprot",
-                                     jalview.datamodel.DBRefSource.UNIPROT);
-      DasCoordinateSystemsLookup.put("EMBL",
-              jalview.datamodel.DBRefSource.EMBL);
-      //DasCoordinateSystemsLookup.put("EMBL",
-      //        jalview.datamodel.DBRefSource.EMBLCDS);
-    }
-
-    String coordsys = (String) DasCoordinateSystemsLookup.get(string.
-        toLowerCase());
-    if (coordsys != null)
+    if (string == null || dBRefEntry == null)
     {
-      return coordsys.equals(dBRefEntry.getSource());
+      return false;
     }
-    return false;
+    String coordsys = dasCoordinateSystemsLookup.get(string
+            .toLowerCase());
+    return coordsys == null ? false : coordsys.equals(dBRefEntry
+            .getSource());
   }
-  public static Hashtable CanonicalSourceNameLookup=null;
+
   /**
-   * look up source in an internal list of database reference sources
-   * and return the canonical jalview name for the source, or the original
-   * string if it has no canonical form.
+   * look up source in an internal list of database reference sources and return
+   * the canonical jalview name for the source, or the original string if it has
+   * no canonical form.
+   * 
    * @param source
-   * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*) or original source
+   * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*)
+   *         or original source
    */
   public static String getCanonicalName(String source)
   {
-    if (CanonicalSourceNameLookup==null) {
-      CanonicalSourceNameLookup = new Hashtable();
-      CanonicalSourceNameLookup.put("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT);
-      CanonicalSourceNameLookup.put("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT);
-      CanonicalSourceNameLookup.put("pdb", jalview.datamodel.DBRefSource.PDB);
-    }
-    String canonical = (String) CanonicalSourceNameLookup.get(source.
-        toLowerCase());
-    if (canonical==null)
+    if (source == null)
     {
-      return source;
+      return null;
     }
-    return canonical;
+    String canonical = canonicalSourceNameLookup.get(source
+            .toLowerCase());
+    return canonical == null ? source : canonical;
   }
+
   /**
-   * find RefEntry corresponding to a particular pattern
-   * the equals method of each entry is used, from String attributes right down to Mapping attributes.
-   * @param ref Set of references to search
-   * @param entry pattern to collect - null any entry for wildcard match
+   * Returns an array of those references that match the given entry, or null if
+   * no matches. Currently uses a comparator which matches if
+   * <ul>
+   * <li>database sources are the same</li>
+   * <li>accession ids are the same</li>
+   * <li>both have no mapping, or the mappings are the same</li>
+   * </ul>
+   * 
+   * @param ref
+   *          Set of references to search
+   * @param entry
+   *          pattern to match
    * @return
    */
   public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
   {
-    return searchRefs(ref, entry, matchDbAndIdAndEitherMapOrEquivalentMapList);
+    return searchRefs(ref, entry,
+            matchDbAndIdAndEitherMapOrEquivalentMapList);
   }
-  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry, DbRefComp comparator)
+
+  /**
+   * Returns an array of those references that match the given entry, according
+   * to the given comparator. Returns null if no matches.
+   * 
+   * @param refs
+   *          an array of database references to search
+   * @param entry
+   *          an entry to compare against
+   * @param comparator
+   * @return
+   */
+  static DBRefEntry[] searchRefs(DBRefEntry[] refs, DBRefEntry entry,
+          DbRefComp comparator)
   {
-    if (ref==null || entry==null)
+    if (refs == null || entry == null)
+    {
       return null;
-    Vector rfs = new Vector();
-    for (int i=0; i<ref.length;i++)
+    }
+    List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+    for (int i = 0; i < refs.length; i++)
     {
-      if (comparator.matches(entry, ref[i]))
+      if (comparator.matches(entry, refs[i]))
       {
-              rfs.addElement(ref[i]);
+        rfs.add(refs[i]);
       }
     }
-    // TODO Auto-generated method stub
-    if (rfs.size()>0)
-    {
-      DBRefEntry[] rf = new DBRefEntry[rfs.size()];
-      rfs.copyInto(rf);
-      return rf;
-    }
-    return null;
+    return rfs.size() == 0 ? null : rfs.toArray(new DBRefEntry[rfs.size()]);
   }
-  public interface DbRefComp {
+
+  interface DbRefComp
+  {
     public boolean matches(DBRefEntry refa, DBRefEntry refb);
   }
+
   /**
    * match on all non-null fields in refa
    */
   public static DbRefComp matchNonNullonA = new DbRefComp()
+  {
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-          public boolean matches(DBRefEntry refa, DBRefEntry refb)
+      if (refa.getSource() == null
+              || refb.getSource().equals(refa.getSource()))
+      {
+        if (refa.getVersion() == null
+                || refb.getVersion().equals(refa.getVersion()))
+        {
+          if (refa.getAccessionId() == null
+                  || refb.getAccessionId().equals(refa.getAccessionId()))
           {
-            if (refa.getSource()==null || refb.getSource().equals(refa.getSource()))
+            if (refa.getMap() == null
+                    || (refb.getMap() != null && refb.getMap().equals(
+                            refa.getMap())))
             {
-              if (refa.getVersion()==null || refb.getVersion().equals(refa.getVersion()))
-              {
-                if (refa.getAccessionId()==null || refb.getAccessionId().equals(refa.getAccessionId()))
-                {
-                  if (refa.getMap()==null || (refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
-                  {
-                    return true; 
-                  }
-                }
-              }
+              return true;
             }
-            return false;
           }
-    };
-    /**
-     * either field is null or field matches for all of source, version, accession id and map.
-     */
-    public static DbRefComp matchEitherNonNull = new DbRefComp()
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * either field is null or field matches for all of source, version, accession
+   * id and map.
+   */
+  public static DbRefComp matchEitherNonNull = new DbRefComp()
+  {
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-          public boolean matches(DBRefEntry refa, DBRefEntry refb)
+      if ((refa.getSource() == null || refb.getSource() == null)
+              || refb.getSource().equals(refa.getSource()))
+      {
+        if ((refa.getVersion() == null || refb.getVersion() == null)
+                || refb.getVersion().equals(refa.getVersion()))
+        {
+          if ((refa.getAccessionId() == null || refb.getAccessionId() == null)
+                  || refb.getAccessionId().equals(refa.getAccessionId()))
           {
-            if ((refa.getSource()==null || refb.getSource()==null) 
-                    || refb.getSource().equals(refa.getSource()))
+            if ((refa.getMap() == null || refb.getMap() == null)
+                    || (refb.getMap() != null && refb.getMap().equals(
+                            refa.getMap())))
             {
-              if ((refa.getVersion()==null || refb.getVersion()==null) 
-                      || refb.getVersion().equals(refa.getVersion()))
-              {
-                if ((refa.getAccessionId()==null || refb.getAccessionId()==null) 
-                        || refb.getAccessionId().equals(refa.getAccessionId()))
-                {
-                  if ((refa.getMap()==null || refb.getMap()==null) 
-                          || (refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
-                  {
-                    return true; 
-                  }
-                }
-              }
+              return true;
             }
-            return false;
           }
-    };
-    /**
-     * accession ID and DB must be identical. Version is ignored. Map is either not defined or is a match (or is compatible?)
-     */
-    public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp()
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * accession ID and DB must be identical. Version is ignored. Map is either
+   * not defined or is a match (or is compatible?)
+   */
+  public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp()
+  {
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-          public boolean matches(DBRefEntry refa, DBRefEntry refb)
+      if (refa.getSource() != null && refb.getSource() != null
+              && refb.getSource().equals(refa.getSource()))
+      {
+        // We dont care about version
+        // if ((refa.getVersion()==null || refb.getVersion()==null)
+        // || refb.getVersion().equals(refa.getVersion()))
+        // {
+        if (refa.getAccessionId() != null && refb.getAccessionId() != null
+                || refb.getAccessionId().equals(refa.getAccessionId()))
+        {
+          if ((refa.getMap() == null || refb.getMap() == null)
+                  || (refa.getMap() != null && refb.getMap() != null && refb
+                          .getMap().equals(refa.getMap())))
           {
-            if (refa.getSource()!=null && refb.getSource()!=null 
-                    && refb.getSource().equals(refa.getSource()))
-            {
-              // We dont care about version
-              //if ((refa.getVersion()==null || refb.getVersion()==null) 
-              //        || refb.getVersion().equals(refa.getVersion()))
-              //{
-              if (refa.getAccessionId()!=null && refb.getAccessionId()!=null 
-                      || refb.getAccessionId().equals(refa.getAccessionId()))
-                {
-                  if ((refa.getMap()==null || refb.getMap()==null) 
-                          || (refa.getMap()!=null && refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
-                  {
-                    return true; 
-                  }
-                }
-              }
-            return false;
+            return true;
           }
-    };
-    /**
-     * accession ID and DB must be identical. Version is ignored. 
-     * No map on either or map but no maplist on either or maplist of map on a is the complement of maplist of map on b.
-     */
-    public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp()
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * accession ID and DB must be identical. Version is ignored. No map on either
+   * or map but no maplist on either or maplist of map on a is the complement of
+   * maplist of map on b.
+   */
+  public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp()
+  {
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-          public boolean matches(DBRefEntry refa, DBRefEntry refb)
+      if (refa.getSource() != null && refb.getSource() != null
+              && refb.getSource().equals(refa.getSource()))
+      {
+        // We dont care about version
+        // if ((refa.getVersion()==null || refb.getVersion()==null)
+        // || refb.getVersion().equals(refa.getVersion()))
+        // {
+        if (refa.getAccessionId() != null && refb.getAccessionId() != null
+                || refb.getAccessionId().equals(refa.getAccessionId()))
+        {
+          if ((refa.getMap() == null && refb.getMap() == null)
+                  || (refa.getMap() != null && refb.getMap() != null))
           {
-            if (refa.getSource()!=null && refb.getSource()!=null 
-                    && refb.getSource().equals(refa.getSource()))
+            if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
+                    || (refb.getMap().getMap() != null
+                            && refa.getMap().getMap() != null && refb
+                            .getMap().getMap().getInverse()
+                            .equals(refa.getMap().getMap())))
             {
-              // We dont care about version
-              //if ((refa.getVersion()==null || refb.getVersion()==null) 
-              //        || refb.getVersion().equals(refa.getVersion()))
-              //{
-              if (refa.getAccessionId()!=null && refb.getAccessionId()!=null 
-                      || refb.getAccessionId().equals(refa.getAccessionId()))
-                {
-                  if ((refa.getMap()==null && refb.getMap()==null) 
-                          || (refa.getMap()!=null && refb.getMap()!=null))
-                    if ((refb.getMap().getMap()==null && refa.getMap().getMap()==null)
-                            || (refb.getMap().getMap()!=null && refa.getMap().getMap()!=null
-                            && refb.getMap().getMap().getInverse().equals(refa.getMap().getMap())))
-                  {
-                    return true; 
-                  }
-                }
-              }
-            return false;
+              return true;
+            }
           }
-    };
-    /**
-     * accession ID and DB must be identical. Version is ignored. 
-     * No map on both or or map but no maplist on either or maplist of map on a is equivalent to the maplist of map on b.
-     */
-    public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp()
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * accession ID and DB must be identical. Version is ignored. No map on both
+   * or or map but no maplist on either or maplist of map on a is equivalent to
+   * the maplist of map on b.
+   */
+  public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp()
+  {
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-          public boolean matches(DBRefEntry refa, DBRefEntry refb)
+      if (refa.getSource() != null && refb.getSource() != null
+              && refb.getSource().equals(refa.getSource()))
+      {
+        // We dont care about version
+        // if ((refa.getVersion()==null || refb.getVersion()==null)
+        // || refb.getVersion().equals(refa.getVersion()))
+        // {
+        if (refa.getAccessionId() != null && refb.getAccessionId() != null
+                || refb.getAccessionId().equals(refa.getAccessionId()))
+        {
+          if (refa.getMap() == null && refb.getMap() == null)
           {
-            if (refa.getSource()!=null && refb.getSource()!=null 
-                    && refb.getSource().equals(refa.getSource()))
-            {
-              // We dont care about version
-              //if ((refa.getVersion()==null || refb.getVersion()==null) 
-              //        || refb.getVersion().equals(refa.getVersion()))
-              //{
-              if (refa.getAccessionId()!=null && refb.getAccessionId()!=null 
-                      || refb.getAccessionId().equals(refa.getAccessionId()))
-                {
-                  if (refa.getMap()==null && refb.getMap()==null)
-                  {
-                    return true;
-                  }
-                  if (refa.getMap()!=null && refb.getMap()!=null
-                          && ((refb.getMap().getMap()==null && refa.getMap().getMap()==null)
-                            || (refb.getMap().getMap()!=null && refa.getMap().getMap()!=null
-                            && refb.getMap().getMap().equals(refa.getMap().getMap()))))
-                  {
-                    return true; 
-                  }
-                }
-              }
-            return false;
+            return true;
+          }
+          if (refa.getMap() != null
+                  && refb.getMap() != null
+                  && ((refb.getMap().getMap() == null && refa.getMap()
+                          .getMap() == null) || (refb.getMap().getMap() != null
+                          && refa.getMap().getMap() != null && refb
+                          .getMap().getMap().equals(refa.getMap().getMap()))))
+          {
+            return true;
           }
-    };
-    /**
-     * accession ID and DB must be identical. Version is ignored. 
-     * No map on either or map but no maplist on either or maplist of map on a is equivalent to the maplist of map on b.
-     */
-    public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * accession ID and DB must be identical. Version is ignored. No map on either
+   * or map but no maplist on either or maplist of map on a is equivalent to the
+   * maplist of map on b.
+   */
+  public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
+  {
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-          public boolean matches(DBRefEntry refa, DBRefEntry refb)
+      // System.err.println("Comparing A: "+refa.getSrcAccString()+(refa.hasMap()?" has map.":"."));
+      // System.err.println("Comparing B: "+refb.getSrcAccString()+(refb.hasMap()?" has map.":"."));
+      if (refa.getSource() != null && refb.getSource() != null
+              && refb.getSource().equals(refa.getSource()))
+      {
+        // We dont care about version
+        // if ((refa.getVersion()==null || refb.getVersion()==null)
+        // || refb.getVersion().equals(refa.getVersion()))
+        // {
+        if (refa.getAccessionId() != null && refb.getAccessionId() != null
+                && refb.getAccessionId().equals(refa.getAccessionId()))
+        {
+          if (refa.getMap() == null || refb.getMap() == null)
           {
-            if (refa.getSource()!=null && refb.getSource()!=null 
-                    && refb.getSource().equals(refa.getSource()))
-            {
-              // We dont care about version
-              //if ((refa.getVersion()==null || refb.getVersion()==null) 
-              //        || refb.getVersion().equals(refa.getVersion()))
-              //{
-              if (refa.getAccessionId()!=null && refb.getAccessionId()!=null 
-                      && refb.getAccessionId().equals(refa.getAccessionId()))
-                {
-                  if (refa.getMap()==null || refb.getMap()==null)
-                  {
-                    return true;
-                  }
-                  if ((refa.getMap()!=null && refb.getMap()!=null)
-                          && (refb.getMap().getMap()==null && refa.getMap().getMap()==null)
-                            || (refb.getMap().getMap()!=null && refa.getMap().getMap()!=null
-                            && refb.getMap().getMap().equals(refa.getMap().getMap())))
-                  {
-                    return true; 
-                  }
-                }
-              }
-            return false;
+            return true;
+          }
+          if ((refa.getMap() != null && refb.getMap() != null)
+                  && (refb.getMap().getMap() == null && refa.getMap()
+                          .getMap() == null)
+                  || (refb.getMap().getMap() != null
+                          && refa.getMap().getMap() != null && (refb
+                          .getMap().getMap().equals(refa.getMap().getMap()))))
+          { // getMap().getMap().containsEither(false,refa.getMap().getMap())
+            return true;
           }
-    };
-    /**
-     * used by file parsers to generate DBRefs from annotation within file (eg stockholm)
-     * @param dbname
-     * @param version
-     * @param acn
-     * @param seq where to anotate 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)
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * 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)
     {
-      DBRefEntry ref = null;
-      if (dbname!=null)
+      String locsrc = DBRefUtils.getCanonicalName(dbname);
+      if (locsrc.equals(DBRefSource.PDB))
       {
-        String locsrc = jalview.util.DBRefUtils
-        .getCanonicalName(dbname);
-        if (locsrc.equals(jalview.datamodel.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()))
         {
-          // check for chaincode and mapping
-          // PFAM style stockhom PDB citation
-          com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex("([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;([0-9]+)-([0-9]+)");
-          if (r.search(acn.trim()))
+          String pdbid = r.stringMatched(1);
+          String chaincode = r.stringMatched(2);
+          if (chaincode==null)
           {
-            String pdbid = r.stringMatched(1);
-            String chaincode = r.stringMatched(2);
-            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);
-            seq.addPDBId(pdbr);
+            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.setProperty(new Hashtable());
+          pdbr.setChainCode(chaincode);
+          // pdbr.getProperty().put("CHAIN", chaincode);
+          seq.addPDBId(pdbr);
         } else {
-          // default:
-          ref = new DBRefEntry(locsrc, version, acn);
+          System.err.println("Malformed PDB DR line:"+acn);
         }
       }
-      if (ref!=null)
+      else
       {
-        seq.addDBRef(ref);
+        // default:
+        ref = new DBRefEntry(locsrc, version, acn);
       }
-      return ref;
     }
-        
-          
+    if (ref != null)
+    {
+      seq.addDBRef(ref);
+    }
+    return ref;
+  }
+
 }