X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=d7d5835a543ead3ed23796749d659a050b490188;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=2f844dafb121c96fa0fff5ef17db88ef1dea5de7;hpb=91416b3038a6f3fc655791512770da07cb6cb251;p=jalview.git

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 2f844da..d7d5835 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,3 +1,20 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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.
+ * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package jalview.util;
 
 import java.util.*;
@@ -6,60 +23,427 @@ import jalview.datamodel.*;
 
 public class DBRefUtils
 {
-    /**
-     * 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
-     * @return Vector
-     */
-    public static Vector selectRefs(java.util.Vector dbrefs, String[] sources) {
-      if (dbrefs==null)
-        return null;
-      if (sources==null)
-        return dbrefs;
-      Hashtable srcs = new Hashtable();
-      Vector res=new Vector();
-      for (int i=0; i<sources.length; i++)
-        srcs.put(new String(sources[i]), new Integer(i));
-      for (int i=0, j=dbrefs.size(); i<j; i++)
-        if (dbrefs.get(i) instanceof jalview.datamodel.DBRefEntry) {
-          jalview.datamodel.DBRefEntry entry = (jalview.datamodel.DBRefEntry) dbrefs.get(i);
-          if (srcs.containsKey(entry.getSource()))
-            res.add(entry);
-        }
-      if (res.size()>0)
-        return res;
-      res = null;
-      // there are probable  memory leaks in the hashtable!
+  /**
+   * 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
+   * @return Vector
+   */
+  public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs,
+          String[] sources)
+  {
+    if (dbrefs == null)
+    {
       return null;
     }
+    if (sources == null)
+    {
+      return dbrefs;
+    }
+    Hashtable srcs = new Hashtable();
+    Vector res = new Vector();
+
+    for (int i = 0; i < sources.length; i++)
+    {
+      srcs.put(new String(sources[i]), new Integer(i));
+    }
+    for (int i = 0, j = dbrefs.length; i < j; i++)
+    {
+      if (srcs.containsKey(dbrefs[i].getSource()))
+      {
+        res.addElement(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;
+    }
+    res = null;
+    // 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
+    if (DasCoordinateSystemsLookup == null)
+    {
+      // TODO: Make a DasCoordinateSystemsLookup properties resource
+      // Initialise
       DasCoordinateSystemsLookup = new Hashtable();
       DasCoordinateSystemsLookup.put("pdbresnum",
-                                     jalview.datamodel.DBRefSource.PDB);
+              jalview.datamodel.DBRefSource.PDB);
       DasCoordinateSystemsLookup.put("uniprot",
-                                     jalview.datamodel.DBRefSource.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)
+    String coordsys = (String) DasCoordinateSystemsLookup.get(string
+            .toLowerCase());
+    if (coordsys != null)
+    {
       return coordsys.equals(dBRefEntry.getSource());
+    }
     return false;
   }
+
+  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.
+   * 
+   * @param 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)
+    {
+      return source;
+    }
+    return 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
+   * @return
+   */
+  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
+  {
+    return searchRefs(ref, entry,
+            matchDbAndIdAndEitherMapOrEquivalentMapList);
+  }
+
+  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry,
+          DbRefComp comparator)
+  {
+    if (ref == null || entry == null)
+      return null;
+    Vector rfs = new Vector();
+    for (int i = 0; i < ref.length; i++)
+    {
+      if (comparator.matches(entry, ref[i]))
+      {
+        rfs.addElement(ref[i]);
+      }
+    }
+    // TODO Auto-generated method stub
+    if (rfs.size() > 0)
+    {
+      DBRefEntry[] rf = new DBRefEntry[rfs.size()];
+      rfs.copyInto(rf);
+      return rf;
+    }
+    return null;
+  }
+
+  public 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)
+    {
+      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.getMap() == null
+                    || (refb.getMap() != null && refb.getMap().equals(
+                            refa.getMap())))
+            {
+              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()
+  {
+    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.getMap() == null || refb.getMap() == null)
+                    || (refb.getMap() != null && refb.getMap().equals(
+                            refa.getMap())))
+            {
+              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()
+  {
+    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())))
+          {
+            return true;
+          }
+        }
+      }
+      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)
+    {
+      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 ((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;
+    }
+  };
+
+  /**
+   * 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)
+    {
+      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;
+    }
+  };
+
+  /**
+   * 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)
+    {
+      // 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)
+          {
+            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;
+          }
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * 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)
+  {
+    DBRefEntry ref = null;
+    if (dbname != null)
+    {
+      String locsrc = jalview.util.DBRefUtils.getCanonicalName(dbname);
+      if (locsrc.equals(jalview.datamodel.DBRefSource.PDB))
+      {
+        // 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);
+          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);
+        }
+      }
+      else
+      {
+        // default:
+        ref = new DBRefEntry(locsrc, version, acn);
+      }
+    }
+    if (ref != null)
+    {
+      seq.addDBRef(ref);
+    }
+    return ref;
+  }
+
 }