+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.util;
-import java.util.Vector;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+
+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
{
- /**
- * Utilities for handling DBRef objects and their collections.
- */
- 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!
+ 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
+ * @return Vector
+ */
+ public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs,
+ String[] sources)
+ {
+ if (dbrefs == null)
+ {
+ return null;
+ }
+ if (sources == null)
+ {
+ return dbrefs;
+ }
+ Map<String, Integer> srcs = new HashMap<String, Integer>();
+ ArrayList<DBRefEntry> res = new ArrayList<DBRefEntry>();
+
+ 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.add(dbrefs[i]);
+ }
+ }
+
+ if (res.size() > 0)
+ {
+ DBRefEntry[] reply = new DBRefEntry[res.size()];
+ return res.toArray(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
+ */
+
+ public static boolean isDasCoordinateSystem(String string,
+ DBRefEntry dBRefEntry)
+ {
+ if (string == null || dBRefEntry == null)
+ {
+ return false;
+ }
+ String coordsys = dasCoordinateSystemsLookup.get(string.toLowerCase());
+ return coordsys == null ? false : coordsys.equals(dBRefEntry
+ .getSource());
+ }
+
+ /**
+ * 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 (source == null)
+ {
return null;
}
+ String canonical = canonicalSourceNameLookup.get(source.toLowerCase());
+ return canonical == null ? source : canonical;
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * 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 (refs == null || entry == null)
+ {
+ return null;
+ }
+ List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+ for (int i = 0; i < refs.length; i++)
+ {
+ if (comparator.matches(entry, refs[i]))
+ {
+ rfs.add(refs[i]);
+ }
+ }
+ return rfs.size() == 0 ? null : rfs.toArray(new DBRefEntry[rfs.size()]);
}
+
+ 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;
+ }
+ };
+
+ /**
+ * 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.setProperty(new Hashtable());
+ pdbr.setChainCode(chaincode);
+ // pdbr.getProperty().put("CHAIN", 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;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff