+/*
+ * 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.
+ *
+ * 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.analysis;
-import java.util.Vector;
-import java.util.Hashtable;
+import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
/**
- * <p>Title: </p>
- * SequenceIdMatcher
- * <p>Description: </p>
- * Routine which does approximate Sequence Id resolution by name using string containment rather than equivalence
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
+ * Routines for approximate Sequence Id resolution by name using string
+ * containment (on word boundaries) rather than equivalence. It also attempts to
+ * resolve ties where no exact match is available by picking the the id closest
+ * to the query.
*/
public class SequenceIdMatcher
{
+ /**
+ * weak hash for each sequence
+ */
+ private HashMap<SeqIdName, Set<SequenceI>> names;
- private class SeqIdName
+ // /**
+ // * cache of values removed for each query string.
+ // */
+ // private HashMap<String, List<SequenceI>> resolved;
+
+ /**
+ * do we index sequences on all 'words' in ID string ?
+ */
+ private boolean wordBased = false;
+
+ /**
+ * Characters that define the end of a unique sequence ID at the beginning of
+ * an arbitrary ID string JBPNote: This is a heuristic that will fail for
+ * arbritrarily extended sequence id's (like portions of an aligned set of
+ * repeats from one sequence)
+ */
+ static String WORD_SEP = "~. |#\\/<>!\"" + ((char) 0x00A4)
+ + "$%^*)}[@',?_";
+
+ /**
+ * @return true if matcher is word-based (ie string key matches one of the
+ * words within the body of one or more sequence IDs)
+ */
+ public boolean isWordBased()
{
- String id;
+ return wordBased;
+ }
+
+ /**
+ * Construct a standard (non-word based) matcher. To configure word based
+ * matching, use the fully qualified constructor
+ *
+ * @param seqs
+ */
+ public SequenceIdMatcher(List<SequenceI> seqs)
+ {
+ this(false, seqs);
+ }
- SeqIdName(String s)
+ /**
+ * construct a new matcher for a set of sequences, configured as required.
+ * Note: enabling word based matching
+ *
+ * @param wordBasedMatch
+ * - when true, "myseq" matches "X|myseq" and "myseq"
+ * @param seqs
+ */
+ public SequenceIdMatcher(boolean wordBasedMatch, List<SequenceI> seqs)
+ {
+ wordBased = wordBasedMatch;
+ names = new HashMap<SeqIdName, Set<SequenceI>>();
+ addAll(seqs);
+ }
+
+ /**
+ * add more sequences to this matcher - also used by the constructor
+ *
+ * @param seqs
+ */
+ public void addAll(List<SequenceI> seqs)
+ {
+ for (SequenceI seq : seqs)
{
- id = new String(s);
+ addSeq(seq);
}
+ }
- public int hashCode()
+ private void addSeqIdName(SeqIdName idname, SequenceI seq)
+ {
+ Set<SequenceI> seqset = names.get(idname);
+ if (seqset == null)
{
- return (id.substring(0, 4).hashCode());
+ seqset = new HashSet<SequenceI>();
+ names.put(idname, seqset);
}
+ seqset.add(seq);
+ }
- public boolean equals(Object s)
+ public void addSeq(SequenceI seq)
+ {
+ // TODO: deal with ID collisions - SequenceI should be appended to list
+ // associated with this key.
+ addSeqIdName(new SeqIdName(seq.getDisplayId(true)), seq);
+ if (wordBased)
{
- if (s instanceof SeqIdName)
+ for (SeqIdName key : getWordsFor(seq))
{
- return this.equals( (SeqIdName) s);
+ addSeqIdName(key, seq);
}
- else
+ }
+ SequenceI dbseq = seq;
+ // TODO add test for database xref resolution
+ while (dbseq.getDatasetSequence() != null)
+ {
+ dbseq = dbseq.getDatasetSequence();
+ }
+ // add in any interesting identifiers
+ if (dbseq.getDBRefs() != null)
+ {
+ DBRefEntry dbr[] = dbseq.getDBRefs();
+ SeqIdName sid = null;
+ for (int r = 0; r < dbr.length; r++)
{
- if (s instanceof String)
+ sid = new SeqIdName(dbr[r].getAccessionId());
+ if (!names.containsKey(sid))
{
- return this.equals( (String) s);
+ addSeqIdName(sid, seq);
}
}
- return false;
}
+ }
- public boolean equals(SeqIdName s)
+ /**
+ * generate word based keys for the given sequence
+ *
+ * @param seq
+ * @return list of split keys
+ */
+ public static List<SeqIdName> getWordsFor(SequenceI seq)
+ {
+ ArrayList<SeqIdName> keys = new ArrayList<SeqIdName>();
+ String name = seq.getName(), limits = "/" + seq.getStart() + "-"
+ + seq.getEnd();
+ int namel = name.length();
+ char[] sep = new char[WORD_SEP.length()];
+ // find only the separators present in the ID.
+ for (int i = 0; i < sep.length; i++)
{
- if (id.startsWith(s.id) || s.id.startsWith(id))
+ sep[i] = WORD_SEP.charAt(i);
+ if (seq.getName().indexOf("" + sep[i]) == -1)
{
- return true;
+ sep[i] = 0;
}
- return false;
}
-
- public boolean equals(String s)
+ ;
+ // make words
+ for (int i = 0; i < sep.length; i++)
{
- if (id.startsWith(s) || s.startsWith(id))
+ if (sep[i] > 0)
{
- return true;
+ int p = 0, m = -1;
+ while ((m = name.indexOf(sep[i], p)) > p)
+ {
+
+ if (m > 0 && m - p > 5)
+ {
+ // split to end of word m with this delimiter
+ keys.add(new SeqIdName(name.substring(p, m - 1) + limits));
+ }
+ if (namel - m > 5)
+ {
+ // index word after this delimiter m
+ keys.add(new SeqIdName(name.substring(m + 1) + limits));
+ }
+ p = m + 1;
+ }
+ if (namel - p > 4)
+ {
+ // index word after this delimiter m
+ keys.add(new SeqIdName(name.substring(p) + limits));
+ }
}
- return false;
}
+ return keys;
+ }
+
+ /**
+ * convenience method to make a matcher from concrete array Note: in order to
+ * support word based matching, use the fully qualified constructor
+ *
+ * @param sequences
+ */
+ public SequenceIdMatcher(SequenceI[] sequences)
+ {
+ this(Arrays.asList(sequences));
}
- private Hashtable names;
+ /**
+ * returns the closest SequenceI in matches to SeqIdName and returns all the
+ * matches to the names hash.
+ *
+ * @param candName
+ * SeqIdName
+ * @param matches
+ * List of SequenceI objects
+ * @return SequenceI closest SequenceI to SeqIdName
+ */
+ private SequenceI pickbestMatch(SeqIdName candName,
+ List<SequenceI> matches)
+ {
+ List<SequenceI> st = pickbestMatches(candName, matches);
+ return st == null || st.size() == 0 ? null : st.get(0);
+ }
- public SequenceIdMatcher(SequenceI[] seqs)
+ /**
+ * returns the closest SequenceI in matches to SeqIdName and returns all the
+ * matches to the names hash.
+ *
+ * @param candName
+ * SeqIdName
+ * @param matches
+ * Vector of SequenceI objects
+ * @return Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[]
+ * ties }
+ */
+ private List<SequenceI> pickbestMatches(SeqIdName candName,
+ List<SequenceI> matches)
{
- names = new Hashtable();
- for (int i = 0; i < seqs.length; i++)
+ ArrayList<SequenceI> best = new ArrayList<SequenceI>();
+ if (candName == null || matches == null || matches.size() == 0)
{
- names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
+ return null;
}
+ SequenceI match = matches.remove(0);
+ best.add(match);
+ addSeq(match);
+ int matchlen = match.getName().length();
+ int namlen = candName.id.length();
+ while (matches.size() > 0)
+ {
+ // look through for a better one.
+ SequenceI cand = matches.remove(0);
+ addSeq(cand);
+ int q, w, candlen = cand.getName().length();
+ // keep the one with an id 'closer' to the given seqnam string
+ boolean is_closer = ((q = Math.abs(matchlen - namlen)) > (w = Math
+ .abs(candlen - namlen)) && candlen > matchlen);
+ // if not closer, then check if current best is actually identical in case
+ // as
+ // well
+ if (is_closer
+ || (candName.equalsCase(cand.getName()) && !candName
+ .equalsCase(best.get(0).getName())))
+ {
+ best.clear();
+ match = cand;
+ matchlen = candlen;
+ best.add(match);
+ }
+ else
+ {
+ if (q == w && candlen == matchlen)
+ {
+ // equivalently good, and matches with case as well. so
+ // record any ties
+ best.add(cand);
+ }
+ }
+ }
+ if (best.size() == 0)
+ {
+ return null;
+ }
+ ;
+ return best;
}
- SequenceI findIdMatch(SequenceI seq)
+ /**
+ * get SequenceI with closest SequenceI.getName() to seq.getName()
+ *
+ * @param seq
+ * SequenceI
+ * @return SequenceI
+ */
+ public SequenceI findIdMatch(SequenceI seq)
{
SeqIdName nam = new SeqIdName(seq.getName());
- if (names.containsKey(nam))
- {
- return (SequenceI) names.get(nam);
- }
- return null;
+ return findIdMatch(nam);
+ }
+
+ public SequenceI findIdMatch(String seqnam)
+ {
+ SeqIdName nam = new SeqIdName(seqnam);
+ return findIdMatch(nam);
}
- SequenceI findIdMatch(String seqnam)
+ /**
+ * Find all matches for a given sequence name.
+ *
+ * @param seqnam
+ * string to query Matcher with.
+ * @return a new array or (possibly) null
+ */
+ public SequenceI[] findAllIdMatches(String seqnam)
{
+
SeqIdName nam = new SeqIdName(seqnam);
- if (names.containsKey(nam))
+ List<SequenceI> m = findAllIdMatches(nam);
+ if (m != null)
{
- return (SequenceI) names.get(nam);
+ return m.toArray(new SequenceI[m.size()]);
}
return null;
}
/**
- * @method findIdMatch
- *
- * Return pointers to sequences (or sequence object containers)
- * which have same Id as a given set of different sequence objects
- *
- * @param seqs SequenceI[]
+ * findIdMatch
+ *
+ * Return pointers to sequences (or sequence object containers) which have
+ * same Id as a given set of different sequence objects
+ *
+ * @param seqs
+ * SequenceI[]
* @return SequenceI[]
*/
-
- SequenceI[] findIdMatch(SequenceI[] seqs)
+ public SequenceI[] findIdMatch(SequenceI[] seqs)
{
- SequenceI[] namedseqs = new SequenceI[seqs.length];
-
+ SequenceI[] namedseqs = null;
int i = 0;
SeqIdName nam;
+
if (seqs.length > 0)
{
+ namedseqs = new SequenceI[seqs.length];
do
{
nam = new SeqIdName(seqs[i].getName());
+
if (names.containsKey(nam))
{
- namedseqs[i] = (SequenceI) names.get(nam);
+ namedseqs[i] = findIdMatch(nam);
}
else
{
namedseqs[i] = null;
}
- }
- while (i++ < seqs.length);
+ } while (++i < seqs.length);
}
+
return namedseqs;
}
+ /**
+ * core findIdMatch search method
+ *
+ * @param nam
+ * SeqIdName
+ * @return SequenceI
+ */
+ private SequenceI findIdMatch(
+ jalview.analysis.SeqIdName nam)
+ {
+ ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
+ while (names.containsKey(nam))
+ {
+ matches.addAll(names.remove(nam));
+ }
+ return pickbestMatch(nam, matches);
+ }
+
+ /**
+ * core findIdMatch search method for finding all equivalent matches
+ *
+ * @param nam
+ * SeqIdName
+ * @return SequenceI[]
+ */
+ private List<SequenceI> findAllIdMatches(
+ jalview.analysis.SeqIdName nam)
+ {
+ ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
+ while (names.containsKey(nam))
+ {
+ matches.addAll(names.remove(nam));
+ }
+ List<SequenceI> r = pickbestMatches(nam, matches);
+ return r;
+ }
}
git://source.jalview.org / jalview.git / blobdiff