+ * 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
+{
+ private HashMap<SeqIdName, SequenceI> names;
+
+ public SequenceIdMatcher(List<SequenceI> seqs)
+ {
+ names = new HashMap<SeqIdName, 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)
+ {
+ // TODO: deal with ID collisions - SequenceI should be appended to list
+ // associated with this key.
+ names.put(new SeqIdName(seq.getDisplayId(true)), seq);
+ SequenceI dbseq = seq;
+ 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++)
+ {
+ sid = new SeqIdName(dbr[r].getAccessionId());
+ if (!names.containsKey(sid))
+ {
+ names.put(sid, seq);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * convenience method to make a matcher from concrete array
+ *
+ * @param sequences
+ */
+ public SequenceIdMatcher(SequenceI[] sequences)
+ {
+ this(Arrays.asList(sequences));
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * 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)
+ {
+ ArrayList<SequenceI> best = new ArrayList<SequenceI>();
+ if (candName == null || matches == null || matches.size() == 0)
+ {
+ return null;
+ }
+ SequenceI match = matches.remove(0);
+ best.add(match);
+ names.put(new SeqIdName(match.getName()), 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);
+ names.put(new SeqIdName(cand.getName()), cand);
+ int q, w, candlen = cand.getName().length();
+ // keep the one with an id 'closer' to the given seqnam string
+ if ((q = Math.abs(matchlen - namlen)) > (w = Math.abs(candlen
+ - namlen))
+ && candlen > matchlen)
+ {
+ best.clear();
+ match = cand;
+ matchlen = candlen;
+ best.add(match);
+ }
+ if (q == w && candlen == matchlen)
+ {
+ // record any ties
+ best.add(cand);
+ }
+ }
+ if (best.size() == 0)
+ {
+ return null;
+ }
+ ;
+ return best;
+ }
+
+ /**
+ * 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());
+ return findIdMatch(nam);
+ }
+
+ public SequenceI findIdMatch(String seqnam)
+ {
+ SeqIdName nam = new SeqIdName(seqnam);
+ return findIdMatch(nam);
+ }
+
+ /**
+ * 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);
+ List<SequenceI> m = findAllIdMatches(nam);
+ if (m != null)
+ {
+ return m.toArray(new SequenceI[m.size()]);
+ }
+ return null;
+ }
+
+ /**
+ * 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[]
+ */
+ public SequenceI[] findIdMatch(SequenceI[] seqs)
+ {
+ 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] = findIdMatch(nam);
+ }
+ else
+ {
+ namedseqs[i] = null;
+ }
+ } while (++i < seqs.length);
+ }
+
+ return namedseqs;
+ }
+
+ /**
+ * core findIdMatch search method
+ *
+ * @param nam
+ * SeqIdName
+ * @return SequenceI
+ */
+ private SequenceI findIdMatch(
+ jalview.analysis.SequenceIdMatcher.SeqIdName nam)
+ {
+ Vector matches = new Vector();
+ while (names.containsKey(nam))
+ {
+ matches.addElement(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.SequenceIdMatcher.SeqIdName nam)
+ {
+ ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
+ while (names.containsKey(nam))
+ {
+ matches.add(names.remove(nam));
+ }
+ List<SequenceI> r = pickbestMatches(nam, matches);
+ return r;
+ }
+
+ class SeqIdName
+ {
+ String id;
+
+ SeqIdName(String s)
+ {
+ if (s != null)
+ {
+ id = new String(s);
+ }
+ else
+ {
+ id = "";
+ }
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id
+ .hashCode());
+ }
+
+ @Override
+ public boolean equals(Object s)
+ {
+ if (s == null)
+ {
+ return false;
+ }
+ if (s instanceof SeqIdName)
+ {
+ return this.equals(((SeqIdName) s).id);
+ }
+ else
+ {
+ if (s instanceof String)
+ {
+ return this.equals((String) s);
+ }
+ }
+
+ return false;
+ }
+