/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* 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.
-*
-* 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
-*/
-
+ * 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.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.List;
+import java.util.Vector;
+
/**
- * <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
{
+ private HashMap<SeqIdName, SequenceI> names;
- private class SeqIdName
+ public SequenceIdMatcher(List<SequenceI> seqs)
{
- String id;
-
- SeqIdName(String s)
- {
- id = new String(s);
- }
-
- public int hashCode()
- {
- return (id.substring(0, 4).hashCode());
- }
+ names = new HashMap<SeqIdName, SequenceI>();
+ addAll(seqs);
+ }
- public boolean equals(Object s)
+ /**
+ * add more sequences to this matcher - also used by the constructor
+ *
+ * @param seqs
+ */
+ public void addAll(List<SequenceI> seqs)
+ {
+ for (SequenceI seq : seqs)
{
- if (s instanceof SeqIdName)
+ // 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)
{
- return this.equals( (SeqIdName) s);
+ dbseq = dbseq.getDatasetSequence();
}
- else
+ // add in any interesting identifiers
+ if (dbseq.getDBRef() != null)
{
- if (s instanceof String)
+ DBRefEntry dbr[] = dbseq.getDBRef();
+ SeqIdName sid = null;
+ for (int r = 0; r < dbr.length; r++)
{
- return this.equals( (String) s);
+ sid = new SeqIdName(dbr[r].getAccessionId());
+ if (!names.containsKey(sid))
+ {
+ names.put(sid, seq);
+ }
}
}
- return false;
}
+ }
- public boolean equals(SeqIdName s)
+ /**
+ * 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)
{
- if (id.startsWith(s.id) || s.id.startsWith(id))
- {
- return true;
- }
- return false;
+ return null;
}
-
- public boolean equals(String s)
+ 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)
{
- if (id.startsWith(s) || s.startsWith(id))
+ // 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)
{
- return true;
+ best.clear();
+ match = cand;
+ matchlen = candlen;
+ best.add(match);
+ }
+ if (q == w && candlen == matchlen)
+ {
+ // record any ties
+ best.add(cand);
}
- return false;
}
- }
-
- private Hashtable names;
-
- public SequenceIdMatcher(SequenceI[] seqs)
- {
- names = new Hashtable();
- for (int i = 0; i < seqs.length; i++)
+ if (best.size() == 0)
{
- names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
+ 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);
}
- SequenceI findIdMatch(String seqnam)
+ public SequenceI findIdMatch(String seqnam)
{
SeqIdName nam = new SeqIdName(seqnam);
- if (names.containsKey(nam))
+ 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 (SequenceI) names.get(nam);
+ 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 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.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;
+ }
+
+ private 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);
+ }
+ else
+ {
+ if (s instanceof String)
+ {
+ return this.equals((String) s);
+ }
+ }
+
+ return 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)
+ */
+ private String WORD_SEP = "~. |#\\/<>!\"" + ((char) 0x00A4)
+ + "$%^*)}[@',?_";
+
+ /**
+ * matches if one ID properly contains another at a whitespace boundary.
+ * TODO: (JBPNote) These are not efficient. should use char[] for speed
+ * todo: (JBPNote) Set separator characters appropriately
+ *
+ * @param s
+ * SeqIdName
+ * @return boolean
+ */
+ public boolean equals(SeqIdName s)
+ {
+ // TODO: JAL-732 patch for cases when name includes a list of IDs, and the
+ // match contains one ID flanked
+ if (id.length() > s.id.length())
+ {
+ return id.startsWith(s.id) ? (WORD_SEP.indexOf(id.charAt(s.id
+ .length())) > -1) : false;
+ }
+ else
+ {
+ return s.id.startsWith(id) ? (s.id.equals(id) ? true : (WORD_SEP
+ .indexOf(s.id.charAt(id.length())) > -1)) : false;
+ }
+ }
+
+ public boolean equals(String s)
+ {
+ if (id.length() > s.length())
+ {
+ return id.startsWith(s) ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
+ : false;
+ }
+ else
+ {
+ return s.startsWith(id) ? (s.equals(id) ? true : (WORD_SEP
+ .indexOf(s.charAt(id.length())) > -1)) : false;
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff