Title:
- * SequenceIdMatcher - *Description:
- * Routine which does approximate Sequence Id resolution by name using - * string containment (on word boundaries) rather than equivalence - *Copyright: Copyright (c) 2004
- * - *Company: Dundee University
- * - * @author not attributable - * @version 1.0 - */ -public class SequenceIdMatcher -{ - private Hashtable names; - - public SequenceIdMatcher(SequenceI[] seqs) - { - names = new Hashtable(); - for (int i = 0; i < seqs.length; i++) - { - names.put(new SeqIdName(seqs[i].getName()), seqs[i]); - } - } - - SequenceI findIdMatch(SequenceI seq) - { - SeqIdName nam = new SeqIdName(seq.getName()); - - if (names.containsKey(nam)) - { - return (SequenceI) names.get(nam); - } - - return null; - } - - SequenceI findIdMatch(String seqnam) - { - SeqIdName nam = new SeqIdName(seqnam); - - if (names.containsKey(nam)) - { - return (SequenceI) names.get(nam); - } - - 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[] - */ - 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] = (SequenceI) names.get(nam); - } - else - { - namedseqs[i] = null; - } - } - while (++i < seqs.length); - } - - return namedseqs; - } - - private class SeqIdName - { - String id; - - SeqIdName(String s) - { - id = new String(s); - } - - public int hashCode() - { - return (id.substring(0, 4).hashCode()); - } - - public boolean equals(Object s) - { - if (s instanceof SeqIdName) - { - return this.equals( (SeqIdName) s); - } - else - { - if (s instanceof String) - { - return this.equals( (String) s); - } - } - - return false; - } - - /** - * matches if one ID properly contains another at a whitespace boundary. - * TODO: (JBPNote) These are not efficient. should use char[] for speed - * @param s SeqIdName - * @return boolean - */ - public boolean equals(SeqIdName s) - { - if (id.length()>s.id.length()) { - return id.startsWith(s.id) ? - (id.equals(s.id) ? true : id.startsWith(s.id+" ")) - : false; - } else - return s.id.startsWith(id) ? - (s.id.equals(id) ? true : s.id.startsWith(id+" ")) - : false; - } - - public boolean equals(String s) - { - if (id.length()>s.length()) { - return id.startsWith(s) ? - (id.equals(s) ? true : id.startsWith(s+" ")) - : false; - } else - return s.startsWith(id) ? - (s.equals(id) ? true : s.startsWith(id+" ")) - : false; - } - } -} +/* + * 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+ * Title: + *
+ * SequenceIdMatcher + *+ * Description: + *
+ * Routine which does 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. + *+ * Copyright: Copyright (c) 2004 + *
+ * + *+ * Company: Dundee University + *
+ * + * @author not attributable + * @version 1.0 + */ +public class SequenceIdMatcher +{ + private Hashtable names; + + public SequenceIdMatcher(SequenceI[] seqs) + { + names = new Hashtable(); + for (int i = 0; i < seqs.length; i++) + { + names.put(new SeqIdName(seqs[i].getName()), seqs[i]); + // add in any interesting identifiers + if (seqs[i].getDBRef() != null) + { + DBRefEntry dbr[] = seqs[i].getDBRef(); + SeqIdName sid = null; + for (int r = 0; r < dbr.length; r++) + { + sid = new SeqIdName(dbr[r].getAccessionId()); + if (!names.contains(sid)) + { + names.put(sid, seqs[i]); + } + } + } + } + } + + /** + * 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 SequenceI closest SequenceI to SeqIdName + */ + private SequenceI pickbestMatch(SeqIdName candName, Vector matches) + { + SequenceI match = null; + if (candName == null || matches == null || matches.size() == 0) + { + return null; + } + match = (SequenceI) matches.elementAt(0); + matches.removeElementAt(0); + 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 = (SequenceI) matches.elementAt(0); + names.put(new SeqIdName(cand.getName()), cand); + int candlen = cand.getName().length(); + // keep the one with an id 'closer' to the given seqnam string + if (Math.abs(matchlen - namlen) > Math.abs(candlen - namlen) + && candlen > matchlen) + { + match = cand; + matchlen = candlen; + } + } + return match; + } + + /** + * get SequenceI with closest SequenceI.getName() to seq.getName() + * + * @param seq + * SequenceI + * @return SequenceI + */ + SequenceI findIdMatch(SequenceI seq) + { + SeqIdName nam = new SeqIdName(seq.getName()); + return findIdMatch(nam); + } + + SequenceI findIdMatch(String seqnam) + { + SeqIdName nam = new SeqIdName(seqnam); + return findIdMatch(nam); + } + + /** + * 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) + { + 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); + } + + private class SeqIdName + { + String id; + + SeqIdName(String s) + { + if (s != null) + { + id = new String(s); + } + else + { + id = ""; + } + } + + public int hashCode() + { + return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id + .hashCode()); + } + + public boolean equals(Object s) + { + 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 = "~. |#\\/<>!\"£$%^*)}[@',?_"; + + /** + * 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) + { + 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; + } + } + } +}