X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=bedce3fd56c3834eaa5a0205a609fb7072cdcf80;hb=e07fc11d5aaf4d1237d83e5f7ea0909dea09902e;hp=0744937743bcba699e34bc0421f06133144b08ca;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java index 0744937..bedce3f 100755 --- a/src/jalview/analysis/SequenceIdMatcher.java +++ b/src/jalview/analysis/SequenceIdMatcher.java @@ -1,246 +1,332 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 - */ -package jalview.analysis; - -import java.util.*; - -import jalview.datamodel.*; - -/** - *
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]); - } - } - - /** - * 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; - } - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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