X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=56b760a59da440099c38598ea4856019db640400;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=f4f305b08da6a19e53c2bd61c0f1c53d4f1e787b;hpb=fbec1b33d0fc169d72be059a5d2cf12b248270e1;p=jalview.git diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java index f4f305b..56b760a 100755 --- a/src/jalview/analysis/SequenceIdMatcher.java +++ b/src/jalview/analysis/SequenceIdMatcher.java @@ -1,185 +1,272 @@ -/* - * 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 - */ -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 - *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) - { - 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 - */ - 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 (Development Version 2.4.1) + * Copyright (C) 2009 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]); + // add in any interesting identifiers + if (seqs[i].getDBRef()!=null) + { + DBRefEntry dbr[] = seqs[i].getDBRef(); + SeqIdName sid=null; + for (int r=0;r