Title:
- * SequenceIdMatcher - *Description:
- * Routine which does approximate Sequence Id resolution by name using string containment rather than equivalence - *Copyright: Copyright (c) 2004
- * - *Company: Dundee University
- * - * @author not attributable - * @version 1.0 - */ -public class SequenceIdMatcher -{ - - 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; - } - - public boolean equals(SeqIdName s) - { - if (id.startsWith(s.id) || s.id.startsWith(id)) - { - return true; - } - return false; - } - - public boolean equals(String s) - { - if (id.startsWith(s) || s.startsWith(id)) - { - return true; - } - return false; - } - } - - 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 = new SequenceI[seqs.length]; - - int i = 0; - SeqIdName nam; - if (seqs.length > 0) - { - 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; - } - -} +/* + * 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 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 = new SequenceI[seqs.length]; + + int i = 0; + SeqIdName nam; + + if (seqs.length > 0) + { + 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; + } + + public boolean equals(SeqIdName s) + { + if (id.startsWith(s.id) || s.id.startsWith(id)) + { + return true; + } + + return false; + } + + public boolean equals(String s) + { + if (id.startsWith(s) || s.startsWith(id)) + { + return true; + } + + return false; + } + } +}