2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.analysis;
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21 import jalview.datamodel.SequenceI;
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23 import java.util.Hashtable;
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24 import java.util.Vector;
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30 * <p>Description: </p>
31 * Routine which does approximate Sequence Id resolution by name using string containment rather than equivalence
32 * <p>Copyright: Copyright (c) 2004</p>
34 * <p>Company: Dundee University</p>
36 * @author not attributable
39 public class SequenceIdMatcher {
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40 private Hashtable names;
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42 public SequenceIdMatcher(SequenceI[] seqs) {
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43 names = new Hashtable();
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45 for (int i = 0; i < seqs.length; i++) {
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46 names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
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50 SequenceI findIdMatch(SequenceI seq) {
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51 SeqIdName nam = new SeqIdName(seq.getName());
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53 if (names.containsKey(nam)) {
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54 return (SequenceI) names.get(nam);
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60 SequenceI findIdMatch(String seqnam) {
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61 SeqIdName nam = new SeqIdName(seqnam);
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63 if (names.containsKey(nam)) {
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64 return (SequenceI) names.get(nam);
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73 * Return pointers to sequences (or sequence object containers)
74 * which have same Id as a given set of different sequence objects
76 * @param seqs SequenceI[]
79 SequenceI[] findIdMatch(SequenceI[] seqs) {
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80 SequenceI[] namedseqs = new SequenceI[seqs.length];
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85 if (seqs.length > 0) {
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87 nam = new SeqIdName(seqs[i].getName());
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89 if (names.containsKey(nam)) {
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90 namedseqs[i] = (SequenceI) names.get(nam);
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92 namedseqs[i] = null;
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94 } while (i++ < seqs.length);
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100 private class SeqIdName {
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103 SeqIdName(String s) {
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104 id = new String(s);
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107 public int hashCode() {
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108 return (id.substring(0, 4).hashCode());
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111 public boolean equals(Object s) {
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112 if (s instanceof SeqIdName) {
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113 return this.equals((SeqIdName) s);
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115 if (s instanceof String) {
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116 return this.equals((String) s);
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123 public boolean equals(SeqIdName s) {
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124 if (id.startsWith(s.id) || s.id.startsWith(id)) {
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131 public boolean equals(String s) {
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132 if (id.startsWith(s) || s.startsWith(id)) {
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