3 // forester -- software libraries and applications
4 // for genomics and evolutionary biology research.
6 // Copyright (C) 2010 Christian M Zmasek
7 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: www.phylosoft.org/forester
27 package org.forester.sequence;
29 import org.forester.util.ForesterUtil;
31 public class BasicSequence implements Sequence {
33 private final char[] _mol_sequence;
34 private final String _identifier;
35 private final TYPE _type;
37 private BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
38 if ( ForesterUtil.isEmpty( identifier ) ) {
39 throw new IllegalArgumentException( "identifier of sequence cannot be empty");
41 if ( ForesterUtil.isEmpty( mol_sequence ) ) {
42 throw new IllegalArgumentException( "molecular sequence cannot be empty");
44 _mol_sequence = mol_sequence.toCharArray();
45 _identifier = identifier;
49 // Only use if you know what you are doing!
50 public BasicSequence( final String identifier, final char[] mol_sequence, final TYPE type ) {
51 if ( ForesterUtil.isEmpty( identifier ) ) {
52 throw new IllegalArgumentException( "identifier of sequence cannot be empty");
54 if ( mol_sequence == null || mol_sequence.length < 1 ) {
55 throw new IllegalArgumentException( "molecular sequence cannot be empty");
57 _mol_sequence = mol_sequence;
58 _identifier = identifier;
63 public String getIdentifier() {
68 public int getLength() {
69 return _mol_sequence.length;
73 public char[] getMolecularSequence() {
78 public char getResidueAt( final int position ) {
79 return _mol_sequence[ position ];
83 public TYPE getType() {
88 public int getNumberOfGapResidues() {
90 for( int i = 0; i < _mol_sequence.length; ++i ) {
91 if ( _mol_sequence[ i ] == GAP ) {
99 public boolean equals(Object obj) {
103 if (obj.getClass() != getClass()) {
106 Sequence other = ( Sequence) obj;
107 if ( getMolecularSequenceAsString() .equals( other.getMolecularSequenceAsString() )) {
114 public int hashCode() {
115 return getMolecularSequenceAsString().hashCode();
120 public String toString() {
121 final StringBuffer sb = new StringBuffer();
122 sb.append( _identifier.toString() );
124 sb.append( getMolecularSequenceAsString() );
125 return sb.toString();
128 public static Sequence copySequence( final Sequence seq ) {
129 final char[] s = new char[ seq.getMolecularSequence().length ];
130 for( int i = 0; i < seq.getMolecularSequence().length; i++ ) {
131 s[ i ] = seq.getMolecularSequence()[ i ];
133 return new BasicSequence( new String( seq.getIdentifier() ), s, seq.getType() );
136 public static Sequence createAaSequence( final String identifier, final String mol_sequence ) {
137 return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
138 .replaceAll( AA_REGEXP, Character.toString( UNSPECIFIED_AA ) ), TYPE.AA );
141 public static Sequence createDnaSequence( final String identifier, final String mol_sequence ) {
142 return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
143 .replaceAll( DNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.DNA );
146 public static Sequence createRnaSequence( final String identifier, final String mol_sequence ) {
147 return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
148 .replaceAll( RNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.RNA );
152 public String getMolecularSequenceAsString() {
154 return new String( getMolecularSequence() );