3 // FORESTER -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2009 Christian M. Zmasek
7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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.protein;
29 import org.forester.go.GoId;
30 import org.forester.util.ForesterUtil;
32 public class BasicDomain implements Domain {
34 final private DomainId _id;
35 final private int _from;
36 final private int _to;
37 final private short _number;
38 final private short _total_count;
39 final private double _per_sequence_evalue;
40 final private double _per_sequence_score;
41 final private double _per_domain_evalue;
42 final private double _per_domain_score;
44 public BasicDomain( final String id_str ) {
45 if ( ForesterUtil.isEmpty( id_str ) ) {
46 throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
48 _id = new DomainId( id_str );
53 _per_sequence_evalue = -1;
54 _per_sequence_score = -1;
55 _per_domain_evalue = -1;
56 _per_domain_score = -1;
59 public BasicDomain( final String id_str,
63 final short total_count,
64 final double per_sequence_evalue,
65 final double per_sequence_score ) {
66 this( id_str, from, to, number, total_count, per_sequence_evalue, per_sequence_score, 0, 0 );
69 public BasicDomain( final String id_str,
73 final short total_count,
74 final double per_sequence_evalue,
75 final double per_sequence_score,
76 final double per_domain_evalue,
77 final double per_domain_score ) {
78 if ( ( from >= to ) || ( from < 0 ) ) {
79 throw new IllegalArgumentException( "attempt to create protein domain from " + from + " to " + to );
81 if ( ForesterUtil.isEmpty( id_str ) ) {
82 throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
84 if ( ( number > total_count ) || ( number < 0 ) ) {
85 throw new IllegalArgumentException( "attempt to create protein domain number " + number + " out of "
88 if ( ( per_sequence_evalue < 0.0 ) || ( per_domain_evalue < 0.0 ) ) {
89 throw new IllegalArgumentException( "attempt to create protein domain with negative E-value" );
91 _id = new DomainId( id_str );
95 _total_count = total_count;
96 _per_sequence_evalue = per_sequence_evalue;
97 _per_sequence_score = per_sequence_score;
98 _per_domain_evalue = per_domain_evalue;
99 _per_domain_score = per_domain_score;
103 public void addGoId( final GoId go_id ) {
104 getDomainId().getGoIds().add( go_id );
108 * Basic domains are compared/sorted based upon their identifiers (case
109 * insensitive) and their numbers.
113 public int compareTo( final Domain domain ) {
114 if ( domain.getClass() != this.getClass() ) {
115 throw new IllegalArgumentException( "attempt to compare [" + domain.getClass() + "] to " + "["
116 + this.getClass() + "]" );
118 if ( this == domain ) {
121 return getDomainId().compareTo( domain.getDomainId() );
125 * Basic domains are considered equal if they have the same identifier (case
130 public boolean equals( final Object o ) {
134 else if ( o == null ) {
135 throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to null" );
137 else if ( o.getClass() != this.getClass() ) {
138 throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to " + o + " ["
139 + o.getClass() + "]" );
142 return getDomainId().equals( ( ( Domain ) o ).getDomainId() );
147 public DomainId getDomainId() {
152 public int getFrom() {
157 public GoId getGoId( final int i ) {
158 return getDomainId().getGoIds().get( i );
162 public short getNumber() {
167 public int getNumberOfGoIds() {
168 return getDomainId().getGoIds().size();
172 public double getPerDomainEvalue() {
173 return _per_domain_evalue;
177 public double getPerDomainScore() {
178 return _per_domain_score;
182 public double getPerSequenceEvalue() {
183 return _per_sequence_evalue;
187 public double getPerSequenceScore() {
188 return _per_sequence_score;
197 public short getTotalCount() {
202 public int hashCode() {
203 return getDomainId().getId().hashCode();
207 public String toString() {
208 return toStringBuffer().toString();
211 public StringBuffer toStringBuffer() {
212 return new StringBuffer( getDomainId().getId() );
216 public int getLength() {
217 return ( 1 + getTo() ) - getFrom();