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: https://sites.google.com/site/cmzmasek/home/software/forester
27 package org.forester.surfacing;
29 import org.forester.protein.Domain;
30 import org.forester.util.ForesterUtil;
33 * A limited implementation of Domain. Its intended use is for when only a
34 * domain identifier is needed. Note intended for general use.
36 public class SimpleDomain implements Domain {
38 final private String _id;
40 public SimpleDomain( final String id ) {
41 if ( ForesterUtil.isEmpty( id ) ) {
42 throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
48 // ^^ public void addGoId( final GoId go_id ) {
49 // ^^ throw new RuntimeException( "method not implemented" );
52 public int compareTo( final Domain domain ) {
53 if ( this == domain ) {
56 return getDomainId().compareTo( domain.getDomainId() );
60 public String getDomainId() {
65 public int getFrom() {
66 throw new RuntimeException( "method not implemented" );
70 // ^^ public GoId getGoId( final int i ) {
71 // ^^ throw new RuntimeException( "method not implemented" );
74 public int getLength() {
75 throw new RuntimeException( "method not implemented" );
79 public short getNumber() {
80 throw new RuntimeException( "method not implemented" );
84 // ^^ public int getNumberOfGoIds() {
85 // ^^ throw new RuntimeException( "method not implemented" );
88 public double getPerDomainEvalue() {
89 throw new RuntimeException( "method not implemented" );
93 public double getPerDomainScore() {
94 throw new RuntimeException( "method not implemented" );
98 public double getPerSequenceEvalue() {
99 throw new RuntimeException( "method not implemented" );
103 public double getPerSequenceScore() {
104 throw new RuntimeException( "method not implemented" );
107 public String getSearchParameter() {
108 throw new RuntimeException( "method not implemented" );
113 throw new RuntimeException( "method not implemented" );
117 public short getTotalCount() {
118 throw new RuntimeException( "method not implemented" );
121 public boolean isCompleteQueryMatch() {
122 throw new RuntimeException( "method not implemented" );
125 public boolean isCompleteTargetMatch() {
126 throw new RuntimeException( "method not implemented" );