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.surfacing;
29 import org.forester.go.GoId;
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 DomainId _id;
40 public SimpleDomain( final String id_str ) {
41 if ( ForesterUtil.isEmpty( id_str ) ) {
42 throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
44 _id = new DomainId( id_str );
48 public void addGoId( final GoId go_id ) {
49 throw new RuntimeException( "method not implemented" );
53 public int compareTo( final Domain domain ) {
54 if ( this == domain ) {
57 return getDomainId().compareTo( domain.getDomainId() );
61 public DomainId getDomainId() {
66 public int getFrom() {
67 throw new RuntimeException( "method not implemented" );
71 public GoId getGoId( final int i ) {
72 throw new RuntimeException( "method not implemented" );
75 public int getLength() {
76 throw new RuntimeException( "method not implemented" );
80 public short getNumber() {
81 throw new RuntimeException( "method not implemented" );
85 public int getNumberOfGoIds() {
86 throw new RuntimeException( "method not implemented" );
90 public double getPerDomainEvalue() {
91 throw new RuntimeException( "method not implemented" );
95 public double getPerDomainScore() {
96 throw new RuntimeException( "method not implemented" );
100 public double getPerSequenceEvalue() {
101 throw new RuntimeException( "method not implemented" );
105 public double getPerSequenceScore() {
106 throw new RuntimeException( "method not implemented" );
109 public String getSearchParameter() {
110 throw new RuntimeException( "method not implemented" );
115 throw new RuntimeException( "method not implemented" );
119 public short getTotalCount() {
120 throw new RuntimeException( "method not implemented" );
123 public boolean isCompleteQueryMatch() {
124 throw new RuntimeException( "method not implemented" );
127 public boolean isCompleteTargetMatch() {
128 throw new RuntimeException( "method not implemented" );