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 java.util.ArrayList;
30 import java.util.Iterator;
31 import java.util.List;
32 import java.util.SortedMap;
33 import java.util.TreeMap;
35 import org.forester.util.DescriptiveStatistics;
37 public class BasicCombinableDomains implements CombinableDomains {
39 final private DomainId _key_domain;
40 private int _key_domain_count;
41 private int _key_domain_proteins_count;
42 final private Species _species;
43 final private TreeMap<DomainId, Integer> _combining_domains;
44 private DescriptiveStatistics _key_domain_confidence_statistics;
46 public BasicCombinableDomains( final DomainId key_domain, final Species species ) {
47 _key_domain = key_domain;
49 _combining_domains = new TreeMap<DomainId, Integer>();
53 public void addCombinableDomain( final DomainId protein_domain ) {
54 if ( getCombiningDomains().containsKey( protein_domain ) ) {
55 getCombiningDomains().put( protein_domain, getCombiningDomains().get( protein_domain ) + 1 );
58 getCombiningDomains().put( protein_domain, 1 );
62 public List<DomainId> getAllDomains() {
63 final List<DomainId> domains = getCombinableDomains();
64 if ( !domains.contains( getKeyDomain() ) ) {
65 domains.add( getKeyDomain() );
70 public List<DomainId> getCombinableDomains() {
71 final List<DomainId> domains = new ArrayList<DomainId>( getNumberOfCombinableDomains() );
72 for( final DomainId domain : getCombiningDomains().keySet() ) {
73 domains.add( domain );
78 public SortedMap<DomainId, Integer> getCombinableDomainsIds() {
79 final SortedMap<DomainId, Integer> ids = new TreeMap<DomainId, Integer>();
80 for( final DomainId domain : getCombiningDomains().keySet() ) {
81 final DomainId pd = domain;
82 ids.put( pd, getCombiningDomains().get( pd ) );
87 public StringBuilder getCombiningDomainIdsAsStringBuilder() {
88 final StringBuilder sb = new StringBuilder();
89 for( final Iterator<DomainId> iter = getCombiningDomains().keySet().iterator(); iter.hasNext(); ) {
90 final DomainId key = iter.next();
91 sb.append( key.toString() );
93 final int count = getCombiningDomains().get( key );
96 if ( iter.hasNext() ) {
103 protected TreeMap<DomainId, Integer> getCombiningDomains() {
104 return _combining_domains;
107 public DomainId getKeyDomain() {
111 public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics() {
112 return _key_domain_confidence_statistics;
115 public int getKeyDomainCount() {
116 return _key_domain_count;
119 public int getKeyDomainProteinsCount() {
120 return _key_domain_proteins_count;
123 public int getNumberOfCombinableDomains() {
124 return _combining_domains.size();
127 public int getNumberOfProteinsExhibitingCombination( final DomainId protein_domain ) {
128 if ( getCombiningDomains().containsKey( protein_domain ) ) {
129 return getCombiningDomains().get( protein_domain );
136 public Species getSpecies() {
140 private void init() {
141 _key_domain_count = 0;
142 _key_domain_proteins_count = 0;
143 _key_domain_confidence_statistics = null;
146 public boolean isCombinable( final DomainId protein_domain ) {
147 return getCombiningDomains().containsKey( protein_domain );
150 public void setKeyDomainConfidenceDescriptiveStatistics( final DescriptiveStatistics key_domain_confidence_statistics ) {
151 _key_domain_confidence_statistics = key_domain_confidence_statistics;
154 public void setKeyDomainCount( final int key_domain_count ) {
155 _key_domain_count = key_domain_count;
158 public void setKeyDomainProteinsCount( final int key_domain_proteins_count ) {
159 _key_domain_proteins_count = key_domain_proteins_count;
163 public List<BinaryDomainCombination> toBinaryDomainCombinations() {
164 final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
165 for( final DomainId domain : getCombiningDomains().keySet() ) {
166 binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
168 return binary_combinations;
172 public String toString() {
173 final StringBuilder sb = new StringBuilder();
174 sb.append( getKeyDomain() );
176 sb.append( getKeyDomainCount() );
178 sb.append( getKeyDomainProteinsCount() );
180 sb.append( getNumberOfCombinableDomains() );
182 sb.append( getCombiningDomainIdsAsStringBuilder() );
183 return sb.toString();