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 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.protein.BinaryDomainCombination;
36 import org.forester.species.Species;
37 import org.forester.util.DescriptiveStatistics;
39 public class BasicCombinableDomains implements CombinableDomains {
41 final private String _key_domain;
42 private int _key_domain_count;
43 private int _key_domain_proteins_count;
44 final private Species _species;
45 final private TreeMap<String, Integer> _combining_domains;
46 private DescriptiveStatistics _key_domain_confidence_statistics;
48 public BasicCombinableDomains( final String key_domain, final Species species ) {
49 _key_domain = key_domain;
51 _combining_domains = new TreeMap<String, Integer>();
56 public void addCombinableDomain( final String protein_domain ) {
57 if ( getCombiningDomains().containsKey( protein_domain ) ) {
58 getCombiningDomains().put( protein_domain, getCombiningDomains().get( protein_domain ) + 1 );
61 getCombiningDomains().put( protein_domain, 1 );
66 public List<String> getAllDomains() {
67 final List<String> domains = getCombinableDomains();
68 if ( !domains.contains( getKeyDomain() ) ) {
69 domains.add( getKeyDomain() );
75 public List<String> getCombinableDomains() {
76 final List<String> domains = new ArrayList<String>( getNumberOfCombinableDomains() );
77 for( final String domain : getCombiningDomains().keySet() ) {
78 domains.add( domain );
84 public SortedMap<String, Integer> getCombinableDomainsIds() {
85 final SortedMap<String, Integer> ids = new TreeMap<String, Integer>();
86 for( final String domain : getCombiningDomains().keySet() ) {
87 final String pd = domain;
88 ids.put( pd, getCombiningDomains().get( pd ) );
94 public StringBuilder getCombiningDomainIdsAsStringBuilder() {
95 final StringBuilder sb = new StringBuilder();
96 for( final Iterator<String> iter = getCombiningDomains().keySet().iterator(); iter.hasNext(); ) {
97 final String key = iter.next();
98 sb.append( key.toString() );
100 final int count = getCombiningDomains().get( key );
103 if ( iter.hasNext() ) {
110 protected TreeMap<String, Integer> getCombiningDomains() {
111 return _combining_domains;
115 public String getKeyDomain() {
120 public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics() {
121 return _key_domain_confidence_statistics;
125 public int getKeyDomainCount() {
126 return _key_domain_count;
130 public int getKeyDomainProteinsCount() {
131 return _key_domain_proteins_count;
135 public int getNumberOfCombinableDomains() {
136 return _combining_domains.size();
140 public int getNumberOfProteinsExhibitingCombination( final String protein_domain ) {
141 if ( getCombiningDomains().containsKey( protein_domain ) ) {
142 return getCombiningDomains().get( protein_domain );
150 public Species getSpecies() {
154 private void init() {
155 _key_domain_count = 0;
156 _key_domain_proteins_count = 0;
157 _key_domain_confidence_statistics = null;
161 public boolean isCombinable( final String protein_domain ) {
162 return getCombiningDomains().containsKey( protein_domain );
166 public void setKeyDomainConfidenceDescriptiveStatistics( final DescriptiveStatistics key_domain_confidence_statistics ) {
167 _key_domain_confidence_statistics = key_domain_confidence_statistics;
171 public void setKeyDomainCount( final int key_domain_count ) {
172 _key_domain_count = key_domain_count;
176 public void setKeyDomainProteinsCount( final int key_domain_proteins_count ) {
177 _key_domain_proteins_count = key_domain_proteins_count;
181 public List<BinaryDomainCombination> toBinaryDomainCombinations() {
182 final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
183 for( final String domain : getCombiningDomains().keySet() ) {
184 binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
186 return binary_combinations;
190 public String toString() {
191 final StringBuilder sb = new StringBuilder();
192 sb.append( getKeyDomain() );
194 sb.append( getKeyDomainCount() );
196 sb.append( getKeyDomainProteinsCount() );
198 sb.append( getNumberOfCombinableDomains() );
200 sb.append( getCombiningDomainIdsAsStringBuilder() );
201 return sb.toString();