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.List;
30 import java.util.SortedMap;
32 import org.forester.util.DescriptiveStatistics;
34 public interface CombinableDomains {
37 * To add a new combinable domain.
39 * @param protein_domain
41 public void addCombinableDomain( final DomainId protein_domain );
45 * This must return all domains in this set of combinable domains (i.e.
46 * the key domain and all domains which can combine with the key domain).
50 List<DomainId> getAllDomains();
52 List<DomainId> getCombinableDomains();
55 * Returns the combinable domain identifiers sorted in alphabetical manner: -
56 * keys are the combinable domain identifiers - values are the counts of
57 * proteins exhibiting a particular combination
59 * @return combining domain identifiers sorted in alphabetical manner
61 public SortedMap<DomainId, Integer> getCombinableDomainsIds();
63 public StringBuilder getCombiningDomainIdsAsStringBuilder();
66 * Returns the domain whose combinable domains are in stored in this
69 * @return the domain identifier
71 public DomainId getKeyDomain();
74 * Gets descriptive statistics for the confidence (i.e. E-values) of the key
78 * @return descriptive statistics for the confidence of the key domain
80 public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics();
83 * Returns how many times the key domain is present in a given species
86 * @return key domain count in species
88 public int getKeyDomainCount();
91 * Returns how many proteins with the key domain are present in a given
94 * @return key domain proteins count in species
96 public int getKeyDomainProteinsCount();
98 public int getNumberOfCombinableDomains();
100 public int getNumberOfProteinsExhibitingCombination( final DomainId protein_domain );
103 * Returns the species of this combinable domains.
105 * @return the species
107 public Species getSpecies();
109 public boolean isCombinable( final DomainId protein_domain );
112 * This is to set descriptive statistics for the confidence (i.e. E-values)
118 void setKeyDomainConfidenceDescriptiveStatistics( final DescriptiveStatistics statistics );
121 * Sets how many times the key domain is present in a given species genome.
123 * @param key_domain_count
124 * key domain count in species
126 void setKeyDomainCount( final int key_domain_count );
129 * Sets how many proteins with the key domain are present in a given species
132 * @param key_domain_proteins_count
133 * key domain protein count in species
135 void setKeyDomainProteinsCount( final int key_domain_proteins_count );
137 public List<BinaryDomainCombination> toBinaryDomainCombinations();