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.protein.BinaryDomainCombination;
33 import org.forester.protein.DomainId;
34 import org.forester.species.Species;
35 import org.forester.util.DescriptiveStatistics;
37 public interface CombinableDomains {
40 * To add a new combinable domain.
42 * @param protein_domain
44 public void addCombinableDomain( final DomainId protein_domain );
48 * This must return all domains in this set of combinable domains (i.e.
49 * the key domain and all domains which can combine with the key domain).
53 List<DomainId> getAllDomains();
55 List<DomainId> getCombinableDomains();
58 * Returns the combinable domain identifiers sorted in alphabetical manner: -
59 * keys are the combinable domain identifiers - values are the counts of
60 * proteins exhibiting a particular combination
62 * @return combining domain identifiers sorted in alphabetical manner
64 public SortedMap<DomainId, Integer> getCombinableDomainsIds();
66 public StringBuilder getCombiningDomainIdsAsStringBuilder();
69 * Returns the domain whose combinable domains are in stored in this
72 * @return the domain identifier
74 public DomainId getKeyDomain();
77 * Gets descriptive statistics for the confidence (i.e. E-values) of the key
81 * @return descriptive statistics for the confidence of the key domain
83 public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics();
86 * Returns how many times the key domain is present in a given species
89 * @return key domain count in species
91 public int getKeyDomainCount();
94 * Returns how many proteins with the key domain are present in a given
97 * @return key domain proteins count in species
99 public int getKeyDomainProteinsCount();
101 public int getNumberOfCombinableDomains();
103 public int getNumberOfProteinsExhibitingCombination( final DomainId protein_domain );
106 * Returns the species of this combinable domains.
108 * @return the species
110 public Species getSpecies();
112 public boolean isCombinable( final DomainId protein_domain );
115 * This is to set descriptive statistics for the confidence (i.e. E-values)
121 void setKeyDomainConfidenceDescriptiveStatistics( final DescriptiveStatistics statistics );
124 * Sets how many times the key domain is present in a given species genome.
126 * @param key_domain_count
127 * key domain count in species
129 void setKeyDomainCount( final int key_domain_count );
132 * Sets how many proteins with the key domain are present in a given species
135 * @param key_domain_proteins_count
136 * key domain protein count in species
138 void setKeyDomainProteinsCount( final int key_domain_proteins_count );
140 public List<BinaryDomainCombination> toBinaryDomainCombinations();