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.List;
30 import java.util.SortedMap;
32 import org.forester.protein.BinaryDomainCombination;
33 import org.forester.species.Species;
34 import org.forester.util.DescriptiveStatistics;
36 public interface CombinableDomains {
39 * To add a new combinable domain.
41 * @param protein_domain
43 public void addCombinableDomain( final String protein_domain );
47 * This must return all domains in this set of combinable domains (i.e.
48 * the key domain and all domains which can combine with the key domain).
52 List<String> getAllDomains();
54 List<String> getCombinableDomains();
57 * Returns the combinable domain identifiers sorted in alphabetical manner: -
58 * keys are the combinable domain identifiers - values are the counts of
59 * proteins exhibiting a particular combination
61 * @return combining domain identifiers sorted in alphabetical manner
63 public SortedMap<String, Integer> getCombinableDomainsIds();
65 public StringBuilder getCombiningDomainIdsAsStringBuilder();
68 * Returns the domain whose combinable domains are in stored in this
71 * @return the domain identifier
73 public String getKeyDomain();
76 * Gets descriptive statistics for the confidence (i.e. E-values) of the key
80 * @return descriptive statistics for the confidence of the key domain
82 public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics();
85 * Returns how many times the key domain is present in a given species
88 * @return key domain count in species
90 public int getKeyDomainCount();
93 * Returns how many proteins with the key domain are present in a given
96 * @return key domain proteins count in species
98 public int getKeyDomainProteinsCount();
100 public int getNumberOfCombinableDomains();
102 public int getNumberOfProteinsExhibitingCombination( final String protein_domain );
105 * Returns the species of this combinable domains.
107 * @return the species
109 public Species getSpecies();
111 public boolean isCombinable( final String protein_domain );
114 * This is to set descriptive statistics for the confidence (i.e. E-values)
120 void setKeyDomainConfidenceDescriptiveStatistics( final DescriptiveStatistics statistics );
123 * Sets how many times the key domain is present in a given species genome.
125 * @param key_domain_count
126 * key domain count in species
128 void setKeyDomainCount( final int key_domain_count );
131 * Sets how many proteins with the key domain are present in a given species
134 * @param key_domain_proteins_count
135 * key domain protein count in species
137 void setKeyDomainProteinsCount( final int key_domain_proteins_count );
139 public List<BinaryDomainCombination> toBinaryDomainCombinations();