org.forester.surfacing.CombinableDomains Maven / Gradle / Ivy
// $Id:
//
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.surfacing;
import java.util.List;
import java.util.Set;
import java.util.SortedMap;
import org.forester.protein.BinaryDomainCombination;
import org.forester.species.Species;
public interface CombinableDomains {
/**
* To add a new combinable domain.
*
* @param protein_domain
*/
public void addCombinableDomain( final String protein_domain );
/**
* Returns the combinable domain identifiers sorted in alphabetical manner: -
* keys are the combinable domain identifiers - values are the counts of
* proteins exhibiting a particular combination
*
* @return combining domain identifiers sorted in alphabetical manner
*/
public SortedMap getCombinableDomainsIds();
public StringBuilder getCombiningDomainIdsAsStringBuilder();
/**
* Returns the domain whose combinable domains are in stored in this
* combinable domains.
*
* @return the domain identifier
*/
public String getKeyDomain();
/**
* Returns how many times the key domain is present in a given species
* genome.
*
* @return key domain count in species
*/
public int getKeyDomainCount();
public Set getKeyDomainProteins();
/**
* Returns how many proteins with the key domain are present in a given
* species genome.
*
* @return key domain proteins count in species
*/
public int getKeyDomainProteinsCount();
public int getNumberOfCombinableDomains();
public int getNumberOfProteinsExhibitingCombination( final String protein_domain );
/**
* Returns the species of this combinable domains.
*
* @return the species
*/
public Species getSpecies();
public boolean isCombinable( final String protein_domain );
public List toBinaryDomainCombinations();
void addKeyDomainProtein( String protein );
/**
*
* This must return all domains in this set of combinable domains (i.e.
* the key domain and all domains which can combine with the key domain).
*
* @return all domains
*/
List getAllDomains();
List getCombinableDomains();
/**
* Sets how many times the key domain is present in a given species genome.
*
* @param key_domain_count
* key domain count in species
*/
void setKeyDomainCount( final int key_domain_count );
}