// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
// 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
// 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
// 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.
// 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
// 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
- public void addCombinableDomain( final DomainId protein_domain );
-
- /**
- *
- * 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<DomainId> getAllDomains();
-
- List<DomainId> getCombinableDomains();
+ public void addCombinableDomain( final String protein_domain );
- public DomainId getKeyDomain();
-
- /**
- * Gets descriptive statistics for the confidence (i.e. E-values) of the key
- * domain.
- *
- *
- * @return descriptive statistics for the confidence of the key domain
- */
- public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics();
+ public String getKeyDomain();
- public boolean isCombinable( final DomainId protein_domain );
+ public boolean isCombinable( final String protein_domain );
+
+ public List<BinaryDomainCombination> toBinaryDomainCombinations();
+
+ void addKeyDomainProtein( String protein );
-
- /**
- * Sets how many proteins with the key domain are present in a given species
- * genome.
- *
- * @param key_domain_proteins_count
- * key domain protein count in species
- */
- void setKeyDomainProteinsCount( final int key_domain_proteins_count );
-
- public List<BinaryDomainCombination> toBinaryDomainCombinations();