// 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
// 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: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.surfacing;
import java.util.SortedMap;
import java.util.SortedSet;
-import org.forester.surfacing.BinaryDomainCombination.DomainCombinationType;
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.protein.BinaryDomainCombination.DomainCombinationType;
+import org.forester.species.Species;
import org.forester.util.DescriptiveStatistics;
public interface GenomeWideCombinableDomains {
- public boolean contains( DomainId key_id );
+ public boolean contains( String key_id );
- public CombinableDomains get( DomainId key_id );
+ public CombinableDomains get( String key_id );
- public SortedMap<DomainId, CombinableDomains> getAllCombinableDomainsIds();
+ public SortedMap<String, CombinableDomains> getAllCombinableDomainsIds();
/**
* This should return all domains ids present in the genome.
*
* @return a sorted set of domains ids
*/
- public SortedSet<DomainId> getAllDomainIds();
+ public SortedSet<String> getAllDomainIds();
public DomainCombinationType getDomainCombinationType();
- SortedSet<DomainId> getMostPromiscuosDomain();
-
/**
* This should return a statistic for per domain
* promiscuity in a genome.
public StringBuilder toStringBuilder( GenomeWideCombinableDomainsSortOrder order );
+ SortedSet<String> getMostPromiscuosDomain();
+
public static enum GenomeWideCombinableDomainsSortOrder {
- ALPHABETICAL_KEY_ID, KEY_DOMAIN_PROTEINS_COUNT, KEY_DOMAIN_COUNT, COMBINATIONS_COUNT
+ ALPHABETICAL_KEY_ID, COMBINATIONS_COUNT, KEY_DOMAIN_COUNT, KEY_DOMAIN_PROTEINS_COUNT
}
}