// 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
package org.forester.surfacing;
import java.util.SortedMap;
import java.util.SortedSet;
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;
* @return descriptive statistics for per domain promiscuity in a genome
*/
public DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics();
* @return descriptive statistics for per domain promiscuity in a genome
*/
public DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics();
* @return a sorted set of binary domain combinations
*/
public SortedSet<BinaryDomainCombination> toBinaryDomainCombinations();
public StringBuilder toStringBuilder( GenomeWideCombinableDomainsSortOrder order );
* @return a sorted set of binary domain combinations
*/
public SortedSet<BinaryDomainCombination> toBinaryDomainCombinations();
public StringBuilder toStringBuilder( GenomeWideCombinableDomainsSortOrder order );
- ALPHABETICAL_KEY_ID, KEY_DOMAIN_PROTEINS_COUNT, KEY_DOMAIN_COUNT, COMBINATIONS_COUNT
+ ALPHABETICAL_KEY_ID, COMBINATIONS_COUNT, KEY_DOMAIN_COUNT, KEY_DOMAIN_PROTEINS_COUNT