// 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.Map;
import java.util.SortedMap;
import java.util.SortedSet;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.species.Species;
+import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
+
/*
* This is to represent a measure of similarity between two or more domains from
* different genomes.
*/
public interface DomainSimilarity extends Comparable<DomainSimilarity> {
- public SortedSet<DomainId> getCombinableDomainIds( final Species species_of_combinable_domain );;
+ static public enum DomainSimilarityScoring {
+ DOMAINS, PROTEINS, COMBINATIONS;
+ }
+
+ public static enum DomainSimilaritySortField {
+ MIN, MAX, SD, MEAN, ABS_MAX_COUNTS_DIFFERENCE, MAX_COUNTS_DIFFERENCE, MAX_DIFFERENCE, SPECIES_COUNT, DOMAIN_ID,
+ }
- public DomainId getDomainId();
+ public SortedSet<String> getCombinableDomainIds( final Species species_of_combinable_domain );
+
+ public String getDomainId();
/**
* For pairwise similarities, this should return the "difference"; for example the difference in counts
*
* @return SortedMap<String, SpeciesSpecificDomainSimilariyData>
*/
- public SortedMap<Species, SpeciesSpecificDomainSimilariyData> getSpeciesData();
+ public SortedMap<Species, SpeciesSpecificDcData> getSpeciesData();
public double getStandardDeviationOfSimilarityScore();
- public StringBuffer toStringBuffer( final PrintableDomainSimilarity.PRINT_OPTION print_option );
-
- static public enum DomainSimilarityScoring {
- DOMAINS, PROTEINS, COMBINATIONS;
- }
-
- public static enum DomainSimilaritySortField {
- MIN, MAX, SD, MEAN, ABS_MAX_COUNTS_DIFFERENCE, MAX_COUNTS_DIFFERENCE, MAX_DIFFERENCE, SPECIES_COUNT, DOMAIN_ID,
- }
+ public StringBuffer toStringBuffer( PRINT_OPTION print_option,
+ Map<String, Integer> tax_code_to_id_map,
+ Phylogeny phy );
}