// 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.List;
+import java.util.Set;
import java.util.SortedMap;
import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
import org.forester.species.Species;
-import org.forester.util.DescriptiveStatistics;
public interface CombinableDomains {
*
* @param protein_domain
*/
- public void addCombinableDomain( final DomainId protein_domain );
+ public void addCombinableDomain( final String protein_domain );
/**
*
*
* @return all domains
*/
- List<DomainId> getAllDomains();
+ List<String> getAllDomains();
- List<DomainId> getCombinableDomains();
+ List<String> getCombinableDomains();
/**
* Returns the combinable domain identifiers sorted in alphabetical manner: -
*
* @return combining domain identifiers sorted in alphabetical manner
*/
- public SortedMap<DomainId, Integer> getCombinableDomainsIds();
+ public SortedMap<String, Integer> getCombinableDomainsIds();
public StringBuilder getCombiningDomainIdsAsStringBuilder();
*
* @return the domain identifier
*/
- 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();
/**
* Returns how many times the key domain is present in a given species
*/
public int getKeyDomainProteinsCount();
+ public Set<String> getKeyDomainProteins();
+
public int getNumberOfCombinableDomains();
- public int getNumberOfProteinsExhibitingCombination( final DomainId protein_domain );
+ public int getNumberOfProteinsExhibitingCombination( final String protein_domain );
/**
* Returns the species of this combinable domains.
*/
public Species getSpecies();
- public boolean isCombinable( final DomainId protein_domain );
-
- /**
- * This is to set descriptive statistics for the confidence (i.e. E-values)
- * of the key domain.
- *
- *
- * @param statistics
- */
- void setKeyDomainConfidenceDescriptiveStatistics( final DescriptiveStatistics statistics );
+ public boolean isCombinable( final String protein_domain );
/**
* Sets how many times the key domain is present in a given species genome.
*/
void setKeyDomainCount( final int key_domain_count );
- /**
- * 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();
+
+ void addKeyDomainProtein( String protein );
}
\ No newline at end of file