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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
surfacing
/
CombinableDomains.java
diff --git
a/forester/java/src/org/forester/surfacing/CombinableDomains.java
b/forester/java/src/org/forester/surfacing/CombinableDomains.java
index
d90eed4
..
028810e
100644
(file)
--- a/
forester/java/src/org/forester/surfacing/CombinableDomains.java
+++ b/
forester/java/src/org/forester/surfacing/CombinableDomains.java
@@
-22,17
+22,16
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// 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;
package org.forester.surfacing;
import java.util.List;
+import java.util.Set;
import java.util.SortedMap;
import org.forester.protein.BinaryDomainCombination;
import java.util.SortedMap;
import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
import org.forester.species.Species;
import org.forester.species.Species;
-import org.forester.util.DescriptiveStatistics;
public interface CombinableDomains {
public interface CombinableDomains {
@@
-41,7
+40,7
@@
public interface CombinableDomains {
*
* @param protein_domain
*/
*
* @param protein_domain
*/
- public void addCombinableDomain( final DomainId protein_domain );
+ public void addCombinableDomain( final String protein_domain );
/**
*
/**
*
@@
-50,9
+49,9
@@
public interface CombinableDomains {
*
* @return all domains
*/
*
* @return all domains
*/
- List<DomainId> getAllDomains();
+ List<String> getAllDomains();
- List<DomainId> getCombinableDomains();
+ List<String> getCombinableDomains();
/**
* Returns the combinable domain identifiers sorted in alphabetical manner: -
/**
* Returns the combinable domain identifiers sorted in alphabetical manner: -
@@
-61,7
+60,7
@@
public interface CombinableDomains {
*
* @return combining 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();
public StringBuilder getCombiningDomainIdsAsStringBuilder();
@@
-71,16
+70,7
@@
public interface CombinableDomains {
*
* @return the domain identifier
*/
*
* @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
/**
* Returns how many times the key domain is present in a given species
@@
-98,9
+88,11
@@
public interface CombinableDomains {
*/
public int getKeyDomainProteinsCount();
*/
public int getKeyDomainProteinsCount();
+ public Set<String> getKeyDomainProteins();
+
public int getNumberOfCombinableDomains();
public int getNumberOfCombinableDomains();
- public int getNumberOfProteinsExhibitingCombination( final DomainId protein_domain );
+ public int getNumberOfProteinsExhibitingCombination( final String protein_domain );
/**
* Returns the species of this combinable domains.
/**
* Returns the species of this combinable domains.
@@
-109,16
+101,7
@@
public interface CombinableDomains {
*/
public Species getSpecies();
*/
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.
/**
* Sets how many times the key domain is present in a given species genome.
@@
-128,14
+111,7
@@
public interface CombinableDomains {
*/
void setKeyDomainCount( final int key_domain_count );
*/
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();
public List<BinaryDomainCombination> toBinaryDomainCombinations();
+
+ void addKeyDomainProtein( String protein );
}
\ No newline at end of file
}
\ No newline at end of file