org.forester.surfacing
Class BasicGenomeWideCombinableDomains
java.lang.Object
org.forester.surfacing.BasicGenomeWideCombinableDomains
- All Implemented Interfaces:
- GenomeWideCombinableDomains
public class BasicGenomeWideCombinableDomains
- extends Object
- implements GenomeWideCombinableDomains
Method Summary |
boolean |
contains(DomainId key_id)
|
static BasicGenomeWideCombinableDomains |
createInstance(List<Protein> protein_list,
boolean ignore_combination_with_same_domain,
Species species)
|
static BasicGenomeWideCombinableDomains |
createInstance(List<Protein> protein_list,
boolean ignore_combination_with_same_domain,
Species species,
BinaryDomainCombination.DomainCombinationType dc_type)
|
static BasicGenomeWideCombinableDomains |
createInstance(List<Protein> protein_list,
boolean ignore_combination_with_same_domain,
Species species,
Map<DomainId,List<GoId>> domain_id_to_go_ids_map,
BinaryDomainCombination.DomainCombinationType dc_type)
|
CombinableDomains |
get(DomainId key_id)
|
SortedMap<DomainId,CombinableDomains> |
getAllCombinableDomainsIds()
|
SortedSet<DomainId> |
getAllDomainIds()
This should return all domains ids present in the genome. |
BinaryDomainCombination.DomainCombinationType |
getDomainCombinationType()
|
SortedSet<DomainId> |
getMostPromiscuosDomain()
|
DescriptiveStatistics |
getPerGenomeDomainPromiscuityStatistics()
This should return a statistic for per domain
promiscuity in a genome. |
int |
getSize()
|
Species |
getSpecies()
|
SortedSet<BinaryDomainCombination> |
toBinaryDomainCombinations()
This should return all binary domain combinations present in the genome. |
String |
toString()
|
StringBuilder |
toStringBuilder(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder sort_order)
|
contains
public boolean contains(DomainId key_id)
- Specified by:
contains
in interface GenomeWideCombinableDomains
get
public CombinableDomains get(DomainId key_id)
- Specified by:
get
in interface GenomeWideCombinableDomains
getAllCombinableDomainsIds
public SortedMap<DomainId,CombinableDomains> getAllCombinableDomainsIds()
- Specified by:
getAllCombinableDomainsIds
in interface GenomeWideCombinableDomains
getAllDomainIds
public SortedSet<DomainId> getAllDomainIds()
- Description copied from interface:
GenomeWideCombinableDomains
- This should return all domains ids present in the genome.
- Specified by:
getAllDomainIds
in interface GenomeWideCombinableDomains
- Returns:
- a sorted set of domains ids
getDomainCombinationType
public BinaryDomainCombination.DomainCombinationType getDomainCombinationType()
- Specified by:
getDomainCombinationType
in interface GenomeWideCombinableDomains
getMostPromiscuosDomain
public SortedSet<DomainId> getMostPromiscuosDomain()
- Specified by:
getMostPromiscuosDomain
in interface GenomeWideCombinableDomains
getPerGenomeDomainPromiscuityStatistics
public DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics()
- Description copied from interface:
GenomeWideCombinableDomains
- This should return a statistic for per domain
promiscuity in a genome.
- Specified by:
getPerGenomeDomainPromiscuityStatistics
in interface GenomeWideCombinableDomains
- Returns:
- descriptive statistics for per domain promiscuity in a genome
getSize
public int getSize()
- Specified by:
getSize
in interface GenomeWideCombinableDomains
getSpecies
public Species getSpecies()
- Specified by:
getSpecies
in interface GenomeWideCombinableDomains
toBinaryDomainCombinations
public SortedSet<BinaryDomainCombination> toBinaryDomainCombinations()
- Description copied from interface:
GenomeWideCombinableDomains
- This should return all binary domain combinations present in the genome.
- Specified by:
toBinaryDomainCombinations
in interface GenomeWideCombinableDomains
- Returns:
- a sorted set of binary domain combinations
toString
public String toString()
- Overrides:
toString
in class Object
toStringBuilder
public StringBuilder toStringBuilder(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder sort_order)
- Specified by:
toStringBuilder
in interface GenomeWideCombinableDomains
createInstance
public static BasicGenomeWideCombinableDomains createInstance(List<Protein> protein_list,
boolean ignore_combination_with_same_domain,
Species species)
createInstance
public static BasicGenomeWideCombinableDomains createInstance(List<Protein> protein_list,
boolean ignore_combination_with_same_domain,
Species species,
BinaryDomainCombination.DomainCombinationType dc_type)
createInstance
public static BasicGenomeWideCombinableDomains createInstance(List<Protein> protein_list,
boolean ignore_combination_with_same_domain,
Species species,
Map<DomainId,List<GoId>> domain_id_to_go_ids_map,
BinaryDomainCombination.DomainCombinationType dc_type)