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