Package org.forester.protein
Interface Protein
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- All Known Implementing Classes:
BasicProtein
public interface Protein
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
addProteinDomain(Domain protein_domain)
boolean
contains(java.util.List<java.lang.String> domains, boolean in_nc_order)
If in_nc_order is set to true, this should return true only and only if the order in List 'domains' and this protein (as determined by the start positions of the domains of this proteins, _not_ by their index) are the same (interspersing, 'other', domains in this are ignored).java.lang.String
getAccession()
java.lang.String
getDescription()
java.util.List<Domain>
getDomainsSortedByPosition()
int
getLength()
java.lang.String
getName()
int
getNumberOfProteinDomains()
Domain
getProteinDomain(int index)
int
getProteinDomainCount(java.lang.String domain_id)
java.util.List<Domain>
getProteinDomains()
java.util.List<Domain>
getProteinDomains(java.lang.String domain_id)
ProteinId
getProteinId()
Species
getSpecies()
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Method Detail
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addProteinDomain
void addProteinDomain(Domain protein_domain)
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contains
boolean contains(java.util.List<java.lang.String> domains, boolean in_nc_order)
If in_nc_order is set to true, this should return true only and only if the order in List 'domains' and this protein (as determined by the start positions of the domains of this proteins, _not_ by their index) are the same (interspersing, 'other', domains in this are ignored). If in_nc_order is set to false, this should return true only and only if this contains all domains listed in 'domains' (order and count do not matter).- Parameters:
domains
- a list of domain ids in a certain order.in_nc_order
- to consider order- Returns:
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getAccession
java.lang.String getAccession()
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getDescription
java.lang.String getDescription()
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getName
java.lang.String getName()
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getNumberOfProteinDomains
int getNumberOfProteinDomains()
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getProteinDomain
Domain getProteinDomain(int index)
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getProteinDomainCount
int getProteinDomainCount(java.lang.String domain_id)
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getProteinDomains
java.util.List<Domain> getProteinDomains()
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getProteinDomains
java.util.List<Domain> getProteinDomains(java.lang.String domain_id)
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getProteinId
ProteinId getProteinId()
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getLength
int getLength()
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getSpecies
Species getSpecies()
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getDomainsSortedByPosition
java.util.List<Domain> getDomainsSortedByPosition()
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