org.forester.protein
Interface Protein

All Known Implementing Classes:

BasicProtein

public interface Protein

Method Summary

void	addProteinDomain(Domain protein_domain)
boolean	contains(java.util.List<DomainId> 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()
int	getLength()
java.lang.String	getName()
int	getNumberOfProteinDomains()
Domain	getProteinDomain(int index)
int	getProteinDomainCount(DomainId domain_id)
java.util.List<Domain>	getProteinDomains()
java.util.List<Domain>	getProteinDomains(DomainId domain_id)
ProteinId	getProteinId()
Species	getSpecies()

Method Detail

addProteinDomain

void addProteinDomain(Domain protein_domain)

contains

boolean contains(java.util.List<DomainId> 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:

getAccession

java.lang.String getAccession()

getDescription

java.lang.String getDescription()

getName

java.lang.String getName()

getNumberOfProteinDomains

int getNumberOfProteinDomains()

getProteinDomain

Domain getProteinDomain(int index)

getProteinDomainCount

int getProteinDomainCount(DomainId domain_id)

getProteinDomains

java.util.List<Domain> getProteinDomains()

getProteinDomains

java.util.List<Domain> getProteinDomains(DomainId domain_id)

getProteinId

ProteinId getProteinId()

getLength

int getLength()

getSpecies

Species getSpecies()