org.forester.surfacing
Interface Protein

All Known Implementing Classes:
BasicProtein

public interface Protein


Method Summary
 void addProteinDomain(Domain protein_domain)
           
 boolean contains(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).
 String getAccession()
           
 String getDescription()
           
 String getName()
           
 int getNumberOfProteinDomains()
           
 Domain getProteinDomain(int index)
           
 int getProteinDomainCount(DomainId domain_id)
           
 List<Domain> getProteinDomains()
           
 List<Domain> getProteinDomains(DomainId domain_id)
           
 ProteinId getProteinId()
           
 Species getSpecies()
           
 

Method Detail

addProteinDomain

void addProteinDomain(Domain protein_domain)

contains

boolean contains(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

String getAccession()

getDescription

String getDescription()

getName

String getName()

getNumberOfProteinDomains

int getNumberOfProteinDomains()

getProteinDomain

Domain getProteinDomain(int index)

getProteinDomainCount

int getProteinDomainCount(DomainId domain_id)

getProteinDomains

List<Domain> getProteinDomains()

getProteinDomains

List<Domain> getProteinDomains(DomainId domain_id)

getProteinId

ProteinId getProteinId()

getSpecies

Species getSpecies()