org.forester.surfacing
Class BasicProtein
java.lang.Object
org.forester.surfacing.BasicProtein
- All Implemented Interfaces:
- Protein
public class BasicProtein
- extends Object
- implements Protein
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
BasicProtein
public BasicProtein(String id_str,
String species_str)
addProteinDomain
public void addProteinDomain(Domain protein_domain)
- Specified by:
addProteinDomain
in interface Protein
contains
public boolean contains(List<DomainId> query_domain_ids,
boolean in_nc_order)
- Description copied from interface:
Protein
- 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).
- Specified by:
contains
in interface Protein
- Parameters:
query_domain_ids
- a list of domain ids in a certain order.in_nc_order
- to consider order
- Returns:
getAccession
public String getAccession()
- Specified by:
getAccession
in interface Protein
getDescription
public String getDescription()
- Specified by:
getDescription
in interface Protein
getName
public String getName()
- Specified by:
getName
in interface Protein
getNumberOfProteinDomains
public int getNumberOfProteinDomains()
- Specified by:
getNumberOfProteinDomains
in interface Protein
getProteinDomain
public Domain getProteinDomain(int index)
- Specified by:
getProteinDomain
in interface Protein
getProteinDomainCount
public int getProteinDomainCount(DomainId domain_id)
- Specified by:
getProteinDomainCount
in interface Protein
getProteinDomains
public List<Domain> getProteinDomains()
- Specified by:
getProteinDomains
in interface Protein
getProteinDomains
public List<Domain> getProteinDomains(DomainId domain_id)
- Specified by:
getProteinDomains
in interface Protein
getProteinId
public ProteinId getProteinId()
- Specified by:
getProteinId
in interface Protein
getSpecies
public Species getSpecies()
- Specified by:
getSpecies
in interface Protein
setAccession
public void setAccession(String accession)
setDescription
public void setDescription(String description)
setName
public void setName(String name)