Modifier and Type | Field and Description |
---|---|
static java.util.Comparator<Domain> |
DomainMidPositionComparator |
Constructor and Description |
---|
BasicProtein(java.lang.String id_str,
java.lang.String species_str,
int length) |
Modifier and Type | Method and Description |
---|---|
void |
addProteinDomain(Domain protein_domain) |
boolean |
contains(java.util.List<java.lang.String> query_domain_ids,
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() |
void |
setAccession(java.lang.String accession) |
void |
setDescription(java.lang.String description) |
void |
setName(java.lang.String name) |
java.lang.String |
toDomainArchitectureString(java.lang.String separator) |
java.lang.String |
toDomainArchitectureString(java.lang.String separator,
int repeats_limit,
java.lang.String repeat_separator) |
java.lang.String |
toString() |
public static java.util.Comparator<Domain> DomainMidPositionComparator
public BasicProtein(java.lang.String id_str, java.lang.String species_str, int length)
public void addProteinDomain(Domain protein_domain)
addProteinDomain
in interface Protein
public boolean contains(java.util.List<java.lang.String> query_domain_ids, boolean in_nc_order)
Protein
public java.lang.String getAccession()
getAccession
in interface Protein
public java.lang.String getDescription()
getDescription
in interface Protein
public java.util.List<Domain> getDomainsSortedByPosition()
getDomainsSortedByPosition
in interface Protein
public int getNumberOfProteinDomains()
getNumberOfProteinDomains
in interface Protein
public Domain getProteinDomain(int index)
getProteinDomain
in interface Protein
public int getProteinDomainCount(java.lang.String domain_id)
getProteinDomainCount
in interface Protein
public java.util.List<Domain> getProteinDomains()
getProteinDomains
in interface Protein
public java.util.List<Domain> getProteinDomains(java.lang.String domain_id)
getProteinDomains
in interface Protein
public ProteinId getProteinId()
getProteinId
in interface Protein
public Species getSpecies()
getSpecies
in interface Protein
public void setAccession(java.lang.String accession)
public void setDescription(java.lang.String description)
public void setName(java.lang.String name)
public java.lang.String toDomainArchitectureString(java.lang.String separator)
public java.lang.String toDomainArchitectureString(java.lang.String separator, int repeats_limit, java.lang.String repeat_separator)
public java.lang.String toString()
toString
in class java.lang.Object