org.forester.protein

Class BasicProtein

java.lang.Object

org.forester.protein.BasicProtein

All Implemented Interfaces:

Protein

public class BasicProtein
extends Object
implements Protein

Field Summary

Fields

Modifier and Type	Field and Description
static Comparator<Domain>	DomainMidPositionComparator

Constructor Summary

Constructors

Constructor and Description
BasicProtein(String id_str, String species_str, int length)

Method Summary

Modifier and Type	Method and Description
void	addProteinDomain(Domain protein_domain)
boolean	contains(List<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).
String	getAccession()
String	getDescription()
List<Domain>	getDomainsSortedByPosition()
int	getLength()
String	getName()
int	getNumberOfProteinDomains()
Domain	getProteinDomain(int index)
int	getProteinDomainCount(String domain_id)
List<Domain>	getProteinDomains()
List<Domain>	getProteinDomains(String domain_id)
ProteinId	getProteinId()
Species	getSpecies()
void	setAccession(String accession)
void	setDescription(String description)
void	setName(String name)
String	toDomainArchitectureString(String separator)
String	toDomainArchitectureString(String separator, int repeats_limit, String repeat_separator)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

DomainMidPositionComparator

public static Comparator<Domain> DomainMidPositionComparator

Constructor Detail

BasicProtein

public BasicProtein(String id_str,
                    String species_str,
                    int length)

Method Detail

addProteinDomain

public void addProteinDomain(Domain protein_domain)

Specified by:

addProteinDomain in interface Protein

contains

public boolean contains(List<String> 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

getDomainsSortedByPosition

public List<Domain> getDomainsSortedByPosition()

Specified by:

getDomainsSortedByPosition in interface Protein

getLength

public int getLength()

Specified by:

getLength 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(String domain_id)

Specified by:

getProteinDomainCount in interface Protein

getProteinDomains

public List<Domain> getProteinDomains()

Specified by:

getProteinDomains in interface Protein

getProteinDomains

public List<Domain> getProteinDomains(String 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)

toDomainArchitectureString

public String toDomainArchitectureString(String separator)

toDomainArchitectureString

public String toDomainArchitectureString(String separator,
                                         int repeats_limit,
                                         String repeat_separator)

toString

public String toString()

Overrides:

toString in class Object