Package org.biojava.bio.program.homologene

Interface HomologeneBuilder

All Known Implementing Classes:

SimpleHomologeneBuilder

public interface HomologeneBuilder

an interface for Homologene dataset Builders

Author:

David Huen

Field Summary

Fields

Modifier and Type	Field	Description
static String	ACCESSION
static String	CURATED
static String	HOMOID
static String	LOCUSID
static String	MULTIPLE
static String	PERCENTIDENTITY
static String	REFERENCE
static String	SIMILARITYTYPE
static String	TAXONID
static String	TWIN

Method Summary

Modifier and Type	Method	Description
void	addOrthologueProperty(String key, String value)	add a property to the current Orthologue
void	addOrthoPairProperty(String key, String value)	add a property to the current OrthoPair
void	addTitle(int taxonID, String homologeneID, String title)	add title information to an Orthologue (this is not in enclosed in the Orthologue element because it comes completely separate in the Homologene data files.
void	endDB()	end of data for DB
void	endGroup()	end of data for group
void	endOrthologue()	end of data for this Orthologue
void	endOrthoPair()	end of data for this OrthoPair
HomologeneDB	getDB()	retrieve the DB that has just been built
void	startDB()	indicates start of data for a HomologeneDB
void	startGroup()	indicates start of data for a OrthoPairSet
void	startOrthologue()	indicates start of data for an orthologue
void	startOrthoPair()	indicates start of data for an OrthoPair

Field Detail

TAXONID

static final String TAXONID

See Also:

Constant Field Values

LOCUSID

static final String LOCUSID

See Also:

Constant Field Values

HOMOID

static final String HOMOID

See Also:

Constant Field Values

ACCESSION

static final String ACCESSION

See Also:

Constant Field Values

SIMILARITYTYPE

static final String SIMILARITYTYPE

See Also:

Constant Field Values

PERCENTIDENTITY

static final String PERCENTIDENTITY

See Also:

Constant Field Values

REFERENCE

static final String REFERENCE

See Also:

Constant Field Values

TWIN

static final String TWIN

See Also:

Constant Field Values

MULTIPLE

static final String MULTIPLE

See Also:

Constant Field Values

CURATED

static final String CURATED

See Also:

Constant Field Values

Method Detail

startDB

void startDB()

indicates start of data for a HomologeneDB

startGroup

void startGroup()

indicates start of data for a OrthoPairSet

startOrthoPair

void startOrthoPair()

indicates start of data for an OrthoPair

startOrthologue

void startOrthologue()

indicates start of data for an orthologue

addOrthologueProperty

void addOrthologueProperty(String key,
                           String value)

add a property to the current Orthologue

endOrthologue

void endOrthologue()

end of data for this Orthologue

addOrthoPairProperty

void addOrthoPairProperty(String key,
                          String value)

add a property to the current OrthoPair

endOrthoPair

void endOrthoPair()

end of data for this OrthoPair

addTitle

void addTitle(int taxonID,
              String homologeneID,
              String title)

add title information to an Orthologue (this is not in enclosed in the Orthologue element because it comes completely separate in the Homologene data files. Go figger.)

endGroup

void endGroup()

end of data for group

endDB

void endDB()

end of data for DB

getDB

HomologeneDB getDB()

retrieve the DB that has just been built