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

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

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

public static final String TAXONID

See Also:

Constant Field Values

LOCUSID

public static final String LOCUSID

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Constant Field Values

HOMOID

public static final String HOMOID

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Constant Field Values

ACCESSION

public static final String ACCESSION

See Also:

Constant Field Values

SIMILARITYTYPE

public static final String SIMILARITYTYPE

See Also:

Constant Field Values

PERCENTIDENTITY

public static final String PERCENTIDENTITY

See Also:

Constant Field Values

REFERENCE

public static final String REFERENCE

See Also:

Constant Field Values

TWIN

public static final String TWIN

See Also:

Constant Field Values

MULTIPLE

public static final String MULTIPLE

See Also:

Constant Field Values

CURATED

public static final String CURATED

See Also:

Constant Field Values

Method Detail

startDB

public void startDB()

indicates start of data for a HomologeneDB

startGroup

public void startGroup()

indicates start of data for a OrthoPairSet

startOrthoPair

public void startOrthoPair()

indicates start of data for an OrthoPair

startOrthologue

public void startOrthologue()

indicates start of data for an orthologue

addOrthologueProperty

public void addOrthologueProperty(String key,
                                  String value)

add a property to the current Orthologue

endOrthologue

public void endOrthologue()

end of data for this Orthologue

addOrthoPairProperty

public void addOrthoPairProperty(String key,
                                 String value)

add a property to the current OrthoPair

endOrthoPair

public void endOrthoPair()

end of data for this OrthoPair

addTitle

public 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

public void endGroup()

end of data for group

endDB

public void endDB()

end of data for DB

getDB

public HomologeneDB getDB()

retrieve the DB that has just been built