sbc.orthoxml
Class Gene

java.lang.Object
  sbc.orthoxml.Gene

public class Gene
extends java.lang.Object

Represent a gene or better molecule in the context of orthology assignments. Can be identified by a gene, protein and transcript identifier.

Author:

Thomas Schmitt

Constructor Summary

Gene(Species species, Database database)
Creates a Gene object from the given database and species

Method Summary

boolean	equals(java.lang.Object obj)
Database	getDatabase() Returns the database the gene stems from.
java.lang.String	getGeneIdentifier() Returns the gene identifier
java.lang.String	getProteinIdentifier() Returns the protein identifier
Species	getSpecies() Returns the species the gene stems from.
java.lang.String	getTranscriptIdentifier() Returns the transcript identifier
int	hashCode()
void	setDatabase(Database database) Sets the database the gene stems from
void	setGeneIdentifier(java.lang.String geneIdentifier) Sets the gene identifier
void	setProteinIdentifier(java.lang.String proteinIdentifier) Sets the protein identifier
void	setSpecies(Species species) Sets the species the gene stems from.
void	setTranscriptIdentifier(java.lang.String transcriptIdentifier) Sets the transcript identifier

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Gene

public Gene(Species species,
            Database database)

Creates a Gene object from the given database and species

Parameters:

species - the species from which the gene stems

database - the database the gene stems from

Method Detail

getGeneIdentifier

public java.lang.String getGeneIdentifier()

Returns the gene identifier

Returns:

the gene identifier

setGeneIdentifier

public void setGeneIdentifier(java.lang.String geneIdentifier)

Sets the gene identifier

Parameters:

geneIdentifier - the gene identifier to set

getProteinIdentifier

public java.lang.String getProteinIdentifier()

Returns the protein identifier

Returns:

the protein identifier

setProteinIdentifier

public void setProteinIdentifier(java.lang.String proteinIdentifier)

Sets the protein identifier

Parameters:

proteinIdentifier - identifier the protein identifier to set

getTranscriptIdentifier

public java.lang.String getTranscriptIdentifier()

Returns the transcript identifier

Returns:

the transcriptIdentifier

setTranscriptIdentifier

public void setTranscriptIdentifier(java.lang.String transcriptIdentifier)

Sets the transcript identifier

Parameters:

transcriptIdentifier - the transcriptIdentifier to set

getDatabase

public Database getDatabase()

Returns the database the gene stems from.

Returns:

the database

setDatabase

public void setDatabase(Database database)

Sets the database the gene stems from

Parameters:

database - the database to set

getSpecies

public Species getSpecies()

Returns the species the gene stems from.

Returns:

the species

setSpecies

public void setSpecies(Species species)

Sets the species the gene stems from.

Parameters:

species - the species to set

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object