A C D E G H M N O S V W

G

Gene - Class in sbc.orthoxml

Represent a gene or better molecule in the context of orthology assignments.

Gene(Species, Database) - Constructor for class sbc.orthoxml.Gene

Creates a Gene object from the given database and species

getChildren() - Method in class sbc.orthoxml.Group

Returns the children (nested groups) of the group.

getDatabase() - Method in class sbc.orthoxml.Gene

Returns the database the gene stems from.

getDefinedScores() - Method in class sbc.orthoxml.Scoreable

Return all scores that are defined for this object.

getDescription() - Method in class sbc.orthoxml.ScoreDefinition

Returns the score description.

getGene() - Method in class sbc.orthoxml.Membership

Returns the gene that this membership stands for.

getGeneIdentifier() - Method in class sbc.orthoxml.Gene

Returns the gene identifier

getGeneLink() - Method in class sbc.orthoxml.Database

Returns the link to the gene in the database how this link is create is source specific.

getGenes() - Method in class sbc.orthoxml.Group

Convenience method to get all genes that are a member of the group without the membership nesting.

getId() - Method in class sbc.orthoxml.Group

Returns the id of the group.

getId() - Method in class sbc.orthoxml.ScoreDefinition

Returns the score identifier.

getMembers() - Method in class sbc.orthoxml.Group

Returns the genes that a member of the group nested into Membership objects.

getName() - Method in class sbc.orthoxml.Database

The name of the database

getName() - Method in class sbc.orthoxml.Species

Returns the name of the species.

getNcbiTaxId() - Method in class sbc.orthoxml.Species

Returns the NCBI taxonomy identifier of the species

getNestedGenes() - Method in class sbc.orthoxml.Group

Convenience method to get all gene in the group and in groups that are nested into the group.

getNestedMembers() - Method in class sbc.orthoxml.Group

Convenience method to get all memberships of the group and of groups that are nested into the group.

getOrigin() - Method in class sbc.orthoxml.io.OrthoXMLReader

Returns the origin of the OrthoXML.

getOriginVersion() - Method in class sbc.orthoxml.io.OrthoXMLReader

Returns the version of the OrthoXML origin.

getParent() - Method in class sbc.orthoxml.Group

Returns the parent of group e.g.

getProperty(String) - Method in class sbc.orthoxml.Group

Returns the value of the property or null if the property has no value or is undefined.

getProteinIdentifier() - Method in class sbc.orthoxml.Gene

Returns the protein identifier

getProtLink() - Method in class sbc.orthoxml.Database

Returns the link to the protein in the database how this link is create is source specific.

getScoreDefinitions() - Method in class sbc.orthoxml.io.OrthoXMLReader

Returns a Map with scores defined in the OrthoXML file.

getScores(ScoreDefinition) - Method in class sbc.orthoxml.Scoreable

Returns the scores for the given type.

getSpecies() - Method in class sbc.orthoxml.Gene

Returns the species the gene stems from.

getSpecies() - Method in class sbc.orthoxml.io.OrthoXMLReader

Returns a list of the species defined in the OrthoXML file.

getTranscriptIdentifier() - Method in class sbc.orthoxml.Gene

Returns the transcript identifier

getTranscriptLink() - Method in class sbc.orthoxml.Database

Returns the link to the transcript in the database how this link is create is source specific.

getType() - Method in class sbc.orthoxml.Group

Returns the type of the group.

getVersion() - Method in class sbc.orthoxml.Database

Returns the version the database;

getVersion() - Method in class sbc.orthoxml.io.OrthoXMLReader

The OrthoXML version.

Group - Class in sbc.orthoxml

The group class represents a group of orthologous or paralogous genes depending on its type.

Group() - Constructor for class sbc.orthoxml.Group

Group.Type - Enum in sbc.orthoxml

The type of a group i.e.