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

S

sbc.orthoxml - package sbc.orthoxml

sbc.orthoxml.io - package sbc.orthoxml.io

Scoreable - Class in sbc.orthoxml

Allows to assign scores to subclasses.

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

ScoreDefinition - Class in sbc.orthoxml

Represent the definition of a score.

ScoreDefinition(String, String) - Constructor for class sbc.orthoxml.ScoreDefinition

Creates a score definition with the given identifier and description.

setChildren(List<Group>) - Method in class sbc.orthoxml.Group

setDatabase(Database) - Method in class sbc.orthoxml.Gene

Sets the database the gene stems from

setGeneIdentifier(String) - Method in class sbc.orthoxml.Gene

Sets the gene identifier

setGeneLink(String) - Method in class sbc.orthoxml.Database

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

setGenes(List<Gene>) - Method in class sbc.orthoxml.Group

Convenience method to set gene members without a score.

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

Sets the id of the group.

setMembers(List<Membership>) - Method in class sbc.orthoxml.Group

Sets the genes that are members of group as Membership objects.

setProperty(String, String) - Method in class sbc.orthoxml.Group

Sets a key-value property.

setProteinIdentifier(String) - Method in class sbc.orthoxml.Gene

Sets the protein identifier

setProtLink(String) - Method in class sbc.orthoxml.Database

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

setSpecies(Species) - Method in class sbc.orthoxml.Gene

Sets the species the gene stems from.

setTranscriptIdentifier(String) - Method in class sbc.orthoxml.Gene

Sets the transcript identifier

setTranscriptLink(String) - Method in class sbc.orthoxml.Database

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

setType(Group.Type) - Method in class sbc.orthoxml.Group

Sets the type of the group.

Species - Class in sbc.orthoxml

Represents a species in the context of orthology assignment.

Species(Integer, String) - Constructor for class sbc.orthoxml.Species

Creates a Species object.