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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.

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