Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Model
v1.09

uk.ac.roslin.ensembl.model.compara
Class HomologyType

java.lang.Object
  extended by uk.ac.roslin.ensembl.config.EnsemblType
      extended by uk.ac.roslin.ensembl.model.relationship.RelationshipType
          extended by uk.ac.roslin.ensembl.model.compara.HomologyType
All Implemented Interfaces:
Serializable, ObjectType

public class HomologyType
extends RelationshipType

See Also:
Serialized Form

Field Summary
static HomologyType APPARENT_ORTHOLOG_ONE2ONE
          two homologous objects derived by speciation Ensembl pipeline annotates as apparent_ortholog_one2one see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
static HomologyType BETWEEN_SPECIES_PARALOG
          two homologous objects derived by duplication Ensembl pipeline annotates as between_species_paralog see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
static HomologyType CONTIGUOUS_GENE_SPLIT
          two homologous objects derived by duplication Ensembl pipeline annotates as contiguous_gene_split see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
static HomologyType ORTHOLOG_MANY2MANY
          two homologous objects derived by speciation Ensembl pipeline annotates as ortholog_many2many see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
static HomologyType ORTHOLOG_ONE2MANY
          two homologous objects derived by speciation Ensembl pipeline annotates as ortholog_one2many see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
static HomologyType ORTHOLOG_ONE2ONE
          two homologous objects derived by speciation Ensembl pipeline annotates as ortholog_one2one see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
static HomologyType OTHER_PARALOG
          two homologous objects derived by duplication Ensembl pipeline annotates as other_paralog see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
static HomologyType POSSIBLE_ORTHOLOG
          two homologous objects derived by speciation Ensembl pipeline annotates as possible_ortholog see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
static HomologyType PUTATIVE_GENE_SPLIT
          two homologous objects derived by duplication Ensembl pipeline annotates as putative_gene_split see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
static HomologyType WITHIN_SPECIES_PARALOG
          two homologous objects derived by duplication Ensembl pipeline annotates as within_species_paralog see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
 
Fields inherited from class uk.ac.roslin.ensembl.model.relationship.RelationshipType
UNKNOWN
 
Fields inherited from class uk.ac.roslin.ensembl.config.EnsemblType
label
 
Method Summary
static Collection<HomologyType> getAllTypes()
           
static HomologyType getHomologyTypeByName(String typeName)
          Checks to see if the supplied type is the name of a valid HomologyType and returns the corresponding HomologyType object if it is.
static HomologyType getRelationshipType(String value)
           
 
Methods inherited from class uk.ac.roslin.ensembl.model.relationship.RelationshipType
equals, hashCode
 
Methods inherited from class uk.ac.roslin.ensembl.config.EnsemblType
toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
 

Field Detail

ORTHOLOG_ONE2ONE

public static final HomologyType ORTHOLOG_ONE2ONE
two homologous objects derived by speciation Ensembl pipeline annotates as ortholog_one2one see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html


ORTHOLOG_ONE2MANY

public static final HomologyType ORTHOLOG_ONE2MANY
two homologous objects derived by speciation Ensembl pipeline annotates as ortholog_one2many see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html


ORTHOLOG_MANY2MANY

public static final HomologyType ORTHOLOG_MANY2MANY
two homologous objects derived by speciation Ensembl pipeline annotates as ortholog_many2many see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html


APPARENT_ORTHOLOG_ONE2ONE

public static final HomologyType APPARENT_ORTHOLOG_ONE2ONE
two homologous objects derived by speciation Ensembl pipeline annotates as apparent_ortholog_one2one see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html


POSSIBLE_ORTHOLOG

public static final HomologyType POSSIBLE_ORTHOLOG
two homologous objects derived by speciation Ensembl pipeline annotates as possible_ortholog see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html


WITHIN_SPECIES_PARALOG

public static final HomologyType WITHIN_SPECIES_PARALOG
two homologous objects derived by duplication Ensembl pipeline annotates as within_species_paralog see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html


BETWEEN_SPECIES_PARALOG

public static final HomologyType BETWEEN_SPECIES_PARALOG
two homologous objects derived by duplication Ensembl pipeline annotates as between_species_paralog see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html


OTHER_PARALOG

public static final HomologyType OTHER_PARALOG
two homologous objects derived by duplication Ensembl pipeline annotates as other_paralog see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html


CONTIGUOUS_GENE_SPLIT

public static final HomologyType CONTIGUOUS_GENE_SPLIT
two homologous objects derived by duplication Ensembl pipeline annotates as contiguous_gene_split see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html


PUTATIVE_GENE_SPLIT

public static final HomologyType PUTATIVE_GENE_SPLIT
two homologous objects derived by duplication Ensembl pipeline annotates as putative_gene_split see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html

Method Detail

getHomologyTypeByName

public static final HomologyType getHomologyTypeByName(String typeName)
Checks to see if the supplied type is the name of a valid HomologyType and returns the corresponding HomologyType object if it is.

Parameters:
typeName -
Returns:
HomologyType - the HomologyType object corresponding to the name supplied

getRelationshipType

public static HomologyType getRelationshipType(String value)

getAllTypes

public static Collection<HomologyType> getAllTypes()

Ensembl Model
v1.09

Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3