HomologyType (JEnsembl: A Java API for Ensembl Data Access 1.78 API)

java.lang.Object
- uk.ac.roslin.ensembl.config.EnsemblType
- - uk.ac.roslin.ensembl.model.relationship.RelationshipType
  - - uk.ac.roslin.ensembl.model.compara.HomologyType

All Implemented Interfaces:

Serializable, ObjectType
```
public class HomologyType
extends RelationshipType
```
See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static HomologyType`	`ALT_ALLELE` Ensembl pipeline annotates alt_allele
`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`	`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`	`GENE_SPLIT` Ensembl pipeline annotates gene_split
`static HomologyType`	`HOMOEOLOG_MANY2MANY` orthology relationships between the component genomes - eg in hexaploid wheat Ensembl pipeline annotates as homoeolog_many2many see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
`static HomologyType`	`HOMOEOLOG_ONE2MANY` orthology relationships between the component genomes - eg in hexaploid wheat Ensembl pipeline annotates as homoeolog_one2many see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
`static HomologyType`	`HOMOEOLOG_ONE2ONE` orthology relationships between the component genomes - eg in hexaploid wheat Ensembl pipeline annotates as homoeolog_one2one 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`	`PROJECTION_ALTERED` relationship between genes on a human chromosome assembly and an assembly patch
`static HomologyType`	`PROJECTION_UNCHANGED` relationship between genes on a human chromosome assembly and an assembly patch
`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`	`UNKNOWN_HOMOLOGY_TYPE` a catch all
`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

Methods
Modifier and Type	Method and Description
`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
  - 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
  - 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
  - GENE_SPLIT
```
public static final HomologyType GENE_SPLIT
```
    Ensembl pipeline annotates gene_split
  - ALT_ALLELE
```
public static final HomologyType ALT_ALLELE
```
    Ensembl pipeline annotates alt_allele
  - HOMOEOLOG_ONE2ONE
```
public static final HomologyType HOMOEOLOG_ONE2ONE
```
    orthology relationships between the component genomes - eg in hexaploid wheat Ensembl pipeline annotates as homoeolog_one2one see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
  - HOMOEOLOG_ONE2MANY
```
public static final HomologyType HOMOEOLOG_ONE2MANY
```
    orthology relationships between the component genomes - eg in hexaploid wheat Ensembl pipeline annotates as homoeolog_one2many see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
  - HOMOEOLOG_MANY2MANY
```
public static final HomologyType HOMOEOLOG_MANY2MANY
```
    orthology relationships between the component genomes - eg in hexaploid wheat Ensembl pipeline annotates as homoeolog_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
  - 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
  - PROJECTION_UNCHANGED
```
public static final HomologyType PROJECTION_UNCHANGED
```
    relationship between genes on a human chromosome assembly and an assembly patch
  - PROJECTION_ALTERED
```
public static final HomologyType PROJECTION_ALTERED
```
    relationship between genes on a human chromosome assembly and an assembly patch
  - UNKNOWN_HOMOLOGY_TYPE
```
public static final HomologyType UNKNOWN_HOMOLOGY_TYPE
```
    a catch all
- 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()
```

Class HomologyType

Field Summary

Fields inherited from class uk.ac.roslin.ensembl.model.relationship.RelationshipType

Fields inherited from class uk.ac.roslin.ensembl.config.EnsemblType

Method Summary

Methods inherited from class uk.ac.roslin.ensembl.model.relationship.RelationshipType

Methods inherited from class uk.ac.roslin.ensembl.config.EnsemblType

Methods inherited from class java.lang.Object

Field Detail

ORTHOLOG_ONE2ONE

ORTHOLOG_ONE2MANY

ORTHOLOG_MANY2MANY

WITHIN_SPECIES_PARALOG

OTHER_PARALOG

GENE_SPLIT

ALT_ALLELE

HOMOEOLOG_ONE2ONE

HOMOEOLOG_ONE2MANY

HOMOEOLOG_MANY2MANY

APPARENT_ORTHOLOG_ONE2ONE

POSSIBLE_ORTHOLOG

CONTIGUOUS_GENE_SPLIT

PUTATIVE_GENE_SPLIT

PROJECTION_UNCHANGED

PROJECTION_ALTERED

UNKNOWN_HOMOLOGY_TYPE

Method Detail

getHomologyTypeByName

getRelationshipType

getAllTypes