GeneSetDao (Gemma 1.31.4-SNAPSHOT API)

All Superinterfaces:

BaseDao<GeneSet>, BaseVoEnabledDao<GeneSet,DatabaseBackedGeneSetValueObject>

All Known Implementing Classes:

GeneSetDaoImpl
```
@ParametersAreNonnullByDefault
public interface GeneSetDao
extends BaseVoEnabledDao<GeneSet,DatabaseBackedGeneSetValueObject>
```
The interface for managing groupings of genes.

Author:

kelsey

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`Collection<GeneSet>`	`findByGene(Gene gene)`
`Collection<GeneSet>`	`findByName(String name)`
`Collection<GeneSet>`	`findByName(String name, Taxon taxon)`
`int`	`getGeneCount(Long id)`	This method does not do any permissions filtering.
`List<Taxon>`	`getTaxa(GeneSet geneSet)`	Return all the taxa of the gene set members.
`Taxon`	`getTaxon(GeneSet geneSet)`	Returns the taxon of an arbitrary member of the set.
`Collection<GeneSet>`	`loadAll(Taxon tax)`
`DatabaseBackedGeneSetValueObject`	`loadValueObjectByIdLite(Long id)`
`List<DatabaseBackedGeneSetValueObject>`	`loadValueObjectsByIdsLite(Collection<Long> geneSetIds)`
`int`	`removeAll()`
`void`	`thaw(GeneSet geneSet)`

Methods inherited from interface ubic.gemma.persistence.service.BaseDao
countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao
loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Method Detail

getGeneCount
```
int getGeneCount(Long id)
```
This method does not do any permissions filtering. It assumes that id the user can see the set, they can see all the members.

Parameters:

id - gene set id

Returns:

integer count of genes in set

getTaxon
```
@Nullable
Taxon getTaxon(GeneSet geneSet)
```
Returns the taxon of an arbitrary member of the set.

Returns:

the taxon, or null if the gene set does not have any member

getTaxa
```
List<Taxon> getTaxa(GeneSet geneSet)
```
Return all the taxa of the gene set members.

loadValueObjectByIdLite

DatabaseBackedGeneSetValueObject loadValueObjectByIdLite(Long id)

loadValueObjectsByIdsLite

List<DatabaseBackedGeneSetValueObject> loadValueObjectsByIdsLite(Collection<Long> geneSetIds)

findByGene

Collection<GeneSet> findByGene(Gene gene)

findByName
```
Collection<GeneSet> findByName(String name)
```
Parameters:

name - uses the given name to do a name* search in the db

Returns:

a collection of geneSets that match the given search term.

findByName

Collection<GeneSet> findByName(String name,
                               @Nullable
                               Taxon taxon)

loadAll

Collection<GeneSet> loadAll(@Nullable
                            Taxon tax)

thaw
```
void thaw(GeneSet geneSet)
```
Parameters:

geneSet - gene set

removeAll
```
int removeAll()
```