SpeciesFactory (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.experiment.biology.taxonomy.SpeciesFactory

```
public class SpeciesFactory
extends Object
```
Class related to the handling of species.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`BIOMART_ENSEMBL_FILENAME` The name of the Ensembl BioMart datasets file.
`static String`	`BIOMART_ENSEMBL_GENOME_FILENAME` The name of the Ensembl Genome BioMart datasets file.
`static String`	`ENSEMBL_GENOME_SPECIES` The names of the Ensembl genome species files.
`static String`	`ENSEMBL_SPECIES` The names of the Ensembl species files.
`static String`	`UNIPROT_TAXONOMY_FILENAME` The name of the UniProt taxonomy file.
`static String`	`UNKNOWN` Tag for unknown species.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static File`	`getBiomartEnsemblGenomeMappingFile(String jarFilePath)` Returns the Ensembl Genome BioMart file.
`static File`	`getBiomartEnsemblMappingFile(String jarFilePath)` Returns the Ensembl BioMart file.
`BiomartMapping`	`getBiomartMapping()` Returns the BioMart mapping.
`String`	`getEnsemblAssembly(Integer taxon)` Returns the Ensembl assembly to use for the given taxon.
`String`	`getEnsemblDataset(Integer taxon)` Returns the Ensembl dataset to use for the given taxon.
`HashMap<String,HashSet<Integer>>`	`getEnsembleSpecies()` Returns a map of the species in Ensembl.
`EnsemblGenomesSpecies`	`getEnsemblGenomesSpecies()` Returns the Ensembl genome species mapping.
`static File`	`getEnsemblGenomesSpeciesFile(String jarFilePath)` Returns the Ensembl genome species file.
`EnsemblSpecies`	`getEnsemblSpecies()` Returns the Ensembl species mapping.
`static File`	`getEnsemblSpeciesFile(String jarFilePath)` Returns the Ensembl species file.
`static SpeciesFactory`	`getInstance()` Static method returning the instance of the factory.
`String`	`getLatinName(Integer taxon)` Returns the Latin name of the species corresponding to the given taxon according to the UniProt mapping.
`String`	`getName(Integer taxon)` Returns the name of the species corresponding to the given taxon according to the UniProt mapping.
`static String`	`getSpeciesDescription(HashMap<String,Integer> speciesOccurrence)` Returns a listing of the species occurrence map provided.
`UniprotTaxonomy`	`getUniprotTaxonomy()` Returns the UniProt taxonomy mapping.
`static File`	`getUniprotTaxonomyFile(String jarFilePath)` Returns the UniProt taxonomy file.
`void`	`initiate(String jarFilePath)` Initiates the factory using the files of the static fields.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - UNKNOWN
```
public static final String UNKNOWN
```
    Tag for unknown species.
    
    See Also:
    
    Constant Field Values
  - UNIPROT_TAXONOMY_FILENAME
```
public static final String UNIPROT_TAXONOMY_FILENAME
```
    The name of the UniProt taxonomy file.
    
    See Also:
    
    Constant Field Values
  - ENSEMBL_SPECIES
```
public static final String ENSEMBL_SPECIES
```
    The names of the Ensembl species files.
    
    See Also:
    
    Constant Field Values
  - ENSEMBL_GENOME_SPECIES
```
public static final String ENSEMBL_GENOME_SPECIES
```
    The names of the Ensembl genome species files.
    
    See Also:
    
    Constant Field Values
  - BIOMART_ENSEMBL_FILENAME
```
public static final String BIOMART_ENSEMBL_FILENAME
```
    The name of the Ensembl BioMart datasets file.
    
    See Also:
    
    Constant Field Values
  - BIOMART_ENSEMBL_GENOME_FILENAME
```
public static final String BIOMART_ENSEMBL_GENOME_FILENAME
```
    The name of the Ensembl Genome BioMart datasets file.
    
    See Also:
    
    Constant Field Values
- Method Detail
  - getInstance
```
public static SpeciesFactory getInstance()
```
    Static method returning the instance of the factory.
    
    Returns:
    
    the instance of the factory
  - initiate
```
public void initiate(String jarFilePath)
              throws IOException
```
    Initiates the factory using the files of the static fields.
    
    Parameters:
    
    jarFilePath - path to the jar file
    
    Throws:
    
    IOException - Exception thrown whenever an error occurred while reading a mapping file.
  - getSpeciesDescription
```
public static String getSpeciesDescription(HashMap<String,Integer> speciesOccurrence)
```
    Returns a listing of the species occurrence map provided.
    
    Parameters:
    
    speciesOccurrence - a map containing the occurrence of different species
    
    Returns:
    
    a listing of the species occurrence map provided
  - getEnsemblSpeciesFile
```
public static File getEnsemblSpeciesFile(String jarFilePath)
```
    Returns the Ensembl species file.
    
    Parameters:
    
    jarFilePath - the path to the jar file
    
    Returns:
    
    the Ensembl species file
  - getEnsemblGenomesSpeciesFile
```
public static File getEnsemblGenomesSpeciesFile(String jarFilePath)
```
    Returns the Ensembl genome species file.
    
    Parameters:
    
    jarFilePath - the path to the jar file
    
    Returns:
    
    the Ensembl genome species file
  - getUniprotTaxonomyFile
```
public static File getUniprotTaxonomyFile(String jarFilePath)
```
    Returns the UniProt taxonomy file.
    
    Parameters:
    
    jarFilePath - the path to the jar file
    
    Returns:
    
    the UniProt taxonomy species file
  - getBiomartEnsemblMappingFile
```
public static File getBiomartEnsemblMappingFile(String jarFilePath)
```
    Returns the Ensembl BioMart file.
    
    Parameters:
    
    jarFilePath - the path to the jar file
    
    Returns:
    
    the Ensembl BioMart file
  - getBiomartEnsemblGenomeMappingFile
```
public static File getBiomartEnsemblGenomeMappingFile(String jarFilePath)
```
    Returns the Ensembl Genome BioMart file.
    
    Parameters:
    
    jarFilePath - the path to the jar file
    
    Returns:
    
    the Ensembl Genome BioMart file
  - getLatinName
```
public String getLatinName(Integer taxon)
```
    Returns the Latin name of the species corresponding to the given taxon according to the UniProt mapping. Null if not found.
    
    Parameters:
    
    taxon - the NCBI taxon ID
    
    Returns:
    
    the Latin name of the species
  - getName
```
public String getName(Integer taxon)
```
    Returns the name of the species corresponding to the given taxon according to the UniProt mapping. Null if not found. For species mapping to plants in the Ensembl genome mapping, the name is Latin name (common name); common name (Latin Name) for the other species. If no common name is present the Latin name is used.
    
    Parameters:
    
    taxon - the NCBI taxon ID
    
    Returns:
    
    the Latin name of the species
  - getEnsemblAssembly
```
public String getEnsemblAssembly(Integer taxon)
```
    Returns the Ensembl assembly to use for the given taxon.
    
    Parameters:
    
    taxon - the taxon number
    
    Returns:
    
    the Ensembl assembly to use
  - getEnsemblDataset
```
public String getEnsemblDataset(Integer taxon)
```
    Returns the Ensembl dataset to use for the given taxon.
    
    Parameters:
    
    taxon - the taxon number
    
    Returns:
    
    the Ensembl dataset to use
  - getEnsemblSpecies
```
public EnsemblSpecies getEnsemblSpecies()
```
    Returns the Ensembl species mapping.
    
    Returns:
    
    the Ensembl species mapping
  - getEnsemblGenomesSpecies
```
public EnsemblGenomesSpecies getEnsemblGenomesSpecies()
```
    Returns the Ensembl genome species mapping.
    
    Returns:
    
    the Ensembl genome species mapping
  - getUniprotTaxonomy
```
public UniprotTaxonomy getUniprotTaxonomy()
```
    Returns the UniProt taxonomy mapping.
    
    Returns:
    
    the UniProt taxonomy mapping
  - getBiomartMapping
```
public BiomartMapping getBiomartMapping()
```
    Returns the BioMart mapping.
    
    Returns:
    
    the BioMart mapping
  - getEnsembleSpecies
```
public HashMap<String,HashSet<Integer>> getEnsembleSpecies()
```
    Returns a map of the species in Ensembl.
    
    Returns:
    
    a map of the species in Ensembl

Class SpeciesFactory

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

UNKNOWN

UNIPROT_TAXONOMY_FILENAME

ENSEMBL_SPECIES

ENSEMBL_GENOME_SPECIES

BIOMART_ENSEMBL_FILENAME

BIOMART_ENSEMBL_GENOME_FILENAME

Method Detail

getInstance

initiate

getSpeciesDescription

getEnsemblSpeciesFile

getEnsemblGenomesSpeciesFile

getUniprotTaxonomyFile

getBiomartEnsemblMappingFile

getBiomartEnsemblGenomeMappingFile

getLatinName

getName

getEnsemblAssembly

getEnsemblDataset

getEnsemblSpecies

getEnsemblGenomesSpecies

getUniprotTaxonomy

getBiomartMapping

getEnsembleSpecies