Class GeneMaps
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.genes.GeneMaps
- All Implemented Interfaces:
Serializable
public class GeneMaps extends ExperimentObject
The gene maps for a given project.
- Author:
- Marc Vaudel, Harald Barsnes
- See Also:
- Serialized Form
-
Field Summary
-
Constructor Summary
Constructors Constructor Description GeneMaps()
Creates new maps. -
Method Summary
Modifier and Type Method Description String
getChromosome(String geneName)
Returns the chromosome corresponding to a given gene name.String
getEnsemblId(String geneName)
Returns the Ensembl ID corresponding to the given gene name.HashMap<String,String>
getEnsemblVersionsMap()
Returns the Ensembl version map.HashMap<String,String>
getGeneNameToChromosomeMap()
Returns the gene name to chromosome map.HashMap<String,String>
getGeneNameToEnsemblIdMap()
Returns the gene name to Ensembl ID map.String
getGoAccession(String goName)
Returns the GO Term accession corresponding to the given name.HashMap<String,HashSet<String>>
getGoAccessionToProteinMap()
Returns the GO to protein accession map.HashSet<String>
getGoNamesForProtein(String proteinAccession)
Returns the go terms names for a protein accession.HashMap<String,String>
getGoNamesMap()
Returns the GO accession to names map.HashSet<String>
getGoTermsForProtein(String proteinAccession)
Returns the go terms accessions for a protein accession.String
getNameForGoTerm(String goAccession)
Returns the name of a GO term.HashSet<String>
getProteinsForGoTerm(String goAccession)
Returns the protein accessions for a GO accession.HashMap<String,HashSet<String>>
getProteinToGoMap()
Returns the protein to GO terms accession map.boolean
hasGoMappings()
Indicates whether the GO maps are populated.void
importMaps(GeneMapping geneMapping)
Imports the gene maps from a gene Mapping.void
setEnsemblVersionsMap(HashMap<String,String> ensemblVersionsMap)
Sets the Ensembl version map.void
setGeneNameToChromosomeMap(HashMap<String,String> geneNameToChromosomeMap)
Sets the gene name to chromosome map.void
setGeneNameToEnsemblIdMap(HashMap<String,String> geneNameToEnsemblIdMap)
Sets the gene name to Ensembl ID map.void
setGoAccessionToProteinMap(HashMap<String,HashSet<String>> goAccessionToProteinMap)
Sets the GO to protein accession map.void
setGoNamesMap(HashMap<String,String> goNamesMap)
Sets the GO accession to names map.void
setMaps(GoMapping goMapping)
Imports the GO maps from a GO mapping.void
setProteinToGoMap(HashMap<String,HashSet<String>> proteinToGoMap)
Sets the protein to GO terms accession map.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
-
Constructor Details
-
GeneMaps
public GeneMaps()Creates new maps.
-
-
Method Details
-
importMaps
Imports the gene maps from a gene Mapping.- Parameters:
geneMapping
- a gene mapping
-
setMaps
Imports the GO maps from a GO mapping.- Parameters:
goMapping
- a go mapping
-
getEnsemblVersionsMap
Returns the Ensembl version map.- Returns:
- the Ensembl version map
-
setEnsemblVersionsMap
Sets the Ensembl version map.- Parameters:
ensemblVersionsMap
- the Ensembl version map
-
getGeneNameToEnsemblIdMap
Returns the gene name to Ensembl ID map.- Returns:
- the gene name to Ensembl ID map
-
setGeneNameToEnsemblIdMap
Sets the gene name to Ensembl ID map.- Parameters:
geneNameToEnsemblIdMap
- the gene name to Ensembl ID map
-
getGeneNameToChromosomeMap
Returns the gene name to chromosome map.- Returns:
- the gene name to chromosome map
-
setGeneNameToChromosomeMap
Sets the gene name to chromosome map.- Parameters:
geneNameToChromosomeMap
- the gene name to chromosome map
-
getProteinToGoMap
Returns the protein to GO terms accession map.- Returns:
- the protein to GO terms accession map
-
setProteinToGoMap
Sets the protein to GO terms accession map.- Parameters:
proteinToGoMap
- the protein to GO terms accession map
-
getGoAccessionToProteinMap
Returns the GO to protein accession map.- Returns:
- the GO to protein accession map
-
setGoAccessionToProteinMap
Sets the GO to protein accession map.- Parameters:
goAccessionToProteinMap
- the GO to protein accession map
-
getGoNamesMap
Returns the GO accession to names map.- Returns:
- the GO accession to names map
-
setGoNamesMap
Sets the GO accession to names map.- Parameters:
goNamesMap
- the GO accession to names map
-
getEnsemblId
Returns the Ensembl ID corresponding to the given gene name. Null if not found.- Parameters:
geneName
- a gene name- Returns:
- the corresponding Ensembl ID
-
getChromosome
Returns the chromosome corresponding to a given gene name.- Parameters:
geneName
- the gene name- Returns:
- the chromosome name
-
getGoTermsForProtein
Returns the go terms accessions for a protein accession. Null if not found.- Parameters:
proteinAccession
- a protein accession- Returns:
- the go terms names
-
getProteinsForGoTerm
Returns the protein accessions for a GO accession. Null if not found.- Parameters:
goAccession
- a GO term accession- Returns:
- the corresponding proteins
-
getNameForGoTerm
Returns the name of a GO term.- Parameters:
goAccession
- the accession of the GO term.- Returns:
- the name of a GO term
-
getGoAccession
Returns the GO Term accession corresponding to the given name. Null if not found.- Parameters:
goName
- the GO name- Returns:
- the corresponding accession
-
getGoNamesForProtein
Returns the go terms names for a protein accession. Null if not found.- Parameters:
proteinAccession
- a protein accession- Returns:
- the go terms names
-
hasGoMappings
public boolean hasGoMappings()Indicates whether the GO maps are populated.- Returns:
- a boolean indicating whether the GO maps are populated
-