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
  • Constructor Details

    • GeneMaps

      public GeneMaps()
      Creates new maps.
  • Method Details

    • importMaps

      public void importMaps​(GeneMapping geneMapping)
      Imports the gene maps from a gene Mapping.
      Parameters:
      geneMapping - a gene mapping
    • setMaps

      public void setMaps​(GoMapping goMapping)
      Imports the GO maps from a GO mapping.
      Parameters:
      goMapping - a go mapping
    • getEnsemblVersionsMap

      public HashMap<String,​String> getEnsemblVersionsMap()
      Returns the Ensembl version map.
      Returns:
      the Ensembl version map
    • setEnsemblVersionsMap

      public void setEnsemblVersionsMap​(HashMap<String,​String> ensemblVersionsMap)
      Sets the Ensembl version map.
      Parameters:
      ensemblVersionsMap - the Ensembl version map
    • getGeneNameToEnsemblIdMap

      public HashMap<String,​String> getGeneNameToEnsemblIdMap()
      Returns the gene name to Ensembl ID map.
      Returns:
      the gene name to Ensembl ID map
    • setGeneNameToEnsemblIdMap

      public void setGeneNameToEnsemblIdMap​(HashMap<String,​String> geneNameToEnsemblIdMap)
      Sets the gene name to Ensembl ID map.
      Parameters:
      geneNameToEnsemblIdMap - the gene name to Ensembl ID map
    • getGeneNameToChromosomeMap

      public HashMap<String,​String> getGeneNameToChromosomeMap()
      Returns the gene name to chromosome map.
      Returns:
      the gene name to chromosome map
    • setGeneNameToChromosomeMap

      public void setGeneNameToChromosomeMap​(HashMap<String,​String> geneNameToChromosomeMap)
      Sets the gene name to chromosome map.
      Parameters:
      geneNameToChromosomeMap - the gene name to chromosome map
    • getProteinToGoMap

      public HashMap<String,​HashSet<String>> getProteinToGoMap()
      Returns the protein to GO terms accession map.
      Returns:
      the protein to GO terms accession map
    • setProteinToGoMap

      public void setProteinToGoMap​(HashMap<String,​HashSet<String>> proteinToGoMap)
      Sets the protein to GO terms accession map.
      Parameters:
      proteinToGoMap - the protein to GO terms accession map
    • getGoAccessionToProteinMap

      public HashMap<String,​HashSet<String>> getGoAccessionToProteinMap()
      Returns the GO to protein accession map.
      Returns:
      the GO to protein accession map
    • setGoAccessionToProteinMap

      public void setGoAccessionToProteinMap​(HashMap<String,​HashSet<String>> goAccessionToProteinMap)
      Sets the GO to protein accession map.
      Parameters:
      goAccessionToProteinMap - the GO to protein accession map
    • getGoNamesMap

      public HashMap<String,​String> getGoNamesMap()
      Returns the GO accession to names map.
      Returns:
      the GO accession to names map
    • setGoNamesMap

      public void setGoNamesMap​(HashMap<String,​String> goNamesMap)
      Sets the GO accession to names map.
      Parameters:
      goNamesMap - the GO accession to names map
    • getEnsemblId

      public String getEnsemblId​(String geneName)
      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

      public String getChromosome​(String geneName)
      Returns the chromosome corresponding to a given gene name.
      Parameters:
      geneName - the gene name
      Returns:
      the chromosome name
    • getGoTermsForProtein

      public HashSet<String> getGoTermsForProtein​(String proteinAccession)
      Returns the go terms accessions for a protein accession. Null if not found.
      Parameters:
      proteinAccession - a protein accession
      Returns:
      the go terms names
    • getProteinsForGoTerm

      public HashSet<String> getProteinsForGoTerm​(String goAccession)
      Returns the protein accessions for a GO accession. Null if not found.
      Parameters:
      goAccession - a GO term accession
      Returns:
      the corresponding proteins
    • getNameForGoTerm

      public String getNameForGoTerm​(String goAccession)
      Returns the name of a GO term.
      Parameters:
      goAccession - the accession of the GO term.
      Returns:
      the name of a GO term
    • getGoAccession

      public String getGoAccession​(String goName)
      Returns the GO Term accession corresponding to the given name. Null if not found.
      Parameters:
      goName - the GO name
      Returns:
      the corresponding accession
    • getGoNamesForProtein

      public HashSet<String> getGoNamesForProtein​(String proteinAccession)
      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