Package com.compomics.util.experiment.biology.genes

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:

  • 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