Package fr.ens.biologie.genomique.eoulsan.data.storages

Class DataFileGenomeIndexStorage

java.lang.Object
fr.ens.biologie.genomique.kenetre.storage.AbstractFileGenomeIndexStorage
fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage
All Implemented Interfaces:
fr.ens.biologie.genomique.kenetre.storage.GenomeIndexStorage
public class DataFileGenomeIndexStorage extends fr.ens.biologie.genomique.kenetre.storage.AbstractFileGenomeIndexStorage
This class define a storage for genome indexes using DataFile API.
Since:
2.6
Author:
Laurent Jourdren

  • Method Summary

    Modifier and Type
    Method
    Description
    DataFile
    getDataFile(fr.ens.biologie.genomique.kenetre.bio.readmapper.MapperInstance mapperInstance, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genome, Map<String,String> additionalDescription)
    Get the DataFile that corresponds to a mapper and a genome
    static fr.ens.biologie.genomique.kenetre.storage.GenomeIndexStorage
    getInstance(String source, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
    Create a GenomeIndexStorage
    void
    put(fr.ens.biologie.genomique.kenetre.bio.readmapper.MapperInstance mapperInstance, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genome, Map<String,String> additionalDescription, DataFile indexArchive)
    Put the index archive in the storage.

    Methods inherited from class fr.ens.biologie.genomique.kenetre.storage.AbstractFileGenomeIndexStorage

    get, put

    Methods inherited from class java.lang.Object

    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Method Details

    • getDataFile

      public DataFile getDataFile(fr.ens.biologie.genomique.kenetre.bio.readmapper.MapperInstance mapperInstance, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genome, Map<String,String> additionalDescription)
      Get the DataFile that corresponds to a mapper and a genome
      Parameters:
      mapperInstance - mapper
      genome - genome description object for the genome
      additionalDescription - description of the additional parameters
      Returns:
      a file that contains the path to the index or null if the index has not yet been computed

    • put

      public void put(fr.ens.biologie.genomique.kenetre.bio.readmapper.MapperInstance mapperInstance, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genome, Map<String,String> additionalDescription, DataFile indexArchive)
      Put the index archive in the storage.
      Parameters:
      mapperInstance - mapper
      genome - genome description object
      additionalDescription - description of the additional parameters
      indexArchive - the file that contains the index

    • getInstance

      public static fr.ens.biologie.genomique.kenetre.storage.GenomeIndexStorage getInstance(String source, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
      Create a GenomeIndexStorage
      Parameters:
      source - the path of the index storage
      logger - the logger
      Returns:
      a GenomeIndexStorage object if the path contains an index storage or null if no index storage is found