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

Interface DataMetadata

public interface DataMetadata
This interface define metadata of data objects.
Since:
2.0
Author:
Laurent Jourdren

  • Field Details

  • Method Details

    • get

      String get(String key)
      Get the value of metadata entry.
      Parameters:
      key - the key
      Returns:
      the value related to key or null if the key does not exists

    • set

      void set(String key, String value)
      Set a metadata entry.
      Parameters:
      key - the key
      value - the value

    • containsKey

      boolean containsKey(String key)
      Test if a key exists.
      Parameters:
      key - the key to test
      Returns:
      true if the key exists

    • removeKey

      boolean removeKey(String key)
      Remove a entry.
      Parameters:
      key - the key of the entry to remove
      Returns:
      true if the entry has been removed

    • set

      void set(DataMetadata metadata)
      The the entries of the metadata with the entries of another metadata object.
      Parameters:
      metadata - the entries to add

    • clear

      void clear()
      Clear the entries of the object.

    • keySet

      Set<String> keySet()
      Get the keys of the entries.
      Returns:
      a set with the keys of the entries

    • isPairedEnd

      boolean isPairedEnd()
      Test if the data is paired end data.
      Returns:
      true if the data is paired end data

    • setPairedEnd

      void setPairedEnd(boolean pairedEnd)
      Set single-end/paired-end data type.
      Parameters:
      pairedEnd - true if data is paired-end data

    • getFastqFormat

      fr.ens.biologie.genomique.kenetre.bio.FastqFormat getFastqFormat()
      Get the FastqFormat. If value not set, the default format is fastq-sanger.
      Returns:
      the fastq format

    • getFastqFormat

      fr.ens.biologie.genomique.kenetre.bio.FastqFormat getFastqFormat(fr.ens.biologie.genomique.kenetre.bio.FastqFormat defaultValue)
      Get the FastqFormat.
      Parameters:
      defaultValue - the default value
      Returns:
      the fastq format

    • setFastqFormat

      void setFastqFormat(fr.ens.biologie.genomique.kenetre.bio.FastqFormat fastqFormat)
      Set the FASTQ format of the data.
      Parameters:
      fastqFormat - the FASTQ format

    • getSampleName

      String getSampleName()
      Get the sample name related to the data.
      Returns:
      a String with the sample name related to the data

    • setSampleName

      void setSampleName(String sampleName)
      Set the sample name related to the data.
      Parameters:
      sampleName - the sample name

    • getSampleId

      String getSampleId()
      Get the sample id related to the data.
      Returns:
      the sample id or null if the value is not set

    • setSampleId

      void setSampleId(String sampleId)
      Set the sample id related to the data
      Parameters:
      sampleId - the sample id

    • getSampleNumber

      int getSampleNumber()
      Get the sample number related to the data.
      Returns:
      the sample number or -1 if the value is not set

    • setSampleNumber

      void setSampleNumber(int sampleNumber)
      Set the sample number related to the data
      Parameters:
      sampleNumber - the sample number