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

    • Method Detail

      • 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