Class FastaHeader


  • public class FastaHeader
    extends java.lang.Object
    This class is used by FastaFormat to determine which fields are in the fasta header. By default they all are except for the sequence name. This is for compliance with fasta files that come from Genbank where the name is derived from the accession number so need not be repeated. The class can be used to customise what appears. Eg if you only want the accession set everything else false. Note that if fields in the RichSequence being parsed by the FastaFormat object then they may not be in the header even if they are specified in this class.
    Since:
    1.6
    Author:
    Mark Schreiber
    • Constructor Detail

      • FastaHeader

        public FastaHeader()
    • Method Detail

      • isShowIdentifier

        public boolean isShowIdentifier()
      • setShowIdentifier

        public void setShowIdentifier​(boolean showIdentifier)
      • isShowNamespace

        public boolean isShowNamespace()
      • setShowNamespace

        public void setShowNamespace​(boolean showNamespace)
      • isShowAccession

        public boolean isShowAccession()
      • setShowAccession

        public void setShowAccession​(boolean showAccession)
      • isShowVersion

        public boolean isShowVersion()
      • setShowVersion

        public void setShowVersion​(boolean showVersion)
        Determines if the version number of a sequence should be displayed. If there is no accession this may not make much sense.
        Parameters:
        showVersion -
      • isShowName

        public boolean isShowName()
      • setShowName

        public void setShowName​(boolean showName)
      • isShowDescription

        public boolean isShowDescription()
      • setShowDescription

        public void setShowDescription​(boolean showDescription)