Class DefaultNucleotideSequence

    • Constructor Detail

      • DefaultNucleotideSequence

        public DefaultNucleotideSequence()
        empty constructor, Plugin document requirement.
      • DefaultNucleotideSequence

        public DefaultNucleotideSequence​(java.lang.String name,
                                         java.lang.CharSequence charSequence)
        Construct a new nucleotide sequence.
        Parameters:
        name - document name (must not be null)
        charSequence - the sequence residues. The length of charSequence and the characters retured from charSequence must not change after calling this method.
      • DefaultNucleotideSequence

        public DefaultNucleotideSequence​(java.lang.String name,
                                         java.lang.String description,
                                         java.lang.CharSequence charSequence,
                                         java.util.Date created)
        Construct a new nucelotide sequence.
        Parameters:
        name - document name (must not be null)
        description - sequence descriptions (may be null or "")
        charSequence - the sequence residues. The length of charSequence and the characters retured from charSequence must not change after calling this method.
        created - sequence creation date. May be null.
      • DefaultNucleotideSequence

        public DefaultNucleotideSequence​(java.lang.String name,
                                         java.lang.String description,
                                         java.lang.CharSequence charSequence,
                                         java.util.Date created,
                                         URN urn)
        Construct a new nucelotide sequence.
        Parameters:
        name - document name (must not be null)
        description - sequence descriptions (may be null or "")
        charSequence - the sequence residues. The length of charSequence and the characters retured from charSequence must not change after calling this method.
        created - sequence creation date. May be null.
      • DefaultNucleotideSequence

        public DefaultNucleotideSequence​(NucleotideSequenceDocument sequence,
                                         java.util.Date created)
        Constructs a DefaultNucleotideSequence as a copy of an existing NucleotideSequenceDocument.
        Parameters:
        sequence - sequence
        created - sequence creation time
      • DefaultNucleotideSequence

        public DefaultNucleotideSequence​(jebl.evolution.sequences.Sequence jeblSequence)
        Construct from a sequence in jebl format.
        Parameters:
        jeblSequence - holds sequence name and sites