Package pal.alignment

Interface Alignment

    • Field Detail

      • UNKNOWN

        static final char UNKNOWN
        character used to designate unknown characters
        See Also:
        Constant Field Values
      • UNKNOWN_TLA

        static final java.lang.String UNKNOWN_TLA
        character used to designate unknown characters
        See Also:
        Constant Field Values
      • GAP_TLA

        static final java.lang.String GAP_TLA
        A three letter acronym version of a gap.
        See Also:
        Constant Field Values
      • GAPS

        static final java.lang.String GAPS
        Characters that might be used as gaps
        See Also:
        Constant Field Values
    • Method Detail

      • getData

        char getData​(int seq,
                     int site)
        sequence alignment at (sequence, site)
      • getSiteCount

        int getSiteCount()
        Returns:
        number of sites for each sequence in this alignment
      • getSequenceCount

        int getSequenceCount()
        Return number of sequences in this alignment
      • getDataType

        DataType getDataType()
        Return DataType of this alignment.
      • getAlignedSequenceString

        java.lang.String getAlignedSequenceString​(int sequence)
        Returns string representation of single sequence in alignment with gap characters included.