Class AlignmentPair

  • All Implemented Interfaces:
    java.io.Serializable, Alignment, SymbolList, Changeable

    public class AlignmentPair
    extends SimpleAlignment
    This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences. Currently, these sequences must have the identical length (this may be changed in the future). A format routine produces a BLAST-like output for the sequences but all necessary information to visualize the alignment are contained in this class.
    Author:
    Andreas Dräger
    See Also:
    Serialized Form
    • Constructor Detail

      • AlignmentPair

        public AlignmentPair​(Sequence query,
                             Sequence subject,
                             int queryStart,
                             int queryEnd,
                             int subjectStart,
                             int subjectEnd,
                             SubstitutionMatrix subMatrix)
                      throws java.lang.IllegalArgumentException,
                             BioException
        Parameters:
        queryStart - the start position in the query, where the alignment starts. For example zero for normal Needleman-Wunsch-Alignments.
        queryEnd - the end position, that means the sequence coordinate, which is the last symbol of the query sequence. Counting starts at zero!
        queryLength - The length of the query sequence without gaps.
        subjectStart - These are all the same for the target. Have a look at these above.
        subjectEnd -
        subMatrix - the subsitution Matrix used for calculating the alignment
        Throws:
        java.lang.IllegalArgumentException
        BioException