Class AlignmentAlgorithm

  • Direct Known Subclasses:
    NeedlemanWunsch, SmithWaterman

    public abstract class AlignmentAlgorithm
    extends java.lang.Object
    This Interface provides methods for the alignment of bio-sequences.
    Author:
    Andreas Dräger , Mark Schreiber
    • Method Detail

      • alignAll

        public java.util.List<AlignmentPairalignAll​(SequenceIterator source,
                                                      SequenceDB subjectDB)
                                               throws java.lang.Exception
        Parameters:
        source - a SequenceIterator containing a set of sequences to be aligned with
        subjectDB - the SequenceDB containing another set of sequences.
        Returns:
        a list containing the results of all single alignments performed by this method.
        Throws:
        java.util.NoSuchElementException
        java.lang.Exception
      • pairwiseAlignment

        public abstract AlignmentPair pairwiseAlignment​(SymbolList query,
                                                        SymbolList subject)
                                                 throws java.lang.Exception
        Performs a pairwise sequence alignment of the two given sequences.
        Parameters:
        query -
        subject -
        Returns:
        score of the alignment or the distance.
        Throws:
        java.lang.Exception