Class SimpleProfilePair<S extends Sequence<C>,​C extends Compound>

    • Constructor Detail

      • SimpleProfilePair

        public SimpleProfilePair​(Profile<S,​C> query,
                                 Profile<S,​C> target,
                                 java.util.List<AlignedSequence.Step> sx,
                                 java.util.List<AlignedSequence.Step> sy)
        Creates a pair profile for the given profiles.
        Parameters:
        query - the first profile of the pair
        target - the second profile of the pair
        sx - lists whether the query profile aligns a Compound or gap at each index of the alignment
        sy - lists whether the target profile aligns a Compound or gap at each index of the alignment
        Throws:
        java.lang.IllegalArgumentException - if alignments differ in size or given profiles do not fit in alignments