It would be great to be able to create sequence aligner objects without specifying target and query sequences, so that the parameters (or options), like gap penalty, alignment type and substitution matrix, are bundled together with the sequence aligner object, before knowing the sequences that will be aligned. This way we could pass the aligner object to another method as input, and the other method will align sequences using this object.

At the moment the sequences need to be known when constructing the aligner object. i think it would be equivalent to create a parameter object that bundles together the options for a sequence aligner, so that is another option.