Data structures and helper functions for calculating alignments
There are two ways to view an alignment: either as a list of edits
(i.e., insertions, deletions, or substitutions), or as a set of sequences
with inserted gaps.
The edit list approach is perhaps more restrictive model but doesn't generalize
to multiple alignments.
The gap approach is more general, and probably more commonly used by other software
(see e.g. the ACE file format).
|Data types for gap-based alignemnts
|Gaps are coded as *s, this function removes them, and returns
the sequence along with the list of gap positions.
|Data types for edit-based alignments
|An Edit is either the insertion, the deletion,
or the replacement of a character.
|An alignment is a sequence of edits.
|A substitution matrix gives scores for replacing a character with another.
Typically, it will be symmetric. It is type-tagged with the alphabet - Nuc or Amino.
|A Selector consists of a zero element, and a funcition
that chooses a possible Edit operation, and generates an updated result.
|The sequence element type, used in alignments.
|Calculate a set of columns containing scores
This represents the columns of the alignment matrix, but will only require linear space
for score calculation.
|Evaluate an Edit based on SubstMx and gap penalty
|True if the Edit is a Repl.
|turn an alignment into sequences with - representing gaps
(for checking, filtering out the - characters should return
the original sequences, provided - isn't part of the sequence
|Produced by Haddock version 2.4.2|