AlignedSequence objects

You really only need to worry about how Twine stores the FASTA alignments if you are going to write plugins.
Basically, each FASTA alignment is parsed into the names of each species sequence (the header, marked by >),
and the sequence data, in gapped and ungapped versions.
The order of the sequences, as specified in the FASTA file, is maintained by the order of a String array
that can be cycled through to get each species name in order.
The currently selected AlignedSequence object can be identified by isSelected().
Each AlignedSequence also contains the same HashMap of all currently loaded Motifs.
Each Motif contains the list of all matches to that motif at the current threshold, for all open AlignedSequence objects, as nested HashMaps,
with keys for the AlignedSequence, then for each species within that AlignedSequence, then for the ungapped position of that match.
In other words,
    alignedSequenceMatchMap is a HashMap in Motif
   where the Keys are AlignedSequence names(String),
    and the values are HashMaps of matches for the species within that AlignedSequence,
    where the keys are Species names (String) and the values are HashMaps,
    where the keys are the location (Integer) and the values are Matches.