I have finished summarizing the methods in Bio::SimpleAlign. The methods are classified into several categories. The classification borrows ideas from Bio::SimpleAlign's original classification, the menu in JalView and my own understanding.
The methods are listed in:
The next step is to sort out how the methods can be classified into different packages. Fucntions reading/writing internal alignment attributes can be transfered to Bio::Align::AlignI. Functions modifying, selecting, and calculating alignment sequences/features can be moved to Bio::Align::Utilities, or made into new packages.
Several new methods will be added.
A text based report will be given in the next couple of days.