[Bioperl-l] moltype() -> alphabet()

[Heikki Lehvaslaiho]

I have now commited the moltype() -> alphabet() changes in bioperl-live.
Calling moltype() will now print a warning unless you set verbose(-1).

I think the new method name reflects better what it does: It tells us what
character encoding (dna, rna, protein) the sequence object is using. The old
name was confusingly leading us to use it to what KIND of biological
molecule we are dealing with (I was confised!). In bioperl, basic sequence
objects are agnostic about it. You can change the sequence string at will
and they will work as long as you call biologically meaningful methods. 

At some level this question is a bit academic since difference between
nucleotides and amino acids is clear and not many people care about DNA/RNA
differences anyway. Hopefully this change will in the long run help to
clarify bioperl syntax.

	-Heikki
	
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     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
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