[Biojava-dev] gaps and holes

[Kalle Näslund]

Matthew Pocock wrote:

>I hope this has made part of the rationalle for structured gaps more clear. I 
>agree that it is a bit strange, but if you want a consistent structure for 
>representing symbols as sets and for representing alignments, it prety much 
>drops out as The One True Way. We can split hairs about exactly when ~ and - 
>get uses, but they are different things, and if you confuse the two then 
>inside things like DP recursions, Very Bad Things happen which require 
>boundary conditions and nasty hacks to correct. Perhaps we need to use a 
>GapSymbol interface or have isGap on Symbol or something to make life easier. 
>It's a pitty the Java type system plays so badly with sets. Pitty ML isn't 
>generally accepted as being a useable language :-(
>
>  
>

Well, atleast it sounds complex and neat =) Jokes aside, i can 
understand the need for
two types of gap symbols, so i agree that we should keep them.

I will try to read your mail, and the javadocs a few more times, until i 
think i understand
how the symbol magic works, and i will then try to figure out where in 
the serialization
stuff goes b0rk. So far it seems that if i take a small DNA SymbolList, 
write it to disk
and then read it. It no longer has the same symbols in it. So im fairly 
sure this realy is
a serialization issue.

/kalle

>Matthew
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