[Biojava-dev] gaps and holes

[Kalle Näslund]

>>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.
>>    
>>
>
>OK. I think the main magic would be to serialize things out as - or ~, and if 
>you have a leading/trailing ~ then it may be reasonable to use {} rather than 
>[] where as internal - is almost certainly meant to be []. Unfortunately, I 
>think we may have lossy serialization here :( Would we need to pass some sort 
>of 'how far through' hint to serialization? that feels sucky.
>
>  
>
The approach i was thinking of was to keep it as it is now. That is that
SimpleSymbolList contains the symbols that was created with, or added 
later on, so there
its up to the user to actualy handle - or ~ as the/she sees fit. This 
seem to have worked
ok up to now.

The GappedSymbolList on the other hand, handles gaps separately from the 
other
symbols. So here it alread uses ~ and - appropriately i think, and the 
serialization
isnt an issue as the gap symbols are never serialized.

This is as it is now in BJ, and from what i understood, the HMM code uses
GappedSymbolLists so it gets the needed ~ and -, and is happy. And 
people doing
simple sequence manipulation only get - and are happy.

Is this ok ?  or am i missing something obvious ?