[Biojava-l] GappedSymbolList

[Matthew Pocock]

Hi Robin,

"Emig, Robin" wrote:

>         Ok, I'm a little confused about how to actually use a
> gappedsymbollist. I can add gaps just fine but what If I wanted to print
> out?
> ACGT------AHXXHFF

You should be able to get this output by calling seqString on the gapped
instance. The gap symbol has a getToken method that returns '-'.

>
>         I have no idea how to do that. Also, the parsers don't understand
> the GapSymbol, ie you can add it to the alphabet, but you cant parse '-'.

This is odd. Could you try the symbol.TestAmbiguity demo? It works for me and
includes a parsed gap character. I am guessing that your sequence is protein
- mabey something is up with how SimpleAlphabet is implemented but is masked
for DNA (somehow...).

Matthew

>
> -Robin
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