On Mon, Oct 22, 2001 at 03:51:14PM -0700, Emig, Robin wrote:
> I use .getToken a lot, about as much as I use .seqString(). I would
> like however there to be somekind of default token set that is easy to use.
It's reasonably easy to get a SymbolTokenization from the
Alphabet you're using, a
: Thomas Down; David Waring; [EMAIL PROTECTED]
Subject: Re: [Biojava-l] IntegerAlphabet IntegerSymbol
On Mon, Oct 22, 2001 at 10:36:22AM +1300, Mark Schreiber wrote:
>
> > 4) get rid of getToken() completely, and change the way that sequences
> >get converted to strings -- replacing
On Mon, Oct 22, 2001 at 10:36:22AM +1300, Mark Schreiber wrote:
>
> > 4) get rid of getToken() completely, and change the way that sequences
> >get converted to strings -- replacing hardwired code in SymbolList
> >implementations with pluggable `stringifiers'.
> >
> > This was the idea of
I second that approach
-Original Message-
From: Mark Schreiber [mailto:[EMAIL PROTECTED]]
Sent: Sunday, October 21, 2001 2:36 PM
To: Thomas Down
Cc: David Waring; [EMAIL PROTECTED]
Subject: Re: [Biojava-l] IntegerAlphabet IntegerSymbol
On Sun, 21 Oct 2001, Thomas Down wrote:
> >
On Sun, 21 Oct 2001, Thomas Down wrote:
> > Three options:
> > 1) Create a new SequenceFormat just for this, and if there will be no other
> > use of IntegerSymbolList perhaps this is the best way to go.
> >
> > 2) Create an IntegerSymbolList that extends SimpleSymbolList overriding
> > seqStrin
On Fri, Oct 19, 2001 at 03:56:54PM -0700, David Waring wrote:
>
> I am working on bio.program.PhredSequence and its friends (for handling the
> qualitative data associated with the output of Phred). PhredSequence uses
> SymbolLists with an IntegerAlphabet. At present the getToken() method of
> In
Hi -
The class PhredTools contains methods to read and write phred quality data
in fasta like format. The issue of spacing integers is handeled by the
PhredFormat class. There are a number of classes that cannot return
sensible results for getToken() such as HMM states.
It is unfortunate that th
I am working on bio.program.PhredSequence and its friends (for handling the
qualitative data associated with the output of Phred). PhredSequence uses
SymbolLists with an IntegerAlphabet. At present the getToken() method of
IntergerAlphabet.IntegerSymbol returns '#'. I guess this is because the
Sy
