Hi Eric,
You can do something like this to check if a particular letter (token)
is in an alphabet:
Alphabet myAlphabet = ... ; // get your alphabet from somewhere
SymbolTokenization st = myAlphabet.getTokenization("token");
String token = "X"; // the token to check for
boolean alphaContainsToken = true;
try {
st.parseToken("X"); // see if your alphabet contains the
letter X
} catch (IllegalSymbolException e) {
alphaContainsToken = false;
}
if (alphaContainsToken) System.out.println("Alphabet DOES
contain token "+token);
else System.out.println("Alphabet DOES NOT contain token
"+token);
cheers,
Richard
Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of
> Eric Buckley
> Sent: Wednesday, September 07, 2005 10:14 PM
> To: biojava-l@biojava.org
> Subject: [Biojava-l] is valid character
>
>
> I was wondering if there is a way to check if a character is
> valid within an
> alphabet. For example I want to do some preprocessing on a
> string before I
> convert the string to a SymbolList using DNATools. However if
> an invalid
> character exists in the string an Exception will be thrown,
> so I would first
> like to remove (or replace) all of the invalid characters.
>
> Eric Buckley
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
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