[Biojava-l] is valid character

[Richard HOLLAND]

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: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> Eric Buckley
> Sent: Wednesday, September 07, 2005 10:14 PM
> To: biojava-l at 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
> 
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