Re: [Biojava-l] SeqIOTools.readXXXXFields() method??

2002-07-26 Thread Mark Fortner
I wonder if it would be worthwhile to have an alphabet like approach to this, where the alphabets are actually field tokens/field names that are either statically defined, or are defined in XML files? For example, you might have entries like You could save subsets of thes

Re: [Biojava-l] adding toSequenceIterator method for Alignment

2002-07-26 Thread Kalle Näslund
Singh, Nimesh wrote: > I've created a class called AlignmentSequenceIterator that I intend to put in >the org.biojava.bio.seq package. It will do the real work. I've also added >public SequenceIterator sequenceIterator() { >return new AlignmentSequenceIterator(this); >

[Biojava-l] SeqIOTools.readXXXXFields() method??

2002-07-26 Thread Roy Park
Hello everyone. I deal with a number of pseudo EMBL/GenBank formatted sequences, and it would be extremely nice (?) to have methods that only attempt to parse out specified fields. The primary reason for this is that, right now, the format.readSequence() throws BioException way too frequently fo