Bio::AlignIO::metafasta - Metafasta MSA Sequence input/output stream Do not use this module directly. Use it via the Bio::AlignIO class. This object can transform Bio::SimpleAlign objects to and from metafasta flat file databases. The format of a metafasta file is >test/1-25 ABCDEFHIJKLMNOPQRSTUVWXYZ &charge NBNAANCNJCNNNONNCNNUNNXNZ &chemical LBSAARCLJCLSMOIMCHHULRXRZ where the sequence block is followed by one or several meta blocks. Each meta block starts with the ampersand character '&' in the first column and is immediately followed by the name of the meta data which continues until the new line. The meta data follows it. All characters, except new line, are important in meta data. Bio::SeqIO::metafasta

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email heikki@ebi.ac.uk The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_aln
Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Returns : L<Bio::Align::AlignI> object - returns 0 on end of file or on error Args : NONE

write_aln
Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in fasta format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object

width
Title : width Usage : $obj->width($newval) Function: Get/Set the line width for METAFASTA output Returns : value of width Args : newvalue (optional)