++ed by:
THALJEF GENEHACK MAJENSEN YUSRIDEB ILUX

11 PAUSE users
14 non-PAUSE users.

Christopher Fields
and 1 contributors

NAME

Bio::AlignIO::fasta - fasta MSA Sequence input/output stream

SYNOPSIS

Do not use this module directly. Use it via the Bio::AlignIO class.

DESCRIPTION

This object can transform Bio::SimpleAlign objects to and from fasta flat file databases. This is for the fasta alignment format, not for the FastA sequence analysis program. To process the alignments from FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module.

FEEDBACK

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 the web:

  http://bugzilla.open-bio.org/

AUTHORS

Peter Schattner

APPENDIX

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 : Bio::Align::AlignI object - returns 0 on end of file
                or on error
 Args    : -width => optional argument to specify the width sequence
           will be written (60 chars by default)

See Bio::Align::AlignI

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

See Bio::Align::AlignI

_get_len

 Title   : _get_len
 Usage   : 
 Function: determine number of alphabetic chars
 Returns : integer
 Args    : sequence string

width

 Title   : width
 Usage   : $obj->width($newwidth)
           $width = $obj->width;
 Function: Get/set width of alignment
 Returns : integer value of width 
 Args    : on set, new value (a scalar or undef, optional)