Bio::AlignIO::msf - msf sequence input/output stream


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


This object can transform Bio::Align::AlignI objects to and from msf flat file databases.



Please direct usage questions or support issues to the mailing list:

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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:

AUTHORS - Peter Schattner



The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream. Tries to read *all* MSF
           It reads all non whitespace characters in the alignment
           area. For MSFs with weird gaps (eg ~~~) map them by using
 Returns : Bio::Align::AlignI object
 Args    : NONE


 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in MSF format
           Sequence type of the alignment is determined by the first sequence.
 Returns : 1 for success and 0 for error
 Args    : Bio::Align::AlignI object