Provided by: libbio-perl-perl_1.7.2-2_all
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.
Support Please direct usage questions or support issues to the mailing list: email@example.com 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: https://github.com/bioperl/bioperl-live/issues
AUTHORS - Peter Schattner
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. 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 $aln->map_chars('~','-') Returns : Bio::Align::AlignI object Args : NONE write_aln 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