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Bio::AlignIO::msf.3pm
Langue: en
Version: 2008-01-11 (mandriva - 01/05/08)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::AlignIO::msf - msf sequence input/output streamSYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.DESCRIPTION
This object can transform Bio::Align::AlignI objects to and from msf flat file databases.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
Email: schattner@alum.mit.eduAPPENDIX
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
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre