Bio::Coordinate::Utils - Additional methods to create Bio::Coordinate objects use Bio::Coordinate::Utils; # get a Bio::Align::AlignI compliant object, $aln, somehow # it could be a Bio::SimpleAlign $mapper = Bio::Coordinate::Utils->from_align($aln, 1); This class is a holder of methods that work on or create Bio::Coordinate::MapperI- compliant objects. . These methods are not part of the Bio::Coordinate::MapperI interface and should in general not be essential to the primary function of sequence objects. If you are thinking of adding essential functions, it might be better to create your own sequence class. See Bio::PrimarySeqI, Bio::PrimarySeq, and Bio::Seq for more.

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists

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 Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

from_align
Title : from_align Usage : $mapper = Bio::Coordinate::Utils->from_align($aln, 1); Function: Create a mapper out of an alignment. The mapper will return a value only when both ends of the input range find a match. Note: This implementation works only on pairwise alignments and is not yet well tested! Returns : A Bio::Coordinate::MapperI Args : Bio::Align::AlignI object Id for the reference sequence, optional