Bio::Coordinate::Utils(3)

NAME
Bio::Coordinate::Utils - Additional methods to create Bio::Coordinate objects

SYNOPSIS
    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);

DESCRIPTION
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.

FEEDBACK

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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.

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AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

APPENDIX
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