/ 
bioperl-1.4
/ Bio::Coordinate::Utils

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

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/

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