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);

           # Build a set of mappers which will map, for each sequence,
           # that sequence position in the alignment (exon position to alignment
           # position)
           my @mappers = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln);

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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho

       Email:  heikki-at-bioperl-dot-org

       Jason Stajich jason at bioperl.org

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

   from_seq_to_alignmentpos
        Title   : from_seq_to_alignmentpos
        Usage   : $mapper = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln, 1);
        Function:
                  Create a mapper out of an alignment.
                  The mapper will map the position of a sequence into that position
                  in the alignment.

                  Will work on alignments of >= 2 sequences
        Returns : An array of Bio::Coordinate::MapperI
        Args    : Bio::Align::AlignI object