Provided by: libbio-perl-perl_1.6.923-1_all bug


       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);

           # 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);


       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.


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AUTHOR - Heikki Lehvaslaiho

       Email:  heikki-at-bioperl-dot-org

       Jason Stajich jason at


       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Title   : from_align
        Usage   : $mapper = Bio::Coordinate::Utils->from_align($aln, 1);
                  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

        Title   : from_seq_to_alignmentpos
        Usage   : $mapper = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln, 1);
                  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