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.

   new
       new() inherited from Root

   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