Provided by: libbio-perl-perl_1.6.901-2_all bug


       Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate sets


         use Bio::Location::Simple;
         use Bio::Coordinate::ExtrapolatingPair;

         $match1 = Bio::Location::Simple->new
           (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
         $match2 = Bio::Location::Simple->new
           (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );

         $pair = Bio::Coordinate::ExtrapolatingPair->
           new(-in => $match1,
               -out => $match2,
               -strict => 1

         $pos = Bio::Location::Simple->new
             (-start => 40, -end => 60, -strand=> 1 );
         $res = $pair->map($pos);
         $res->start eq 20;
         $res->end eq 20;


       This class represents a one continuous match between two coordinate systems represented by
       Bio::Location::Simple objects. The relationship is directed and reversible. It implements
       methods to ensure internal consistency, and map continuous and split locations from one
       coordinate system to another.

       This class is an elaboration of Bio::Coordinate::Pair. The map function returns only
       matches which is the mode needed most of tehtime. By default the matching regions between
       coordinate systems are boundless, so that you can say e.g. that gene starts from here in
       the chromosomal coordinate system and extends indefinetely in both directions. If you want
       to define the matching regions exactly, you can do that and set strict() to true.


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AUTHOR - Heikki Lehvaslaiho

       Email:  heikki-at-bioperl-dot-org


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

        Title   : strict
        Usage   : $obj->strict(1);
        Function: Set and read the strictness of the coordinate system.
        Example :
        Returns : value of input system
        Args    : boolean

        Title   : map
        Usage   : $newpos = $obj->map($loc);
        Function: Map the location from the input coordinate system
                  to a new value in the output coordinate system.

                  In extrapolating coodinate system there is no location zero.
                  Locations are...
        Example :
        Returns : new location in the output coordinate system or undef
        Args    : Bio::Location::Simple

        Title   : _map
        Usage   : $newpos = $obj->_map($simpleloc);
        Function: Internal method that does the actual mapping. Called
                  multiple times by map() if the location to be mapped is a
                  split location

        Example :
        Returns : new location in the output coordinate system or undef
        Args    : Bio::Location::Simple