bionic (3) Bio::Coordinate::ExtrapolatingPair.3pm.gz

NAME

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

VERSION

       version 1.007001

SYNOPSIS

         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;

DESCRIPTION

       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.

METHODS

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

   map
        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

INTERNAL METHODS

   _map
        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

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 the Bioperl mailing list.  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 of the bugs and their resolution.
       Bug reports can be submitted via the web:

         https://github.com/bioperl/%%7Bdist%7D

AUTHOR

       Heikki Lehvaslaiho <heikki@bioperl.org>

COPYRIGHT

       This software is copyright (c) by Heikki Lehvaslaiho.

       This software is available under the same terms as the perl 5 programming language system itself.