bio::location::avwithincoordpolicy(3pm) [debian man page]

Bio::Location::AvWithinCoordPolicy(3pm) 		User Contributed Perl Documentation		   Bio::Location::AvWithinCoordPolicy(3pm)

NAME

       Bio::Location::AvWithinCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible
       and reasonable range otherwise

SYNOPSIS

       See Bio::Location::CoordinatePolicyI

DESCRIPTION

       CoordinatePolicyI implementing objects are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked
       for it.

       This class will compute the coordinates such that for fuzzy locations of type WITHIN and BETWEEN the average of the two limits will be
       returned, and for all other locations it will return the widest possible range, but by using some common sense. This means that e.g.
       locations like "<5..100" (start before position 5) will return 5 as start (returned values have to be positive integers).

FEEDBACK

       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 - Hilmar Lapp, Jason Stajich
       Email <hlapp-at-gmx-dot-net>, <jason-at-bioperl-dot-org>

APPENDIX

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

   start
	 Title	 : start
	 Usage	 : $start = $policy->start($location);
	 Function: Get the integer-valued start coordinate of the given location as
		   computed by this computation policy.
	 Returns : A positive integer number.
	 Args	 : A Bio::LocationI implementing object.

   end
	 Title	 : end
	 Usage	 : $end = $policy->end($location);
	 Function: Get the integer-valued end coordinate of the given location as
		   computed by this computation policy.
	 Returns : A positive integer number.
	 Args	 : A Bio::LocationI implementing object.

perl v5.14.2							    2012-03-02				   Bio::Location::AvWithinCoordPolicy(3pm)

Bio::Coordinate::Pair(3pm)				User Contributed Perl Documentation				Bio::Coordinate::Pair(3pm)

NAME

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

SYNOPSIS

	 use Bio::Location::Simple;
	 use Bio::Coordinate::Pair;

	 my $match1 = Bio::Location::Simple->new
	     (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
	 my $match2 = Bio::Location::Simple->new
	     (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
	 my $pair = Bio::Coordinate::Pair->new(-in => $match1,
					       -out => $match2
					       );
	 # location to match
	 $pos = Bio::Location::Simple->new
	     (-start => 25, -end => 25, -strand=> -1 );

	 # results are in a Bio::Coordinate::Result
	 # they can be Matches and Gaps; are  Bio::LocationIs
	 $res = $pair->map($pos);
	 $res->isa('Bio::Coordinate::Result');
	 $res->each_match == 1;
	 $res->each_gap == 0;
	 $res->each_Location == 1;
	 $res->match->start == 5;
	 $res->match->end == 5;
	 $res->match->strand == -1;
	 $res->match->seq_id eq 'peptide';

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.

       The map() method returns Bio::Coordinate::Results with Bio::Coordinate::Result::Gaps. The calling code have to deal (process or ignore)
       them.

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 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

APPENDIX

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

   in
	Title	: in
	Usage	: $obj->in('peptide');
	Function: Set and read the input coordinate system.
	Example :
	Returns : value of input system
	Args	: new value (optional), Bio::LocationI

   out
	Title	: out
	Usage	: $obj->out('peptide');
	Function: Set and read the output coordinate system.
	Example :
	Returns : value of output system
	Args	: new value (optional), Bio::LocationI

   swap
	Title	: swap
	Usage	: $obj->swap;
	Function: Swap the direction of mapping; input <-> output
	Example :
	Returns : 1
	Args	:

   strand
	Title	: strand
	Usage	: $obj->strand;
	Function: Get strand value for the pair
	Example :
	Returns : ( 1 | 0 | -1 )
	Args	:

   test
	Title	: test
	Usage	: $obj->test;
	Function: test that both components are of the same length
	Example :
	Returns : ( 1 | undef )
	Args	:

   map
	Title	: map
	Usage	: $newpos = $obj->map($pos);
	Function: Map the location from the input coordinate system
		  to a new value in the output coordinate system.
	Example :
	Returns : new Bio::LocationI in the output coordinate system or undef
	Args	: Bio::LocationI object

   _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

perl v5.14.2							    2012-03-02						Bio::Coordinate::Pair(3pm)