Bio::Location AvWithinCoordPolicy
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Summary
Bio::Location::AvWithinCoordPolicy - class implementing
Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
Package variables
No package variables defined.
Inherit
Bio::Location::WidestCoordPolicy
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).
Methods
new
No description
Code
startDescriptionCode
endDescriptionCode
Methods description
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  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.
endcodeprevnextTop
  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.
Methods code
newdescriptionprevnextTop
sub new {
     my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    return $self;
}
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sub start {
    my ($self,$loc) = @_;

    if(($loc->start_pos_type() eq 'WITHIN') ||
       ($loc->start_pos_type() eq 'BETWEEN')) {
	my ($min, $max) = ($loc->min_start(), $loc->max_start());
	return int(($min+$max)/2) if($min && $max);
} return $self->SUPER::start($loc);
}
enddescriptionprevnextTop
sub end {
    my ($self,$loc) = @_;

    if(($loc->end_pos_type() eq 'WITHIN') ||
       ($loc->end_pos_type() eq 'BETWEEN')) {
	my ($min, $max) = ($loc->min_end(), $loc->max_end());
	return int(($min+$max)/2) if($min && $max);
} return $self->SUPER::end($loc); } 1;
}
General documentation
FEEDBACKTop
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 Top
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 BugsTop
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 StajichTop
Email <hlapp-at-gmx-dot-net>, <jason-at-bioperl-dot-org>
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _