Bio::Location
FuzzyLocationI
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Summary
Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence
which has unclear start/end location
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# Get a FuzzyLocationI object somehow
print "Fuzzy FT location string is ", $location->to_FTstring();
print "location is of the type ", $location->loc_type, "\n";
Description
This interface encapsulates the necessary methods for representing a
Fuzzy Location, one that does not have clear start and/or end points.
This will initially serve to handle features from Genbank/EMBL feature
tables that are written as 1^100 meaning between bases 1 and 100 or
<100..300 meaning it starts somewhere before 100. Advanced
implementations of this interface may be able to handle the necessary
logic of overlaps/intersection/contains/union. It was constructed to
handle fuzzy locations that can be represented in Genbank/EMBL.
Methods
Methods description
Title : loc_type
Usage : my $location_type = $location->location_type();
Function: Get location type encoded as text
Returns : string ('EXACT', 'WITHIN', 'BETWEEN')
Args : none |
Methods code
sub location_type
{ my ($self) = @_;
$self->throw_not_implemented();} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
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bioperl-l@bioperl.org - General discussion
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Report bugs to the Bioperl bug tracking system to help us keep track
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| AUTHOR - Jason Stajich | Top |
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
| Bio::LocationI methods | Top |
Bio::LocationI methods follow
Title : min_start
Usage : my $minstart = $location->min_start();
Function: Get minimum starting location of feature startpoint
Returns : integer or undef if no maximum starting point.
Args : none
Title : max_start
Usage : my $maxstart = $location->max_start();
Function: Get maximum starting location of feature startpoint
Returns : integer or undef if no maximum starting point.
Args : none
Title : start_pos_type
Usage : my $start_pos_type = $location->start_pos_type();
Function: Get start position type (ie <,>, ^)
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
Title : min_end
Usage : my $minend = $location->min_end();
Function: Get minimum ending location of feature endpoint
Returns : integer or undef if no minimum ending point.
Args : none
Title : max_end
Usage : my $maxend = $location->max_end();
Function: Get maximum ending location of feature endpoint
Returns : integer or undef if no maximum ending point.
Args : none
Title : end_pos_type
Usage : my $end_pos_type = $location->end_pos_type();
Function: Get end position type (ie <,>, ^)
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
Title : seq_id
Usage : my $seqid = $location->seq_id();
Function: Get/Set seq_id that location refers to
Returns : seq_id
Args : [optional] seq_id value to set
Title : coordinate_policy
Usage : $policy = $location->coordinate_policy();
$location->coordinate_policy($mypolicy); # set may not be possible
Function: Get the coordinate computing policy employed by this object.
See Bio::Location::CoordinatePolicyI for documentation about
the policy object and its use.
The interface *does not* require implementing classes to accept
setting of a different policy. The implementation provided here
does, however, allow to do so.
Implementors of this interface are expected to initialize every
new instance with a CoordinatePolicyI object. The implementation
provided here will return a default policy object if none has
been set yet. To change this default policy object call this
method as a class method with an appropriate argument. Note that
in this case only subsequently created Location objects will be
affected.
Returns : A Bio::Location::CoordinatePolicyI implementing object.
Args : On set, a Bio::Location::CoordinatePolicyI implementing object.
Title : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none