- AUTHOR - Jason Stajich
- LocationI methods
- Bio::LocationI methods
Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence which has unclear start/end location
# Get a FuzzyLocationI object somehow print "Fuzzy FT location string is ", $location->to_FTstring(); print "location is of the type ", $location->loc_type, "\n";
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : loc_type Usage : my $location_type = $location->location_type(); Function: Get location type encoded as text Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN') Args : none
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 one 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