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BioPerl-1.6.920
River stage two • 60 direct dependents • 65 total dependents
/ Bio::LocationI

NAME

Bio::LocationI - Abstract interface of a Location on a Sequence

SYNOPSIS

    # get a LocationI somehow
    printf( "start = %d, end = %d, strand = %s, seq_id = %s\n", 
	    $location->start, $location->end, $location->strand,
	    $location->seq_id);
    print "location str is ", $location->to_FTstring(), "\n";

DESCRIPTION

This Interface defines the methods for a Bio::LocationI, an object which encapsulates a location on a biological sequence. Locations need not be attached to actual sequences as they are stand alone objects. LocationI objects are used by Bio::SeqFeatureI objects to manage and represent locations for a Sequence Feature.

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 - Jason Stajich

Email jason-at-bioperl-dot-org

APPENDIX

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

location_type

Title   : location_type
Usage   : my $location_type = $location->location_type();
Function: Get location type encoded as text
Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN')
Args    : none

start

Title   : start
Usage   : $start = $location->start();
Function: Get the start coordinate of this location as defined by
          the currently active coordinate computation policy. In
          simple cases, this will return the same number as
          min_start() and max_start(), in more ambiguous cases like
          fuzzy locations the number may be equal to one or neither
          of both.

          We override this here from RangeI in order to delegate
          'get' to a L<Bio::Location::CoordinatePolicy> implementing
          object.  Implementing classes may also wish to provide
          'set' functionality, in which case they *must* override
          this method. The implementation provided here will throw
          an exception if called with arguments.

Returns : A positive integer value.
Args    : none

See Bio::Location::CoordinatePolicy for more information

end

Title   : end
Usage   : $end = $location->end();
Function: Get the end coordinate of this location as defined by the
          currently active coordinate computation policy. In simple
          cases, this will return the same number as min_end() and
          max_end(), in more ambiguous cases like fuzzy locations
          the number may be equal to one or neither of both.

          We override this here from Bio::RangeI in order to delegate
          'get' to a L<Bio::Location::CoordinatePolicy> implementing
          object. Implementing classes may also wish to provide
          'set' functionality, in which case they *must* override
          this method. The implementation provided here will throw
          an exception if called with arguments.

Returns : A positive integer value.
Args    : none

See Bio::Location::CoordinatePolicy and Bio::RangeI for more information

min_start

Title   : min_start
Usage   : my $minstart = $location->min_start();
Function: Get minimum starting point of feature.

          Note that an implementation must not call start() in this method.

Returns : integer or undef if no minimum starting point.
Args    : none

max_start

Title   : max_start
Usage   : my $maxstart = $location->max_start();
Function: Get maximum starting point of feature.

          Note that an implementation must not call start() in this method
          unless start() is overridden such as not to delegate to the
          coordinate computation policy object.

Returns : integer or undef if no maximum starting point.
Args    : none

start_pos_type

Title   : start_pos_type
Usage   : my $start_pos_type = $location->start_pos_type();
Function: Get start position type encoded as text

          Known valid values are 'BEFORE' (<5..100), 'AFTER' (>5..100), 
          'EXACT' (5..100), 'WITHIN' ((5.10)..100), 'BETWEEN', (5^6), with
          their meaning best explained by their GenBank/EMBL location string
          encoding in brackets.

Returns : string ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args    : none

flip_strand

Title   : flip_strand
Usage   : $location->flip_strand();
Function: Flip-flop a strand to the opposite
Returns : None
Args    : None

min_end

Title   : min_end
Usage   : my $minend = $location->min_end();
Function: Get minimum ending point of feature. 

          Note that an implementation must not call end() in this method
          unless end() is overridden such as not to delegate to the
          coordinate computation policy object.

Returns : integer or undef if no minimum ending point.
Args    : none

max_end

Title   : max_end
Usage   : my $maxend = $location->max_end();
Function: Get maximum ending point of feature.

          Note that an implementation must not call end() in this method
          unless end() is overridden such as not to delegate to the
          coordinate computation policy object.

Returns : integer or undef if no maximum ending point.
Args    : none

end_pos_type

Title   : end_pos_type
Usage   : my $end_pos_type = $location->end_pos_type();
Function: Get end position encoded as text.

          Known valid values are 'BEFORE' (5..<100), 'AFTER' (5..>100), 
          'EXACT' (5..100), 'WITHIN' (5..(90.100)), 'BETWEEN', (5^6), with
          their meaning best explained by their GenBank/EMBL location string
          encoding in brackets.

Returns : string ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args    : none

seq_id

Title   : seq_id
Usage   : my $seqid = $location->seq_id();
Function: Get/Set seq_id that location refers to
Returns : seq_id (a string)
Args    : [optional] seq_id value to set

is_remote

Title   : is_remote
Usage   : $is_remote_loc = $loc->is_remote()
Function: Whether or not a location is a remote location.

          A location is said to be remote if it is on a different
          'object' than the object which 'has' this
          location. Typically, features on a sequence will sometimes
          have a remote location, which means that the location of
          the feature is on a different sequence than the one that is
          attached to the feature. In such a case, $loc->seq_id will
          be different from $feat->seq_id (usually they will be the
          same).

          While this may sound weird, it reflects the location of the
          kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL
          feature tables.

Example : 
Returns : TRUE if the location is a remote location, and FALSE otherwise
Args    : Value to set to

coordinate_policy

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 L<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
          L<Bio::Location::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 L<Bio::Location::CoordinatePolicyI> implementing object.
Args    : On set, a L<Bio::Location::CoordinatePolicyI> implementing object.

See Bio::Location::CoordinatePolicyI for more information

to_FTstring

Title   : to_FTstring
Usage   : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args    : none

each_Location

Title   : each_Location
Usage   : @locations = $locObject->each_Location($order);
Function: Conserved function call across Location:: modules - will
          return an array containing the component Location(s) in
          that object, regardless if the calling object is itself a
          single location or one containing sublocations.
Returns : an array of Bio::LocationI implementing objects
Args    : Optional sort order to be passed to sub_Location() for Splits

valid_Location

Title   : valid_Location
Usage   : if ($location->valid_location) {...};
Function: boolean method to determine whether location is considered valid
          (has minimum requirements for a specific LocationI implementation)
Returns : Boolean value: true if location is valid, false otherwise
Args    : none