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Man Pages


Manual Reference Pages  -  BIO::LOCATIONI (3)

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NAME

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

CONTENTS

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://github.com/bioperl/bioperl-live/issues



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



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