Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::LocationI.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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 AB18375:450-900 which can be found in GenBank/EMBL
            feature tables.
 
  Example : 
  Returns : TRUE if the location is a remote location, and FALSE otherwise
  Args    :
 
 

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