Bio::LocationI(3)

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://bio.perl.org/MailList.html - About the mailing lists

  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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Jason Stajich
Email jason@chg.mc.duke.edu

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

  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 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

  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 RangeI in order to delegate 'get' to
            a 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

  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

  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

  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 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.

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