/ 
bioperl-0.7.0
/ 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://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