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Bio::Map::PositionI.3pm

NAME

Bio::Map::PositionI - Abstracts the notion of a position having a value in the context of a marker and a Map

SYNOPSIS

     # do not use this module directly
     # See Bio::Map::Position for an example of
     # implementation.
 
 

DESCRIPTION

This object stores one of the postions that a mappable object (e.g. Marker) may have in a map.

Positions can have non-numeric values or other methods to store the locations, so they have a method numeric() which does the conversion. numeric() returns the position in a form that can be compared between other positions of the same type. It is not necessarily a value suitable for sorting positions (it may be the distance from the previous position); for that purpose the result of sortable() should be used.

A 'position', in addition to being a single point, can also be an area and so can be imagined as a range and compared with other positions on the basis of overlap, intersection etc.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. 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 of 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.org

CONTRIBUTORS

Lincoln Stein, lstein-at-cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Sendu Bala, bix@sendu.me.uk

APPENDIX

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

EntityI methods

  These are fundamental to coordination of Positions and other entities, so are
  implemented at the interface level
 
 

get_position_handler

  Title   : get_position_handler
  Usage   : my $position_handler = $entity->get_position_handler();
  Function: Gets a PositionHandlerI that $entity is registered with.
  Returns : Bio::Map::PositionHandlerI object
  Args    : none
 
 

PositionHandlerI-related methods

  These are fundamental to coordination of Positions and other entities, so are
  implemented at the interface level
 
 

map

  Title   : map
  Usage   : my $map = $position->map();
            $position->map($map);
  Function: Get/Set the map the position is in.
  Returns : L<Bio::Map::MapI>
  Args    : none to get
            new L<Bio::Map::MapI> to set
 
 

element

  Title   : element
  Usage   : my $element = $position->element();
            $position->element($element);
  Function: Get/Set the element the position is for.
  Returns : L<Bio::Map::MappableI>
  Args    : none to get
            new L<Bio::Map::MappableI> to set
 
 

marker

  Title   : marker
  Function: This is a synonym of the element() method
  Status  : deprecated, will be removed in the next version
 
 

PositionI-specific methods

value

  Title   : value
  Usage   : my $pos = $position->value();
  Function: Get/Set the value for this position
  Returns : scalar, value
  Args    : [optional] new value to set
 
 

numeric

  Title   : numeric
  Usage   : my $num = $position->numeric;
  Function: Read-only method that is guaranteed to return a numeric 
            representation of the start of this position. 
  Returns : scalar numeric
  Args    : none to get the co-ordinate normally (see absolute() method), OR
            Bio::Map::RelativeI to get the co-ordinate converted to be
            relative to what this Relative describes.
 
 

sortable

  Title   : sortable
  Usage   : my $num = $position->sortable();
  Function: Read-only method that is guaranteed to return a value suitable
            for correctly sorting this kind of position amongst other positions
            of the same kind on the same map. Note that sorting different kinds
            of position together is unlikely to give sane results.
  Returns : numeric
  Args    : none
 
 

relative

   Title   : relative
   Usage   : my $relative = $position->relative();
             $position->relative($relative);
   Function: Get/set the thing this Position's coordinates (numerical(), start(),
             end()) are relative to, as described by a Relative object.
   Returns : Bio::Map::RelativeI (default is one describing "relative to the
             start of the Position's map")
   Args    : none to get, OR
             Bio::Map::RelativeI to set
 
 

absolute

   Title   : absolute
   Usage   : my $absolute = $position->absolute();
             $position->absolute($absolute);
   Function: Get/set how this Position's co-ordinates (numerical(), start(),
             end()) are reported. When absolute is off, co-ordinates are
             relative to the thing described by relative(). Ie. the value
             returned by start() will be the same as the value you set start()
             to. When absolute is on, co-ordinates are converted to be relative
             to the start of the map.
 
             So if relative() currently points to a Relative object describing
             "relative to another position which is 100 bp from the start of
             the map", this Position's start() had been set to 50 and absolute()
             returns 1, $position->start() will return 150. If absolute() returns
             0 in the same situation, $position->start() would return 50.
 
   Returns : boolean (default 0)
   Args    : none to get, OR
             boolean to set
 
 

RangeI-based methods

start

   Title   : start
   Usage   : my $start = $position->start();
             $position->start($start);
   Function: Get/set the start co-ordinate of this position.
   Returns : the start of this position
   Args    : scalar numeric to set, OR
             none to get the co-ordinate normally (see absolute() method), OR
             Bio::Map::RelativeI to get the co-ordinate converted to be
             relative to what this Relative describes.
 
 

end

   Title   : end
   Usage   : my $end = $position->end();
             $position->end($end);
   Function: Get/set the end co-ordinate of this position.
   Returns : the end of this position
   Args    : scalar numeric to set, OR
             none to get the co-ordinate normally (see absolute() method), OR
             Bio::Map::RelativeI to get the co-ordinate converted to be
             relative to what this Relative describes.
 
 

length

   Title   : length
   Usage   : $length = $position->length();
   Function: Get the length of this position.
   Returns : the length of this position
   Args    : none
 
 

strand

   Title   : strand
   Usage   : $strand = $position->strand();
   Function: Get the strand of this position; it is always 1 since maps to not
             have strands.
   Returns : 1
   Args    : none
 
 

toString

   Title   : toString
   Usage   : print $position->toString(), "\n";
   Function: stringifies this range
   Returns : a string representation of the range of this Position
   Args    : optional Bio::Map::RelativeI to have the co-ordinates reported
             relative to the thing described by that Relative
 
 

RangeI-related methods

These methods work by considering only the values of start() and end(), as modified by considering every such co-ordinate relative to the start of the map (ie. absolute(1) is set temporarily during the calculation), or any supplied Relative. For the boolean methods, when the comparison Position is on the same map as the calling Position, there is no point supplying a Relative since the answer will be the same as without. Relative is most useful when comparing Positions on different maps and you have a Relative that describes some special place on each map like 'the start of the gene', where the actual start of the gene relative to the start of the map is different for each map.

The methods do not consider maps during their calculations - things on different maps can overlap/contain/intersect/etc. each other.

The geometrical methods (intersect, union etc.) do things to the geometry of ranges, and return Bio::Map::PositionI compliant objects or triplets (start, stop, strand) from which new positions could be built. When a PositionI is made it will have a map transferred to it if all the arguments shared the same map. If a Relative was supplied the result will have that same Relative.

Note that the strand-testing args are there for compatability with the RangeI interface. They have no meaning when only using PositionI objects since maps do not have strands. Typically you will just set the argument to undef if you want to supply the argument after it.

equals

   Title   : equals
   Usage   : if ($p1->equals($p2)) {...}
   Function: Test whether $p1 has the same start, end, length as $p2.
   Returns : true if they are describing the same position (regardless of map)
   Args    : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
                      one to (mandatory)
             arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
             arg #3 = optional Bio::Map::RelativeI to ask if the Positions
                      equal in terms of their relative position to the thing
                      described by that Relative
 
 

less_than

  Title   : less_than
  Usage   : if ($position->less_than($other_position)) {...}
  Function: Ask if this Position ends before another starts.
  Returns : boolean
  Args    : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
                     one to (mandatory)
            arg #2 = optional Bio::Map::RelativeI to ask if the Position is less
                     in terms of their relative position to the thing described
                     by that Relative
 
 

greater_than

  Title   : greater_than
  Usage   : if ($position->greater_than($other_position)) {...}
  Function: Ask if this Position starts after another ends.
  Returns : boolean
  Args    : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
                     one to (mandatory)
            arg #2 = optional Bio::Map::RelativeI to ask if the Position is
                     greater in terms of their relative position to the thing
                     described by that Relative
 
 

overlaps

   Title   : overlaps
   Usage   : if ($p1->overlaps($p2)) {...}
   Function: Tests if $p1 overlaps $p2.
   Returns : True if the positions overlap (regardless of map), false otherwise
   Args    : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
                      one to (mandatory)
             arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
             arg #3 = optional Bio::Map::RelativeI to ask if the Positions
                      overlap in terms of their relative position to the thing
                      described by that Relative
             arg #4 = optional minimum percentage length of the overlap before
                      reporting an overlap exists (default 0)
 
 

contains

   Title   : contains
   Usage   : if ($p1->contains($p2)) {...}
   Function: Tests whether $p1 totally contains $p2.
   Returns : true if the argument is totally contained within this position
             (regardless of map), false otherwise
   Args    : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
                      one to, or scalar number (mandatory)
             arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
             arg #3 = optional Bio::Map::RelativeI to ask if the Position
                      is contained in terms of their relative position to the
                      thing described by that Relative
 
 

intersection

  Title   : intersection
  Usage   : ($start, $stop, $strand) = $p1->intersection($p2)
            ($start, $stop, $strand) = Bio::Map::Position->intersection(\@positions);
            $mappable = $p1->intersection($p2, undef, $relative);
            $mappable = Bio::Map::Position->intersection(\@positions);
  Function: gives the range that is contained by all ranges
  Returns : undef if they do not overlap, OR
            Bio::Map::Mappable object who's positions are the
            cross-map-calculated intersection of the input positions on all the
            maps that the input positions belong to, OR, in list context, a three
            element array (start, end, strand)
  Args    : arg #1 = [REQUIRED] a Bio::RangeI (eg. a Bio::Map::Position) to
                     compare this one to, or an array ref of Bio::RangeI
            arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
            arg #3 = optional Bio::Map::RelativeI to ask how the Positions
                     intersect in terms of their relative position to the thing
                     described by that Relative
 
 

union

  Title   : union
  Usage   : ($start, $stop, $strand) = $p1->union($p2);
            ($start, $stop, $strand) = Bio::Map::Position->union(@positions);
            my $mappable = $p1->union($p2);
            my $mappable = Bio::Map::Position->union(@positions);
  Function: finds the minimal position/range that contains all of the positions
  Returns : Bio::Map::Mappable object who's positions are the
            cross-map-calculated union of the input positions on all the maps
            that the input positions belong to, OR, in list context, a three
            element array (start, end, strand)
  Args    : a Bio::Map::PositionI to compare this one to, or a list of such
            OR
            a single Bio::Map::PositionI or array ref of such AND a
            Bio::Map::RelativeI to ask for the Position's union in terms of their
            relative position to the thing described by that Relative
 
 

overlap_extent

  Title   : overlap_extent
  Usage   : ($a_unique,$common,$b_unique) = $a->overlap_extent($b)
  Function: Provides actual amount of overlap between two different
            positions
  Example :
  Returns : array of values containing the length unique to the calling 
            position, the length common to both, and the length unique to 
            the argument position
  Args    : a position
 
 

disconnected_ranges

  Title   : disconnected_ranges
  Usage   : my @disc_ranges = Bio::Map::Position->disconnected_ranges(@ranges);
  Function: Creates the minimal set of positions such that each input position is
            fully contained by at least one output position, and none of the
            output positions overlap.
  Returns : Bio::Map::Mappable with the calculated disconnected ranges
  Args    : a Bio::Map::PositionI to compare this one to, or a list of such,
            OR
            a single Bio::Map::PositionI or array ref of such AND a
            Bio::Map::RelativeI to consider all Position's co-ordinates in terms
            of their relative position to the thing described by that Relative,
            AND, optionally, an int for the minimum percentage of overlap that
            must be present before considering two ranges to be overlapping
            (default 0)