Bio::Map::PositionI3pm

Abstracts the notion of a position having a value in the context of a marker and a map

Usage

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

Overview

This object stores one of the positions 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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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:

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

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

Contributors

Lincoln Stein, lstein-at-cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Sendu Bala, [email protected]

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 compatibility 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)

Releases

7 releases since Debian 3.0 (Woody); the text changed 6 times.