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BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Map::PositionI

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:

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, 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
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)