Provided by: libbio-perl-perl_1.6.901-2_all bug

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://redmine.open-bio.org/projects/bioperl/

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 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)