Bio::Map::PositionI(3pm) | User Contributed Perl Documentation | Bio::Map::PositionI(3pm) |
Bio::Map::PositionI - Abstracts the notion of a position having a value in the context of a marker and a Map
# do not use this module directly # See Bio::Map::Position for an example of # implementation.
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.
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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:
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Email jason-at-bioperl.org
Lincoln Stein, lstein-at-cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Sendu Bala, bix@sendu.me.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
These are fundamental to coordination of Positions and other entities, so are implemented at the interface level
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
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
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
Title : marker Function: This is a synonym of the element() method Status : deprecated, will be removed in the next version
Title : value Usage : my $pos = $position->value(); Function: Get/Set the value for this position Returns : scalar, value Args : [optional] new value to set
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.
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
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
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
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.
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.
Title : length Usage : $length = $position->length(); Function: Get the length of this position. Returns : the length of this position Args : none
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
Title : toString Usage : print $position->toString(), "\n"; Function: stringifies this range Returns : a string representation of the range of this Position Args : optional Bio::Map::RelativeI to have the co-ordinates reported relative to the thing described by that Relative
These methods work by considering only the values of start() and end(), as modified by considering every such co-ordinate relative to the start of the map (ie. absolute(1) is set temporarily during the calculation), or any supplied Relative. For the boolean methods, when the comparison Position is on the same map as the calling Position, there is no point supplying a Relative since the answer will be the same as without. Relative is most useful when comparing Positions on different maps and you have a Relative that describes some special place on each map like 'the start of the gene', where the actual start of the gene relative to the start of the map is different for each map.
The methods do not consider maps during their calculations - things on different maps can overlap/contain/intersect/etc. each other.
The geometrical methods (intersect, union etc.) do things to the geometry of ranges, and return Bio::Map::PositionI compliant objects or triplets (start, stop, strand) from which new positions could be built. When a PositionI is made it will have a map transferred to it if all the arguments shared the same map. If a Relative was supplied the result will have that same Relative.
Note that the strand-testing args are there for compatibility with the RangeI interface. They have no meaning when only using PositionI objects since maps do not have strands. Typically you will just set the argument to undef if you want to supply the argument after it.
Title : equals Usage : if ($p1->equals($p2)) {...} Function: Test whether $p1 has the same start, end, length as $p2. Returns : true if they are describing the same position (regardless of map) Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this one to (mandatory) arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore') arg #3 = optional Bio::Map::RelativeI to ask if the Positions equal in terms of their relative position to the thing described by that Relative
Title : less_than Usage : if ($position->less_than($other_position)) {...} Function: Ask if this Position ends before another starts. Returns : boolean Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this one to (mandatory) arg #2 = optional Bio::Map::RelativeI to ask if the Position is less in terms of their relative position to the thing described by that Relative
Title : greater_than Usage : if ($position->greater_than($other_position)) {...} Function: Ask if this Position starts after another ends. Returns : boolean Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this one to (mandatory) arg #2 = optional Bio::Map::RelativeI to ask if the Position is greater in terms of their relative position to the thing described by that Relative
Title : overlaps Usage : if ($p1->overlaps($p2)) {...} Function: Tests if $p1 overlaps $p2. Returns : True if the positions overlap (regardless of map), false otherwise Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this one to (mandatory) arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore') arg #3 = optional Bio::Map::RelativeI to ask if the Positions overlap in terms of their relative position to the thing described by that Relative arg #4 = optional minimum percentage length of the overlap before reporting an overlap exists (default 0)
Title : contains Usage : if ($p1->contains($p2)) {...} Function: Tests whether $p1 totally contains $p2. Returns : true if the argument is totally contained within this position (regardless of map), false otherwise Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this one to, or scalar number (mandatory) arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore') arg #3 = optional Bio::Map::RelativeI to ask if the Position is contained in terms of their relative position to the thing described by that Relative
Title : intersection Usage : ($start, $stop, $strand) = $p1->intersection($p2) ($start, $stop, $strand) = Bio::Map::Position->intersection(\@positions); $mappable = $p1->intersection($p2, undef, $relative); $mappable = Bio::Map::Position->intersection(\@positions); Function: gives the range that is contained by all ranges Returns : undef if they do not overlap, OR Bio::Map::Mappable object who's positions are the cross-map-calculated intersection of the input positions on all the maps that the input positions belong to, OR, in list context, a three element array (start, end, strand) Args : arg #1 = [REQUIRED] a Bio::RangeI (eg. a Bio::Map::Position) to compare this one to, or an array ref of Bio::RangeI arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore') arg #3 = optional Bio::Map::RelativeI to ask how the Positions intersect in terms of their relative position to the thing described by that Relative
Title : union Usage : ($start, $stop, $strand) = $p1->union($p2); ($start, $stop, $strand) = Bio::Map::Position->union(@positions); my $mappable = $p1->union($p2); my $mappable = Bio::Map::Position->union(@positions); Function: finds the minimal position/range that contains all of the positions Returns : Bio::Map::Mappable object who's positions are the cross-map-calculated union of the input positions on all the maps that the input positions belong to, OR, in list context, a three element array (start, end, strand) Args : a Bio::Map::PositionI to compare this one to, or a list of such OR a single Bio::Map::PositionI or array ref of such AND a Bio::Map::RelativeI to ask for the Position's union in terms of their relative position to the thing described by that Relative
Title : overlap_extent Usage : ($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
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)
2018-10-27 | perl v5.26.2 |