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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::Map::MappableI \- An object that can be placed in a map .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 3 \& # do not use this module directly \& # See Bio::Map::Mappable for an example of \& # implementation. .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" This object handles the generic notion of an element placed on a (linear) Map. A Mappable can have multiple positions in multiple maps, such as is the case of Restriction enzyme cut sites on sequence maps. For exact information about a mappable's position in a map one must query the associate PositionI objects which are accessible through the \fIget_positions()\fR method. .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "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. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Support" .IX Subsection "Support" Please direct usage questions or support issues to the mailing list: .PP \&\fIbioperl\-l@bioperl.org\fR .PP 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. .SS "Reporting Bugs" .IX Subsection "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: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHOR \- Jason Stajich" .IX Header "AUTHOR - Jason Stajich" Email jason@bioperl.org .SH "CONTRIBUTORS" .IX Header "CONTRIBUTORS" Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.org Sendu Bala bix@sendu.me.uk .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SS "EntityI methods" .IX Subsection "EntityI methods" .Vb 2 \& These are fundamental to coordination of Mappables and other entities, so are \& implemented at the interface level .Ve .SS "get_position_handler" .IX Subsection "get_position_handler" .Vb 5 \& 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 .Ve .SS "PositionHandlerI-related methods" .IX Subsection "PositionHandlerI-related methods" .Vb 2 \& These are fundamental to coordination of Mappables and other entities, so are \& implemented at the interface level .Ve .SS "add_position" .IX Subsection "add_position" .Vb 5 \& Title : add_position \& Usage : $mappable\->add_position($position); \& Function: Add a position to this mappable (defining where on which map it is). \& Returns : n/a \& Args : L object .Ve .SS "get_positions" .IX Subsection "get_positions" .Vb 7 \& Title : get_positions \& Usage : my @positions = $mappable\->get_positions(); \& Function: Get all the Positions of this Mappable (sorted). \& Returns : Array of L objects \& Args : none for all, OR \& L object for positions on the given map, AND/OR some \& other true value to avoid sorting .Ve .SS "each_position" .IX Subsection "each_position" .Vb 3 \& Title : each_position \& Function: Synonym of the get_positions() method. \& Status : deprecated, will be removed in next version .Ve .SS "purge_positions" .IX Subsection "purge_positions" .Vb 8 \& Title : purge_positions \& Usage : $mappable\->purge_positions(); \& Function: Remove positions from this mappable. \& Returns : n/a \& Args : none to remove all positions, OR \& L object to remove just that Position, OR \& L object to remove only those positions on the given \& map .Ve .SS "known_maps" .IX Subsection "known_maps" .Vb 5 \& Title : known_maps \& Usage : my @maps = $marker\->known_maps() \& Function: Returns the maps that this mappable is found on \& Returns : Array of L objects \& Args : none .Ve .SS "MappableI-specific methods" .IX Subsection "MappableI-specific methods" .SS "name" .IX Subsection "name" .Vb 7 \& Title : name \& Usage : my $name = $marker\->name(); \& $marker\->name($new_name); \& Function: Get/Set the name for this Mappable. \& Returns : A scalar representing the current name of this Mappable \& Args : none to get \& string to set .Ve .SS "id" .IX Subsection "id" .Vb 7 \& Title : id \& Usage : my $id = $marker\->id(); \& $marker\->id($new_id); \& Function: Get/Set the id for this Mappable. \& Returns : A scalar representing the current id of this Mappable \& Args : none to get \& string to set .Ve .SS "in_map" .IX Subsection "in_map" .Vb 5 \& Title : in_map \& Usage : if ($marker\->in_map($map)) {...} \& Function: Tests if this mappable is found on a specific map \& Returns : boolean \& Args : L .Ve .SH "RangeI-related Methods" .IX Header "RangeI-related Methods" They throw an error if start and end are not defined in the Positions of the Mappables supplied. .SS "equals" .IX Subsection "equals" .Vb 10 \& Title : equals \& Usage : if ($mappable\->equals($other_mappable)) {...} \& my @equal_positions = $mappable\->equals($other_mappable); \& Function: Finds the positions in this mappable that are equal to any \& comparison positions. \& Returns : array of L objects \& Args : arg #1 = L OR L to compare \& this one to (mandatory) \& arg #2 = optionally, the key => value pairs below \& \-map => Bio::Map::MapI : optionally a Map to only consider \& positions on the given map \& \-relative => Bio::Map::RelativeI : optionally a Relative to ask if \& the Positions equal in terms of \& their relative position to the \& thing described by that Relative .Ve .SS "overlaps" .IX Subsection "overlaps" .Vb 10 \& Title : overlaps \& Usage : if ($mappable\->overlaps($other_mappable)) {...} \& my @overlapping_positions = $mappable\->overlaps($other_mappable); \& Function: Finds the positions in this mappable that overlap with any \& comparison positions. \& Returns : array of L objects \& Args : arg #1 = L OR L to compare \& this one to (mandatory) \& arg #2 = optionally, the key => value pairs below \& \-map => Bio::Map::MapI : optionally a Map to only consider \& positions on the given map \& \-relative => Bio::Map::RelativeI : optionally a Relative to ask if \& the Positions overlap in terms of \& their relative position to the \& thing described by that Relative .Ve .SS "contains" .IX Subsection "contains" .Vb 10 \& Title : contains \& Usage : if ($mappable\->contains($other_mappable)) {...} \& my @container_positions = $mappable\->contains($other_mappable); \& Function: Finds the positions in this mappable that contain any comparison \& positions. \& Returns : array of L objects \& Args : arg #1 = L OR L to compare \& this one to (mandatory) \& arg #2 = optionally, the key => value pairs below \& \-map => Bio::Map::MapI : optionally a Map to only consider \& positions on the given map \& \-relative => Bio::Map::RelativeI : optionally a Relative to ask if \& the Positions contains in terms of \& their relative position to the \& thing described by that Relative .Ve .SS "intersection" .IX Subsection "intersection" .Vb 10 \& Title : intersection \& Usage : my $position = $mappable\->intersection($other_mappable); \& my $position = Bio::Map::Mappable\->intersection(\e@mappables); \& Function: Make the position that is at the intersection of all positions of all \& supplied mappables. \& Returns : L object or undef (if not all positions overlap) \& Args : arg #1 = L OR L to compare \& this one to, or an array ref of such objects (mandatory) \& arg #2 = optionally, the key => value pairs below \& \-map => Bio::Map::MapI : optionally a Map to only consider \& positions on the given map \& \-relative => Bio::Map::RelativeI : optionally a Relative to to ask \& how the Positions intersect in \& terms of their relative position \& to the thing described by that \& Relative .Ve .SS "union" .IX Subsection "union" .Vb 10 \& Title : union \& Usage : my $position = $mappable\->union($other_mappable); \& my $position = Bio::Map::Mappable\->union(@mappables); \& Function: Make the minimal position that contains all of the positions of all \& supplied mappables. \& Returns : L object or undef (if not all positions overlap) \& Args : arg #1 = L OR L to compare \& this one to, or an array ref of such objects (mandatory) \& arg #2 = optionally, the key => value pairs below \& \-map => Bio::Map::MapI : optionally a Map to only consider \& positions on the given map \& \-relative => Bio::Map::RelativeI : optionally a Relative to to ask \& if the union of the Positions in \& terms of their relative position \& to the thing described by that \& Relative .Ve