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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::Mappable \- An object representing a generic map element that can have multiple locations in several maps. .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 5 \& # a map element in two different positions on the same map \& $map1 = Bio::Map::SimpleMap\->new(); \& $position1 = Bio::Map::Position\->new(\-map => $map1, \-value => 100); \& $position2 = Bio::Map::Position\->new(\-map => $map1, \-value => 200); \& $mappable = Bio::Map::Mappable\->new(\-positions => [$position1, $position2] ); \& \& # add another position on a different map \& $map2 = Bio::Map::SimpleMap\->new(); \& $position3 = Bio::Map::Position\->new(\-map => $map2, $value => 50); \& $mappable\->add_position($position3); \& \& # get all the places our map element is found, on a particular map of interest \& foreach $pos ($mappable\->get_positions($map1)) { \& print $pos\->value, "\en"; \& } .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" This object handles the notion of a generic map element. Mappables are entities with one or more positions on one or more maps. .PP This object is a pure perl implementation of Bio::Map::MappableI. That interface implements some of its own methods so check the docs there for those. .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 \- Sendu Bala" .IX Header "AUTHOR - Sendu Bala" Email 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 "new" .IX Subsection "new" .Vb 6 \& Title : new \& Usage : my $mappable = Bio::Map::Mappable\->new(); \& Function: Builds a new Bio::Map::Mappable object \& Returns : Bio::Map::Mappable \& Args : \-name => string : name of the mappable element \& \-id => string : id of the mappable element .Ve .SS "name" .IX Subsection "name" .Vb 7 \& Title : name \& Usage : $mappable\->name($new_name); \& my $name = $mappable\->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 = $mappable\->id(); \& $mappable\->id($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 ($mappable\->in_map($map)) {...} \& Function: Tests if this mappable is found on a specific map \& Returns : boolean \& Args : L .Ve .SS "Comparison methods" .IX Subsection "Comparison methods" .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, one or more of the key => value pairs below \& \-map => MapI : a Bio::Map::MapI to only consider positions \& on the given map \& \-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms \& of each Position\*(Aqs relative position to the \& thing described by that Relative .Ve .SS "less_than" .IX Subsection "less_than" .Vb 10 \& Title : less_than \& Usage : if ($mappable\->less_than($other_mappable)) {...} \& my @lesser_positions = $mappable\->less_than($other_mappable); \& Function: Finds the positions in this mappable that are less than all \& comparison positions. \& Returns : array of L objects \& Args : arg #1 = L OR L to compare \& this one to (mandatory) \& arg #2 = optionally, one or more of the key => value pairs below \& \-map => MapI : a Bio::Map::MapI to only consider positions \& on the given map \& \-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms \& of each Position\*(Aqs relative position to the \& thing described by that Relative .Ve .SS "greater_than" .IX Subsection "greater_than" .Vb 10 \& Title : greater_than \& Usage : if ($mappable\->greater_than($other_mappable)) {...} \& my @greater_positions = $mappable\->greater_than($other_mappable); \& Function: Finds the positions in this mappable that are greater than all \& comparison positions. \& Returns : array of L objects \& Args : arg #1 = L OR L to compare \& this one to (mandatory) \& arg #2 = optionally, one or more of the key => value pairs below \& \-map => MapI : a Bio::Map::MapI to only consider positions \& on the given map \& \-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms \& of each Position\*(Aqs 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, one or more of the key => value pairs below \& \-map => MapI : a Bio::Map::MapI to only consider positions \& on the given map \& \-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms \& of each Position\*(Aqs 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, one or more of the key => value pairs below \& \-map => MapI : a Bio::Map::MapI to only consider positions \& on the given map \& \-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms \& of each Position\*(Aqs relative position to the \& thing described by that Relative .Ve .SS "overlapping_groups" .IX Subsection "overlapping_groups" .Vb 10 \& Title : overlapping_groups \& Usage : my @groups = $mappable\->overlapping_groups($other_mappable); \& my @groups = Bio::Map::Mappable\->overlapping_groups(\e@mappables); \& Function: Look at all the positions of all the supplied mappables and group \& them according to overlap. \& Returns : array of array refs, each ref containing the Bio::Map::PositionI \& objects that overlap with each other \& Args : arg #1 = L OR L to compare \& this one to, or an array ref of such objects (mandatory) \& arg #2 = optionally, one or more of the key => value pairs below \& \-map => MapI : a Bio::Map::MapI to only consider positions \& on the given map \& \-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms \& of each Position\*(Aqs relative position to the \& thing described by that Relative \& \-min_pos_num => int : the minimum number of positions that must \& be in a group before it will be returned \& [default is 1] \& \-min_mappables_num => int : the minimum number of different \& mappables represented by the \& positions in a group before it \& will be returned [default is 1] \& \-min_mappables_percent => number : as above, but the minimum \& percentage of input mappables \& [default is 0] \& \-min_map_num => int : the minimum number of different \& maps represented by the positions \& in a group before it will be \& returned [default is 1] \& \-min_map_percent => number : as above, but the minimum \& percentage of maps known by the \& input mappables [default is 0] \& \-require_self => 1|0 : require that at least one of the \& calling object\*(Aqs positions be in \& each group [default is 1, has no \& effect when the second usage form \& is used] \& \-required => \e@mappables : require that at least one position \& for each mappable supplied in this \& array ref be in each group .Ve .SS "disconnected_intersections" .IX Subsection "disconnected_intersections" .Vb 10 \& Title : disconnected_intersections \& Usage : @positions = $mappable\->disconnected_intersections($other_mappable); \& @positions = Bio::Map::Mappable\->disconnected_intersections(\e@mappables); \& Function: Make the positions that are at the intersection of each group of \& overlapping positions, considering all the positions of the supplied \& mappables. \& Returns : new Bio::Map::Mappable who\*(Aqs positions on maps are the calculated \& disconnected unions \& Args : arg #1 = L OR L to compare \& this one to, or an array ref of such objects (mandatory) \& arg #2 = optionally, one or more of the key => value pairs below \& \-map => MapI : a Bio::Map::MapI to only consider positions \& on the given map \& \-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms \& of each Position\*(Aqs relative position to the \& thing described by that Relative \& \-min_pos_num => int : the minimum number of positions that must \& be in a group before the intersection will \& be calculated and returned [default is 1] \& \-min_mappables_num => int : the minimum number of different \& mappables represented by the \& positions in a group before the \& intersection will be calculated \& and returned [default is 1] \& \-min_mappables_percent => number : as above, but the minimum \& percentage of input mappables \& [default is 0] \& \-min_map_num => int : the minimum number of different \& maps represented by the positions \& in a group before the intersection \& will be calculated and returned \& [default is 1] \& \-min_map_percent => number : as above, but the minimum \& percentage of maps known by the \& input mappables [default is 0] \& \-require_self => 1|0 : require that at least one of the \& calling object\*(Aqs positions be in \& each group [default is 1, has no \& effect when the second usage form \& is used] \& \-required => \e@mappables : require that at least one position \& for each mappable supplied in this \& array ref be in each group .Ve .SS "disconnected_unions" .IX Subsection "disconnected_unions" .Vb 10 \& Title : disconnected_unions \& Usage : my @positions = $mappable\->disconnected_unions($other_mappable); \& my @positions = Bio::Map::Mappable\->disconnected_unions(\e@mappables); \& Function: Make the positions that are the union of each group of overlapping \& positions, considering all the positions of the supplied mappables. \& Returns : new Bio::Map::Mappable who\*(Aqs positions on maps are the calculated \& disconnected unions \& Args : arg #1 = L OR L to compare \& this one to, or an array ref of such objects (mandatory) \& arg #2 = optionally, one or more of the key => value pairs below \& \-map => MapI : a Bio::Map::MapI to only consider positions \& on the given map \& \-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms \& of each Position\*(Aqs relative position to the \& thing described by that Relative \& \-min_pos_num => int : the minimum number of positions that must \& be in a group before the union will be \& calculated and returned [default is 1] \& \-min_mappables_num => int : the minimum number of different \& mappables represented by the \& positions in a group before the \& union will be calculated and \& returned [default is 1] \& \-min_mappables_percent => number : as above, but the minimum \& percentage of input mappables \& [default is 0] \& \-min_map_num => int : the minimum number of different \& maps represented by the positions \& in a group before the union will \& be calculated and returned \& [default is 1] \& \-min_map_percent => number : as above, but the minimum \& percentage of maps known by the \& input mappables [default is 0] \& \-require_self => 1|0 : require that at least one of the \& calling object\*(Aqs positions be in \& each group [default is 1, has no \& effect when the second usage form \& is used] \& \-required => \e@mappables : require that at least one position \& for each mappable supplied in this \& array ref be in each group .Ve .SS "tuple" .IX Subsection "tuple" .Vb 7 \& Title : tuple \& Usage : Do Not Use! \& Function: tuple was supposed to be a private method; this method no longer \& does anything \& Returns : warning \& Args : none \& Status : deprecated, will be removed in next version .Ve .SS "annotation" .IX Subsection "annotation" .Vb 8 \& Title : annotation \& Usage : $mappable\->annotation($an_col); \& my $an_col = $mappable\->annotation(); \& Function: Get the annotation collection (see Bio::AnnotationCollectionI) \& for this annotatable object. \& Returns : a Bio::AnnotationCollectionI implementing object, or undef \& Args : none to get, OR \& a Bio::AnnotationCollectionI implementing object to set .Ve