module Bio::Map::ActsLikeMarker

Description¶ ↑

The Bio::Map::ActsLikeMarker module contains methods that are typical for marker-like things:

map it to one or more maps
check if it’s mapped to a given map and can be mixed into other classes (e.g. Bio::Map::Marker)

Classes that include this mixin should provide an array property called mappings_as_marker.

For example:

class MyMarkerThing
  include Bio::Map::ActsLikeMarker

  def initialize(name)
    @name = name
    @mappings_as_marker = Array.new
  end
  attr_accessor :name, :mappings_as_marker
 end

Public Instance Methods

add_mapping_as_marker(map, location = nil) click to toggle source

Description¶ ↑

Adds a Bio::Map::Mappings object to its array of mappings.

Usage¶ ↑

# suppose we have a Bio::Map::Marker object called marker_a
marker_a.add_mapping_as_marker(Bio::Map::SimpleMap.new('my_map'), '5')

Arguments:

map (required): Bio::Map::SimpleMap object
location: location of mapping. Should be a string, not a number.

Returns: itself

    # File lib/bio/map.rb
203 def add_mapping_as_marker(map, location = nil)
204   unless map.class.include?(Bio::Map::ActsLikeMap)
205     raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
206   end
207   my_mapping = (location.nil?) ? Bio::Map::Mappings.new(map, self, nil) : Bio::Map::Mapping.new(map, self, Bio::Locations.new(location))
208   if ! self.mapped_to?(map)
209     self.mappings_as_marker.push(my_mapping)
210     map.mappings_as_map.push(my_mapping)
211   else
212     already_mapped = false
213     self.positions_on(map).each do |loc|
214       if loc.equals?(Bio::Locations.new(location))
215         already_mapped = true
216       end
217     end
218     if ! already_mapped
219       self.mappings_as_marker.push(my_mapping)
220       map.mappings_as_map.push(my_mapping)
221     end
222   end
223 end

mapped_to?(map) click to toggle source

Check whether this marker is mapped to a given Bio::Map::SimpleMap.

Arguments:

map: a Bio::Map::SimpleMap object

Returns: true or false

    # File lib/bio/map.rb
230 def mapped_to?(map)
231   unless map.class.include?(Bio::Map::ActsLikeMap)
232     raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
233   end
234           
235   mapped = false
236   self.mappings_as_marker.each do |mapping|
237     if mapping.map == map
238       mapped = true
239       return mapped
240     end
241   end
242 
243   return mapped
244 end

mappings_on(map) click to toggle source

Return all mappings of this marker on a given map.

Arguments:

map: an object that mixes in Bio::Map::ActsLikeMap

Returns: array of Bio::Map::Mapping objects

    # File lib/bio/map.rb
271 def mappings_on(map)
272   unless map.class.include?(Bio::Map::ActsLikeMap)
273     raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
274   end
275   
276   m = Array.new
277   self.mappings_as_marker.each do |mapping|
278     if mapping.map == map
279       m.push(mapping)
280     end
281   end
282   
283   return m
284 end

positions_on(map) click to toggle source

Return all positions of this marker on a given map.

Arguments:

map: an object that mixes in Bio::Map::ActsLikeMap

Returns: array of Bio::Location objects

    # File lib/bio/map.rb
251 def positions_on(map)
252   unless map.class.include?(Bio::Map::ActsLikeMap)
253     raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
254   end
255   
256   positions = Array.new
257   self.mappings_as_marker.each do |mapping|
258     if mapping.map == map
259       positions.push(mapping.location)
260     end
261   end
262   
263   return positions
264 end