Module | Bio::Map::ActsLikeMap |
In: |
lib/bio/map.rb
|
The Bio::Map::ActsLikeMap module contains methods that are typical for map-like things:
Classes that include this mixin should provide an array property called mappings_as_map.
For example:
class MyMapThing include Bio::Map::ActsLikeMap def initialize (name) @name = name @mappings_as_maps = Array.new end attr_accessor :name, :mappings_as_map end
Adds a Bio::Map::Mappings object to its array of mappings.
# suppose we have a Bio::Map::SimpleMap object called my_map my_map.add_mapping_as_map(Bio::Map::Marker.new('marker_a'), '5')
Arguments:
Returns: | itself |
# File lib/bio/map.rb, line 116 116: def add_mapping_as_map(marker, location = nil) 117: unless marker.class.include?(Bio::Map::ActsLikeMarker) 118: raise "[Error] marker is not object that implements Bio::Map::ActsLikeMarker" 119: end 120: my_mapping = ( location.nil? ) ? Bio::Map::Mapping.new(self, marker, nil) : Bio::Map::Mapping.new(self, marker, Bio::Locations.new(location)) 121: if ! marker.mapped_to?(self) 122: self.mappings_as_map.push(my_mapping) 123: marker.mappings_as_marker.push(my_mapping) 124: else 125: already_mapped = false 126: marker.positions_on(self).each do |loc| 127: if loc.equals?(Bio::Locations.new(location)) 128: already_mapped = true 129: end 130: end 131: if ! already_mapped 132: self.mappings_as_map.push(my_mapping) 133: marker.mappings_as_marker.push(my_mapping) 134: end 135: end 136: 137: return self 138: end
Checks whether a Bio::Map::Marker is mapped to this Bio::Map::SimpleMap.
Arguments:
Returns: | true or false |
# File lib/bio/map.rb, line 147 147: def contains_marker?(marker) 148: unless marker.class.include?(Bio::Map::ActsLikeMarker) 149: raise "[Error] marker is not object that implements Bio::Map::ActsLikeMarker" 150: end 151: contains = false 152: self.mappings_as_map.each do |mapping| 153: if mapping.marker == marker 154: contains = true 155: return contains 156: end 157: end 158: return contains 159: end