class Bio::PhyloXML::SequenceRelation
Description¶ ↑
This is used to express a typed relationship between two sequences. For example it could be used to describe an orthology (in which case attribute ‘type’ is ‘orthology’).
Attributes
distance[R]
Float
id_ref_0[RW]
String
id_ref_1[RW]
String
type[R]
String. Allowed values: “orthology”, “one_to_one_orthology”, “super_orthology”, “paralogy”, “ultra_paralogy”, “xenology”, “unknown”, “other”
Public Instance Methods
distance=(str)
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@todo it has Confidences objects.
# File lib/bio-phyloxml/phyloxml_elements.rb 1125 def distance=(str) 1126 @distance = str.to_f if str != nil 1127 end
to_xml()
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Converts elements to xml representation. Called by PhyloXML::Writer
class.
# File lib/bio-phyloxml/phyloxml_elements.rb 1145 def to_xml 1146 if @id_ref_0 == nil or @id_ref_1 == nil or @type == nil 1147 raise "Attributes id_ref_0, id_ref_1, type are required elements by SequenceRelation element." 1148 else 1149 sr = LibXML::XML::Node.new('sequence_relation') 1150 sr['id_ref_0'] = @id_ref_0 1151 sr['id_ref_1'] = @id_ref_1 1152 sr['distance'] = @distance.to_s if (defined? @distance) && @distance 1153 sr['type'] = @type 1154 return sr 1155 end 1156 end
type=(str)
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String. Allowed values: “orthology”, “one_to_one_orthology”, “super_orthology”, “paralogy”, “ultra_paralogy”, “xenology”, “unknown”, “other”
# File lib/bio-phyloxml/phyloxml_elements.rb 1132 def type=(str) 1133 #@todo do warning instead? 1134 #@todo do validation at actually writing xml 1135 allowed_values = ["orthology", "one_to_one_orthology", "super_orthology", "paralogy", 1136 "ultra_paralogy", "xenology", "unknown", "other"] 1137 if not allowed_values.include? str 1138 raise "SequenceRelation#type has to be one one of #{allowed_values.join("; ")}" 1139 else 1140 @type = str 1141 end 1142 end