Class Bio::FANTOM::MaXML::Cluster
In: lib/bio/db/fantom.rb
Parent: MaXML

Methods

Constants

Data_XPath = 'maxml-clusters/cluster'   (MaXML cluster) fantom2.gsc.riken.go.jp/fantom/2.1/allclust.sep.xml.gz

Public Instance methods

[Source]

     # File lib/bio/db/fantom.rb, line 145
145:         def representative_annotations
146:           e = representative_sequence
147:           e ? e.annotations : nil
148:         end
representative_clone()

[Source]

     # File lib/bio/db/fantom.rb, line 150
150:         def representative_cloneid
151:           e = representative_sequence
152:           e ? e.cloneid : nil
153:         end

[Source]

     # File lib/bio/db/fantom.rb, line 116
116:         def representative_seqid
117:           unless defined?(@representative_seqid)
118:             @representative_seqid =
119:               gsub_entities(@elem.text('representative-seqid'))
120:           end
121:           @representative_seqid
122:         end

[Source]

     # File lib/bio/db/fantom.rb, line 135
135:         def representative_sequence
136:           unless defined?(@representative_sequence)
137:             rid = representative_seqid
138:             @representative_sequence =
139:               rid ? sequences[representative_seqid] : nil
140:           end
141:           @representative_sequence
142:         end

[Source]

     # File lib/bio/db/fantom.rb, line 131
131:         def sequence(idstr = nil)
132:           idstr ? sequences[idstr] : representative_sequence
133:         end

[Source]

     # File lib/bio/db/fantom.rb, line 124
124:         def sequences
125:           unless defined?(@sequences)
126:             @sequences = MaXML::Sequences.new(@elem)
127:           end
128:           @sequences
129:         end

[Validate]