module GenomerPluginView::GffRecordHelper
Constants
- DEFAULT_GFF_MAPPING
- GFF_TO_TABLE
Public Instance Methods
coordinates()
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# File lib/genomer-plugin-view/gff_record_helper.rb, line 27 def coordinates if negative_strand? [self.end,self.start,self.feature] else [self.start,self.end,self.feature] end end
negative_strand?()
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# File lib/genomer-plugin-view/gff_record_helper.rb, line 23 def negative_strand? self.strand == '-' end
table_attributes()
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# File lib/genomer-plugin-view/gff_record_helper.rb, line 50 def table_attributes raise Genomer::Error, "Unknown feature type '#{feature}'" unless valid? attributes.map do |(k,v)| k = GFF_TO_TABLE[feature][k] k.nil? ? nil : [k,v] end.compact end
to_genbank_table_entry()
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# File lib/genomer-plugin-view/gff_record_helper.rb, line 35 def to_genbank_table_entry delimiter = "\t" indent = delimiter * 2 entries = table_attributes.inject([coordinates]) do |array,atr| array << atr.unshift(indent) end return entries.map{|line| line * delimiter} * "\n" + "\n" end
valid?()
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# File lib/genomer-plugin-view/gff_record_helper.rb, line 46 def valid? GFF_TO_TABLE.include?(feature) end