Module: RGFA::Lines
- Included in:
- RGFA
- Defined in:
- lib/rgfa/lines.rb
Overview
Methods for the RGFA class, which allow to handle lines of multiple types.
Instance Method Summary collapse
-
#<<(gfa_line) ⇒ RGFA
Add a line to a RGFA.
-
#rename(old_name, new_name) ⇒ RGFA
Rename a segment or a path.
-
#rm(x, *args) ⇒ RGFA
Delete elements from the RGFA graph.
Instance Method Details
#<<(gfa_line_string) ⇒ RGFA #<<(gfa_line) ⇒ RGFA
Add a line to a RGFA
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# File 'lib/rgfa/lines.rb', line 17 def <<(gfa_line) gfa_line = gfa_line.to_rgfa_line(validate: @validate) rt = gfa_line.record_type case rt when :H add_header(gfa_line) when :S add_segment(gfa_line) when :L add_link(gfa_line) when :C add_containment(gfa_line) when :P add_path(gfa_line) when :"#" add_comment(gfa_line) else raise # this never happens, as already catched by gfa_line init end return self end |
#rename(old_name, new_name) ⇒ RGFA
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# File 'lib/rgfa/lines.rb', line 118 def rename(old_name, new_name) old_name = old_name.to_sym new_name = new_name.to_sym s = segment(old_name) pt = nil if s.nil? pt = path(old_name) if pt.nil? raise RGFA::LineMissingError, "#{old_name} is not a path or segment name" end end if segment(new_name) or path(new_name) raise RGFA::DuplicatedLabelError, "#{new_name} is already a path or segment name" end if s s.name = new_name @segments.delete(old_name) @segments[new_name] = s else pt.path_name = new_name @paths.delete(old_name) @paths[new_name] = pt end self end |
#rm(segment) ⇒ RGFA #rm(path) ⇒ RGFA #rm(link) ⇒ RGFA #rm(containment) ⇒ RGFA #rm(: headers) ⇒ RGFA #rm(array) ⇒ RGFA #rm(method_name, *args) ⇒ RGFA
Delete elements from the RGFA graph
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# File 'lib/rgfa/lines.rb', line 58 def rm(x, *args) if x.kind_of?(RGFA::Line) raise ArgumentError, "One argument required if first RGFA::Line" if !args.empty? case x.record_type when :H then raise ArgumentError, "Cannot remove single header lines" when :S then delete_segment(x) when :P then delete_path(x) when :L then delete_link(x) when :C then delete_containment(x) when :"#" then delete_comment(x) end elsif x.kind_of?(Symbol) if @segments.has_key?(x) if !args.empty? raise ArgumentError, "One arguments required if first segment name" end delete_segment(x) elsif @paths.has_key?(x) if !args.empty? raise ArgumentError, "One argument required if first path name" end delete_path(x) elsif x == :headers if !args.empty? raise ArgumentError, "One argument required if first :headers" end delete_headers elsif x == :comments if !args.empty? raise ArgumentError, "One argument required if first :comments" end delete_comments else if respond_to?(x) rm(send(x, *args)) else raise ArgumentError, "Cannot remove #{x.inspect}" end end elsif x.kind_of?(String) rm(x.to_sym, *args) elsif x.kind_of?(Array) x.each {|elem| rm(elem, *args)} elsif x.nil? return self else raise ArgumentError, "Cannot remove #{x.inspect}" end return self end |