bio-restriction_enzyme 1.0.0
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- data/.document +5 -0
- data/COPYING.txt +121 -0
- data/Gemfile +10 -0
- data/LICENSE.txt +7 -0
- data/README.rdoc +22 -0
- data/Rakefile +53 -0
- data/VERSION +1 -0
- data/bio-restriction_enzyme.gemspec +99 -0
- data/lib/bio-restriction_enzyme.rb +1 -0
- data/lib/bio/util/restriction_enzyme.rb +218 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +241 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +209 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +99 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +313 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +127 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +95 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +30 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +68 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +99 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +16 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +39 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +59 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +249 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +236 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +43 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +33 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +69 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +193 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +127 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +15 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +103 -0
- data/test/bio-restriction_enzyme/analysis/test_calculated_cuts.rb +281 -0
- data/test/bio-restriction_enzyme/analysis/test_cut_ranges.rb +87 -0
- data/test/bio-restriction_enzyme/analysis/test_sequence_range.rb +223 -0
- data/test/bio-restriction_enzyme/double_stranded/test_aligned_strands.rb +84 -0
- data/test/bio-restriction_enzyme/double_stranded/test_cut_location_pair.rb +58 -0
- data/test/bio-restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +56 -0
- data/test/bio-restriction_enzyme/double_stranded/test_cut_locations.rb +35 -0
- data/test/bio-restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +87 -0
- data/test/bio-restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +66 -0
- data/test/bio-restriction_enzyme/test_analysis.rb +228 -0
- data/test/bio-restriction_enzyme/test_cut_symbol.rb +27 -0
- data/test/bio-restriction_enzyme/test_double_stranded.rb +98 -0
- data/test/bio-restriction_enzyme/test_single_strand.rb +131 -0
- data/test/bio-restriction_enzyme/test_single_strand_complement.rb +131 -0
- data/test/bio-restriction_enzyme/test_string_formatting.rb +43 -0
- data/test/helper.rb +17 -0
- data/test/test_bio-restriction_enzyme.rb +21 -0
- metadata +153 -0
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# bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb - The cut locations, in enzyme notation
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require 'bio/util/restriction_enzyme'
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module Bio
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class RestrictionEnzyme
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class SingleStrand
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# Stores the cut location in thier enzyme index notation
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#
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# May be initialized with a series of cuts or an enzyme pattern marked
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# with cut symbols.
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#
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# Enzyme index notation:: 1.._n_, value before 1 is -1
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#
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# example:: [-3][-2][-1][1][2][3][4][5]
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#
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# Negative values are used to indicate when a cut may occur at a specified
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# distance before the sequence begins. This would be padded with 'n'
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# nucleotides to represent wildcards.
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#
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# Notes:
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# * <code>0</code> is invalid as it does not refer to any index
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# * +nil+ is not allowed here as it has no meaning
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# * +nil+ values are kept track of in DoubleStranded::CutLocations as they
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# need a reference point on the correlating strand. In
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# DoubleStranded::CutLocations +nil+ represents no cut or a partial
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# digestion.
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#
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class CutLocationsInEnzymeNotation < Array
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include CutSymbol
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extend CutSymbol
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# First cut, in enzyme-index notation
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attr_reader :min
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# Last cut, in enzyme-index notation
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attr_reader :max
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# Constructor for CutLocationsInEnzymeNotation
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#
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# ---
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# *Arguments*
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# * +a+: Locations of cuts represented as a string with cuts or an array of values
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# Examples:
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# * n^ng^arraxt^n
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# * 2
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# * -1, 5
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# * [-1, 5]
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# *Returns*:: nothing
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def initialize(*a)
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a.flatten! # in case an array was passed as an argument
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if a.size == 1 and a[0].kind_of? String and a[0] =~ re_cut_symbol
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# Initialize with a cut symbol pattern such as 'n^ng^arraxt^n'
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s = a[0]
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a = []
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i = -( s.tr(cut_symbol, '') =~ %r{[^n]} ) # First character that's not 'n'
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s.each_byte { |c| (a << i; next) if c.chr == cut_symbol; i += 1 }
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a.collect! { |n| n <= 0 ? n-1 : n } # 0 is not a valid enzyme index, decrement from 0 and all negative
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else
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a.collect! { |n| n.to_i } # Cut locations are always integers
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end
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validate_cut_locations( a )
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super(a)
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self.sort!
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@min = self.first
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@max = self.last
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self.freeze
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end
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# Transform the cut locations from enzyme index notation to 0-based index
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# notation.
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#
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# input -> output
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# [ 1, 2, 3 ] -> [ 0, 1, 2 ]
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# [ 1, 3, 5 ] -> [ 0, 2, 4 ]
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# [ -1, 1, 2 ] -> [ 0, 1, 2 ]
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# [ -2, 1, 3 ] -> [ 0, 2, 4 ]
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#
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# ---
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# *Arguments*
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# * _none_
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# *Returns*:: +Array+ of cuts in 0-based index notation
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def to_array_index
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return [] if @min == nil
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if @min < 0
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calc = lambda do |n|
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n -= 1 unless n < 0
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n + @min.abs
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end
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else
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calc = lambda { |n| n - 1 }
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end
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self.collect(&calc)
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end
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#########
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protected
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#########
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def validate_cut_locations( input_cut_locations )
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unless input_cut_locations == input_cut_locations.uniq
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err = "The cut locations supplied contain duplicate values. Redundant / undefined meaning.\n"
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err += "cuts: #{input_cut_locations.inspect}\n"
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err += "unique: #{input_cut_locations.uniq.inspect}"
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raise ArgumentError, err
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end
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if input_cut_locations.include?(nil)
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err = "The cut locations supplied contained a nil. nil has no index for enzyme notation, alternative meaning is 'no cut'.\n"
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err += "cuts: #{input_cut_locations.inspect}"
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raise ArgumentError, err
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end
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if input_cut_locations.include?(0)
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err = "The cut locations supplied contained a '0'. '0' has no index for enzyme notation, alternative meaning is 'no cut'.\n"
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err += "cuts: #{input_cut_locations.inspect}"
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raise ArgumentError, err
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end
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end
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end # CutLocationsInEnzymeNotation
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end # SingleStrand
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end # RestrictionEnzyme
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end # Bio
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# bio/util/restriction_enzyme/single_strand_complement.rb - Single strand restriction enzyme sequence in complement orientation
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require 'bio/util/restriction_enzyme'
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module Bio
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class RestrictionEnzyme
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# A single strand of restriction enzyme sequence pattern with a 3' to 5' orientation.
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#
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class SingleStrandComplement < SingleStrand
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# Orientation of the strand, 3' to 5'
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def orientation; [3, 5]; end
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end # SingleStrandComplement
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end # RestrictionEnzyme
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end # Bio
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# bio/util/restriction_enzyme/string_formatting.rb - Useful functions for string manipulation
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require 'bio/util/restriction_enzyme'
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module Bio
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class RestrictionEnzyme
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module StringFormatting
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include CutSymbol
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extend CutSymbol
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# Return the sequence with spacing for alignment. Does not add whitespace
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# around cut symbols.
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#
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# Example:
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# pattern = 'n^ng^arraxt^n'
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# add_spacing( pattern ) # => "n^n g^a r r a x t^n"
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#
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# ---
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# *Arguments*
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# * +seq+: sequence with cut symbols
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# * +cs+: (_optional_) Cut symbol along the string. The reason this is
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# definable outside of CutSymbol is that this is a utility function used
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# to form vertical and horizontal cuts such as:
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#
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# a|t g c
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# +---+
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# t a c|g
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# *Returns*:: +String+ sequence with single character distance between bases
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def add_spacing( seq, cs = cut_symbol )
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str = ''
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flag = false
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seq.each_byte do |c|
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c = c.chr
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if c == cs
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str += c
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flag = false
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elsif flag
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str += ' ' + c
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else
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str += c
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flag = true
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end
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end
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str
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end
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# Remove extraneous nucleic acid wildcards ('n' padding) from the
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# left and right sides
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#
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# ---
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# *Arguments*
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# * +s+: sequence with extraneous 'n' padding
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# *Returns*:: +String+ sequence without 'n' padding on the sides
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def strip_padding( s )
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if s[0].chr == 'n'
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s =~ %r{(n+)(.+)}
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s = $2
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end
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if s[-1].chr == 'n'
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s =~ %r{(.+?)(n+)$}
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s = $1
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end
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s
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end
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# Remove extraneous nucleic acid wildcards ('n' padding) from the
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# left and right sides and remove cut symbols
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#
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# ---
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# *Arguments*
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# * +s+: sequence with extraneous 'n' padding and cut symbols
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# *Returns*:: +String+ sequence without 'n' padding on the sides or cut symbols
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def strip_cuts_and_padding( s )
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strip_padding( s.tr(cut_symbol, '') )
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end
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# Return the 'n' padding on the left side of the strand
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#
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# ---
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# *Arguments*
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# * +s+: sequence with extraneous 'n' padding on the left side of the strand
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# *Returns*:: +String+ the 'n' padding from the left side
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def left_padding( s )
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s =~ %r{^n+}
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ret = $&
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ret ? ret : '' # Don't pass nil values
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end
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# Return the 'n' padding on the right side of the strand
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#
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# ---
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# *Arguments*
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# * +s+: sequence with extraneous 'n' padding on the right side of the strand
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# *Returns*:: +String+ the 'n' padding from the right side
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def right_padding( s )
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s =~ %r{n+$}
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ret = $&
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ret ? ret : '' # Don't pass nil values
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end
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end # StringFormatting
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end # RestrictionEnzyme
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end # Bio
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load Pathname.new(File.join(File.dirname(__FILE__), ['..']*2, 'helper.rb')).cleanpath.to_s
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require 'bio/util/restriction_enzyme/range/sequence_range/calculated_cuts'
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require 'bio/util/restriction_enzyme/range/cut_range'
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require 'bio/util/restriction_enzyme/range/cut_ranges'
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require 'bio/util/restriction_enzyme/range/horizontal_cut_range'
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require 'bio/util/restriction_enzyme/range/vertical_cut_range'
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class TestBioRestrictionEnzymeAnalysisCalculatedCuts < Test::Unit::TestCase
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def setup
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@t = Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
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@vcr = Bio::RestrictionEnzyme::Range::VerticalCutRange
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@crs = Bio::RestrictionEnzyme::Range::CutRanges
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@hcr = Bio::RestrictionEnzyme::Range::HorizontalCutRange
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#a.add_cut_range(p_cut_left, p_cut_right, c_cut_left, c_cut_right )
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@obj_1 = @t.new(6)
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@obj_1.add_cuts_from_cut_ranges( @crs.new( [@vcr.new(0,nil,nil,3), @vcr.new(nil,2,nil,nil)] ))
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@obj_1b = @obj_1.dup
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@obj_1b.remove_incomplete_cuts
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@obj_2 = @t.new(6)
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@obj_2.add_cuts_from_cut_ranges( @crs.new( [@vcr.new(0,2,nil,nil), @vcr.new(3,nil,4,nil)] ))
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@obj_2b = @obj_2.dup
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@obj_2b.remove_incomplete_cuts
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@obj_3 = @t.new(6)
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@obj_3.add_cuts_from_cut_ranges( @crs.new( [@vcr.new(0,2,nil,nil), @vcr.new(3,nil,4,nil)] ))
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@obj_3.add_cuts_from_cut_ranges( @crs.new( [@hcr.new(0), @hcr.new(5)] ))
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@obj_3b = @obj_3.dup
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@obj_3b.remove_incomplete_cuts
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@obj_4 = @t.new(6)
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@obj_4.add_cuts_from_cut_ranges( @crs.new( [@vcr.new(0,2,1,3)] ))
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@obj_4b = @obj_4.dup
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@obj_4b.remove_incomplete_cuts
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# Same thing, declared a different way
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@obj_4_c1 = @t.new(6)
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@obj_4_c1.add_cuts_from_cut_ranges( @crs.new( [@vcr.new(nil,nil,1,3), @vcr.new(0,2,nil,nil)] ))
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@obj_4b_c1 = @obj_4_c1.dup
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@obj_4b_c1.remove_incomplete_cuts
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# Same thing, declared a different way
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@obj_4_c2 = @t.new(6)
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@obj_4_c2.add_cuts_from_cut_ranges( @crs.new( [@vcr.new(0,nil,nil,3), @vcr.new(nil,2,1,nil)] ))
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@obj_4b_c2 = @obj_4_c2.dup
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@obj_4b_c2.remove_incomplete_cuts
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@obj_5 = @t.new(6)
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@obj_5.add_cuts_from_cut_ranges( @crs.new( [@vcr.new(0,nil,nil,nil), @vcr.new(nil,4,3,nil), @hcr.new(1,2)] ))
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@obj_5b = @obj_5.dup
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@obj_5b.remove_incomplete_cuts
|
56
|
+
|
57
|
+
@obj_6 = @t.new(6)
|
58
|
+
@obj_6.add_cuts_from_cut_ranges( @crs.new( [@vcr.new(nil,nil,0,nil), @hcr.new(1,2), @vcr.new(nil,4,3,nil)] ))
|
59
|
+
@obj_6b = @obj_6.dup
|
60
|
+
@obj_6b.remove_incomplete_cuts
|
61
|
+
|
62
|
+
@obj_7 = @t.new(6)
|
63
|
+
@obj_7.add_cuts_from_cut_ranges( @crs.new( [@vcr.new(nil,2,nil,nil), @hcr.new(0,2)] ))
|
64
|
+
@obj_7b = @obj_7.dup
|
65
|
+
@obj_7b.remove_incomplete_cuts
|
66
|
+
|
67
|
+
@obj_8 = @t.new(12)
|
68
|
+
@obj_8.add_cuts_from_cut_ranges( @crs.new( [@hcr.new(0,1), @vcr.new(nil,nil,nil,5), @hcr.new(7,8), @hcr.new(10), @vcr.new(nil,10,nil,nil)] ))
|
69
|
+
@obj_8b = @obj_8.dup
|
70
|
+
@obj_8b.remove_incomplete_cuts
|
71
|
+
|
72
|
+
@obj_9 = @t.new(6)
|
73
|
+
@obj_9.add_cuts_from_cut_ranges( @crs.new( [@vcr.new(nil,3,nil,3)] ))
|
74
|
+
@obj_9b = @obj_9.dup
|
75
|
+
@obj_9b.remove_incomplete_cuts
|
76
|
+
|
77
|
+
@obj_10 = @t.new(6)
|
78
|
+
@obj_10.add_cuts_from_cut_ranges( @crs.new( [@vcr.new(0,nil,nil,3), @vcr.new(nil,2,nil,2)] ))
|
79
|
+
@obj_10b = @obj_10.dup
|
80
|
+
@obj_10b.remove_incomplete_cuts
|
81
|
+
|
82
|
+
|
83
|
+
end
|
84
|
+
|
85
|
+
def test_cuts
|
86
|
+
x = @obj_1
|
87
|
+
assert_equal([0,2], x.vc_primary)
|
88
|
+
assert_equal([3], x.vc_complement)
|
89
|
+
assert_equal([1,2,3], x.hc_between_strands)
|
90
|
+
|
91
|
+
x = @obj_2
|
92
|
+
assert_equal([0,2,3], x.vc_primary)
|
93
|
+
assert_equal([4], x.vc_complement)
|
94
|
+
assert_equal([1,2,4], x.hc_between_strands)
|
95
|
+
|
96
|
+
x = @obj_3
|
97
|
+
assert_equal([0,2,3], x.vc_primary)
|
98
|
+
assert_equal([4], x.vc_complement)
|
99
|
+
assert_equal([0,1,2,4,5], x.hc_between_strands)
|
100
|
+
|
101
|
+
x = @obj_4
|
102
|
+
assert_equal([0,2], x.vc_primary)
|
103
|
+
assert_equal([1,3], x.vc_complement)
|
104
|
+
assert_equal([1,2,3], x.hc_between_strands)
|
105
|
+
|
106
|
+
x = @obj_4_c1
|
107
|
+
assert_equal([0,2], x.vc_primary)
|
108
|
+
assert_equal([1,3], x.vc_complement)
|
109
|
+
assert_equal([1,2,3], x.hc_between_strands)
|
110
|
+
|
111
|
+
x = @obj_4_c2
|
112
|
+
assert_equal([0,2], x.vc_primary)
|
113
|
+
assert_equal([1,3], x.vc_complement)
|
114
|
+
assert_equal([1,2,3], x.hc_between_strands)
|
115
|
+
|
116
|
+
x = @obj_5
|
117
|
+
assert_equal([0,4], x.vc_primary)
|
118
|
+
assert_equal([3], x.vc_complement)
|
119
|
+
assert_equal([1,2,4], x.hc_between_strands)
|
120
|
+
|
121
|
+
x = @obj_6
|
122
|
+
assert_equal([4], x.vc_primary)
|
123
|
+
assert_equal([0,3], x.vc_complement)
|
124
|
+
assert_equal([1,2,4], x.hc_between_strands)
|
125
|
+
|
126
|
+
x = @obj_7
|
127
|
+
assert_equal([2], x.vc_primary)
|
128
|
+
assert_equal([], x.vc_complement)
|
129
|
+
assert_equal([0,1,2], x.hc_between_strands)
|
130
|
+
|
131
|
+
x = @obj_8
|
132
|
+
assert_equal([10], x.vc_primary)
|
133
|
+
assert_equal([5], x.vc_complement)
|
134
|
+
assert_equal([0,1,7,8,10], x.hc_between_strands)
|
135
|
+
|
136
|
+
x = @obj_9
|
137
|
+
assert_equal([3], x.vc_primary)
|
138
|
+
assert_equal([3], x.vc_complement)
|
139
|
+
assert_equal([], x.hc_between_strands)
|
140
|
+
|
141
|
+
x = @obj_10
|
142
|
+
assert_equal([0,2], x.vc_primary)
|
143
|
+
assert_equal([2,3], x.vc_complement)
|
144
|
+
assert_equal([1,2,3], x.hc_between_strands)
|
145
|
+
end
|
146
|
+
|
147
|
+
def test_cuts_after_remove_incomplete_cuts
|
148
|
+
x = @obj_1b
|
149
|
+
assert_equal([0,2], x.vc_primary)
|
150
|
+
assert_equal([3], x.vc_complement)
|
151
|
+
assert_equal([1,2,3], x.hc_between_strands)
|
152
|
+
end
|
153
|
+
|
154
|
+
def test_strands_for_display_current
|
155
|
+
#check object_id
|
156
|
+
end
|
157
|
+
|
158
|
+
def test_strands_for_display
|
159
|
+
x = @obj_1
|
160
|
+
assert_equal('0|1 2|3 4 5', x.strands_for_display[0])
|
161
|
+
assert_equal(' +---+-+ ', x.strands_for_display[1])
|
162
|
+
assert_equal('0 1 2 3|4 5', x.strands_for_display[2])
|
163
|
+
|
164
|
+
x = @obj_1b
|
165
|
+
assert_equal('0|1 2|3 4 5', x.strands_for_display[0])
|
166
|
+
assert_equal(' +---+-+ ', x.strands_for_display[1])
|
167
|
+
assert_equal('0 1 2 3|4 5', x.strands_for_display[2])
|
168
|
+
|
169
|
+
x = @obj_2
|
170
|
+
assert_equal('0|1 2|3|4 5', x.strands_for_display[0])
|
171
|
+
assert_equal(' +---+ +-+ ', x.strands_for_display[1])
|
172
|
+
assert_equal('0 1 2 3 4|5', x.strands_for_display[2])
|
173
|
+
|
174
|
+
x = @obj_2b
|
175
|
+
assert_equal('0|1 2|3|4 5', x.strands_for_display[0])
|
176
|
+
assert_equal(' +---+ +-+ ', x.strands_for_display[1])
|
177
|
+
assert_equal('0 1 2 3 4|5', x.strands_for_display[2])
|
178
|
+
|
179
|
+
x = @obj_3
|
180
|
+
assert_equal('0|1 2|3|4 5', x.strands_for_display[0])
|
181
|
+
assert_equal('-+---+ +-+-', x.strands_for_display[1])
|
182
|
+
assert_equal('0 1 2 3 4|5', x.strands_for_display[2])
|
183
|
+
|
184
|
+
x = @obj_3b
|
185
|
+
assert_equal('0|1 2|3|4 5', x.strands_for_display[0])
|
186
|
+
assert_equal('-+---+ +-+-', x.strands_for_display[1])
|
187
|
+
assert_equal('0 1 2 3 4|5', x.strands_for_display[2])
|
188
|
+
|
189
|
+
x = @obj_4
|
190
|
+
assert_equal('0|1 2|3 4 5', x.strands_for_display[0])
|
191
|
+
assert_equal(' +-+-+-+ ', x.strands_for_display[1])
|
192
|
+
assert_equal('0 1|2 3|4 5', x.strands_for_display[2])
|
193
|
+
|
194
|
+
x = @obj_4b
|
195
|
+
assert_equal('0|1 2|3 4 5', x.strands_for_display[0])
|
196
|
+
assert_equal(' +-+-+-+ ', x.strands_for_display[1])
|
197
|
+
assert_equal('0 1|2 3|4 5', x.strands_for_display[2])
|
198
|
+
|
199
|
+
x = @obj_4_c1
|
200
|
+
assert_equal('0|1 2|3 4 5', x.strands_for_display[0])
|
201
|
+
assert_equal(' +-+-+-+ ', x.strands_for_display[1])
|
202
|
+
assert_equal('0 1|2 3|4 5', x.strands_for_display[2])
|
203
|
+
|
204
|
+
x = @obj_4b_c1
|
205
|
+
assert_equal('0|1 2|3 4 5', x.strands_for_display[0])
|
206
|
+
assert_equal(' +-+-+-+ ', x.strands_for_display[1])
|
207
|
+
assert_equal('0 1|2 3|4 5', x.strands_for_display[2])
|
208
|
+
|
209
|
+
x = @obj_4_c2
|
210
|
+
assert_equal('0|1 2|3 4 5', x.strands_for_display[0])
|
211
|
+
assert_equal(' +-+-+-+ ', x.strands_for_display[1])
|
212
|
+
assert_equal('0 1|2 3|4 5', x.strands_for_display[2])
|
213
|
+
|
214
|
+
x = @obj_4b_c2
|
215
|
+
assert_equal('0|1 2|3 4 5', x.strands_for_display[0])
|
216
|
+
assert_equal(' +-+-+-+ ', x.strands_for_display[1])
|
217
|
+
assert_equal('0 1|2 3|4 5', x.strands_for_display[2])
|
218
|
+
|
219
|
+
x = @obj_5
|
220
|
+
assert_equal('0|1 2 3 4|5', x.strands_for_display[0])
|
221
|
+
assert_equal(' +--- +-+ ', x.strands_for_display[1])
|
222
|
+
assert_equal('0 1 2 3|4 5', x.strands_for_display[2])
|
223
|
+
|
224
|
+
x = @obj_5b
|
225
|
+
assert_equal('0 1 2 3 4|5', x.strands_for_display[0])
|
226
|
+
assert_equal(' +-+ ', x.strands_for_display[1])
|
227
|
+
assert_equal('0 1 2 3|4 5', x.strands_for_display[2])
|
228
|
+
|
229
|
+
x = @obj_6
|
230
|
+
assert_equal('0 1 2 3 4|5', x.strands_for_display[0])
|
231
|
+
assert_equal(' +--- +-+ ', x.strands_for_display[1])
|
232
|
+
assert_equal('0|1 2 3|4 5', x.strands_for_display[2])
|
233
|
+
|
234
|
+
x = @obj_6b
|
235
|
+
assert_equal('0 1 2 3 4|5', x.strands_for_display[0])
|
236
|
+
assert_equal(' +-+ ', x.strands_for_display[1])
|
237
|
+
assert_equal('0 1 2 3|4 5', x.strands_for_display[2])
|
238
|
+
|
239
|
+
x = @obj_7
|
240
|
+
assert_equal('0 1 2|3 4 5', x.strands_for_display[0])
|
241
|
+
assert_equal('-----+ ', x.strands_for_display[1])
|
242
|
+
assert_equal('0 1 2 3 4 5', x.strands_for_display[2])
|
243
|
+
|
244
|
+
x = @obj_7b
|
245
|
+
assert_equal('0 1 2|3 4 5', x.strands_for_display[0])
|
246
|
+
assert_equal('-----+ ', x.strands_for_display[1])
|
247
|
+
assert_equal('0 1 2 3 4 5', x.strands_for_display[2])
|
248
|
+
|
249
|
+
x = @obj_8
|
250
|
+
assert_equal('0 1 2 3 4 5 6 7 8 9 0|1', x.strands_for_display[0])
|
251
|
+
assert_equal('--- + --- -+ ', x.strands_for_display[1])
|
252
|
+
assert_equal('0 1 2 3 4 5|6 7 8 9 0 1', x.strands_for_display[2])
|
253
|
+
|
254
|
+
x = @obj_8b
|
255
|
+
assert_equal('0 1 2 3 4 5 6 7 8 9 0 1', x.strands_for_display[0])
|
256
|
+
assert_equal(' ', x.strands_for_display[1])
|
257
|
+
assert_equal('0 1 2 3 4 5 6 7 8 9 0 1', x.strands_for_display[2])
|
258
|
+
|
259
|
+
x = @obj_9
|
260
|
+
assert_equal('0 1 2 3|4 5', x.strands_for_display[0])
|
261
|
+
assert_equal(' + ', x.strands_for_display[1])
|
262
|
+
assert_equal('0 1 2 3|4 5', x.strands_for_display[2])
|
263
|
+
|
264
|
+
x = @obj_9b
|
265
|
+
assert_equal('0 1 2 3|4 5', x.strands_for_display[0])
|
266
|
+
assert_equal(' + ', x.strands_for_display[1])
|
267
|
+
assert_equal('0 1 2 3|4 5', x.strands_for_display[2])
|
268
|
+
|
269
|
+
x = @obj_10
|
270
|
+
assert_equal('0|1 2|3 4 5', x.strands_for_display[0])
|
271
|
+
assert_equal(' +---+-+ ', x.strands_for_display[1])
|
272
|
+
assert_equal('0 1 2|3|4 5', x.strands_for_display[2])
|
273
|
+
|
274
|
+
x = @obj_10b
|
275
|
+
assert_equal('0|1 2|3 4 5', x.strands_for_display[0])
|
276
|
+
assert_equal(' +---+-+ ', x.strands_for_display[1])
|
277
|
+
assert_equal('0 1 2|3|4 5', x.strands_for_display[2])
|
278
|
+
|
279
|
+
end
|
280
|
+
|
281
|
+
end
|