### Home Classes Methods

### In Files

- lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
- lib/bio/util/restriction_enzyme/single_strand.rb

### Parent

Bio::Sequence::NA

### Namespace

- CLASS Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation

### Methods

- ::new
- #orientation
- #palindromic?
- #pattern
- #validate_args
- #with_cut_symbols
- #with_spaces

### Included Modules

- Bio::RestrictionEnzyme::CutSymbol
- Bio::RestrictionEnzyme::StringFormatting

### Files

- KNOWN_ISSUES.rdoc
- README.rdoc
- README_DEV.rdoc
- RELEASE_NOTES.rdoc
- Changes-1.3.rdoc
- RELEASE_NOTES-1.4.0.rdoc
- RELEASE_NOTES-1.4.1.rdoc
- RELEASE_NOTES-1.4.2.rdoc

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No matching classes.

# Bio::RestrictionEnzyme::SingleStrand

A single strand of restriction enzyme sequence pattern with a 5' to 3' orientation.

DoubleStranded puts the SingleStrand and SingleStrandComplement together to create the sequence pattern with cuts on both strands.

### Attributes

cut_locations[R]

The cut locations transformed from enzyme index notation to 0-based array index notation. Contains an Array.

cut_locations_in_enzyme_notation[R]

The cut locations in enzyme notation. Contains a CutLocationsInEnzymeNotation object set when the SingleStrand object is initialized.

stripped[R]

Sequence pattern with no cut symbols and no 'n' padding.

- `SingleStrand.new('garraxt', [-2, 1, 7]).stripped # => "garraxt"`

### Public Class Methods

new( sequence, *c ) click to toggle source

Constructor for a Bio::RestrictionEnzyme::StingleStrand object.

A single strand of restriction enzyme sequence pattern with a 5' to 3' orientation.

Arguments

- `sequence`: (required) The enzyme sequence.

- `c`: (optional) Cut locations in enzyme notation. See Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation

Constraints

- `sequence` cannot contain immediately adjacent cut symbols (ex. atg^^c).

- `c` is in enzyme index notation and therefore cannot contain a 0.

- If `c` is omitted, `sequence` must contain a cut symbol.

- You cannot provide both a sequence with cut symbols and provide cut locations - ambiguous.

`sequence` must be a kind of:

- String

- Bio::Sequence::NA

- Bio::RestrictionEnzyme::SingleStrand

`c` must be a kind of:

- Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation

- Integer, one or more

- Array

Returns | nothing

    # File lib/bio/util/restriction_enzyme/single_strand.rb, line 69
    def initialize( sequence, *c )
      c.flatten! # if an array was supplied as an argument
    # NOTE t| 2009-09-19 commented out for library efficiency
      # validate_args(sequence, c)
      sequence = sequence.downcase

      if sequence =~ re_cut_symbol
        @cut_locations_in_enzyme_notation = CutLocationsInEnzymeNotation.new( strip_padding(sequence) )
      else
        @cut_locations_in_enzyme_notation = CutLocationsInEnzymeNotation.new( c )
      end

      @stripped = Bio::Sequence::NA.new( strip_cuts_and_padding( sequence ) )
      super( pattern )
      @cut_locations = @cut_locations_in_enzyme_notation.to_array_index
      return
    end

### Public Instance Methods

orientation() click to toggle source

Orientation of the strand, 5' to 3'

    # File lib/bio/util/restriction_enzyme/single_strand.rb, line 40
    def orientation; [5,3]; end

palindromic?() click to toggle source

Returns true if this enzyme is palindromic with its reverse complement. Does not report if the `cut_locations` are palindromic or not.

Examples:

- This would be palindromic:

      5' - ATGCAT - 3'
           TACGTA

- This would not be palindromic:

      5' - ATGCGTA - 3'
           TACGCAT

Arguments

- none

Returns | `true` or `false`

    # File lib/bio/util/restriction_enzyme/single_strand.rb, line 103
    def palindromic?
      @stripped.reverse_complement == @stripped
    end

pattern() click to toggle source

The sequence with 'n' padding on the left and right for cuts larger than the sequence.

- `SingleStrand.new('garraxt', [-2, 1, 7]).pattern # => "nngarraxtn"`

Arguments

- none

Returns | The sequence with 'n' padding on the left and right for cuts larger than the sequence.

    # File lib/bio/util/restriction_enzyme/single_strand.rb, line 131
    def pattern
      return stripped if @cut_locations_in_enzyme_notation.min == nil
      left = (@cut_locations_in_enzyme_notation.min < 0 ? 'n' * @cut_locations_in_enzyme_notation.min.abs : '')

      # Add one more 'n' if a cut is at the last position
      right = ( (@cut_locations_in_enzyme_notation.max >= @stripped.length) ? ('n' * (@cut_locations_in_enzyme_notation.max - @stripped.length + 1)) : '')
      [left, stripped, right].join('')
    end

with_cut_symbols() click to toggle source

The sequence with 'n' padding and cut symbols.

- `SingleStrand.new('garraxt', [-2, 1, 7]).with_cut_symbols # => "n^ng^arraxt^n"`

Arguments

- none

Returns | The sequence with 'n' padding and cut symbols.

    # File lib/bio/util/restriction_enzyme/single_strand.rb, line 118
    def with_cut_symbols
      s = pattern
      @cut_locations_in_enzyme_notation.to_array_index.sort.reverse.each { |c| s.insert(c+1, cut_symbol) }
      s
    end

with_spaces() click to toggle source

The sequence with 'n' pads, cut symbols, and spacing for alignment.

- `SingleStrand.new('garraxt', [-2, 1, 7]).with_spaces # => "n^n g^a r r a x t^n"`

Arguments

- none

Returns | The sequence with 'n' pads, cut symbols, and spacing for alignment.

    # File lib/bio/util/restriction_enzyme/single_strand.rb, line 147
    def with_spaces
      add_spacing( with_cut_symbols )
    end

### Protected Instance Methods

validate_args( input_pattern, input_cut_locations ) click to toggle source

    # File lib/bio/util/restriction_enzyme/single_strand.rb, line 155
    def validate_args( input_pattern, input_cut_locations )
      unless input_pattern.kind_of?(String)
        err = "input_pattern is not a String, Bio::Sequence::NA, or Bio::RestrictionEnzyme::SingleStrand object\n"
        err += "pattern: #{input_pattern}\n"
        err += "class: #{input_pattern.class}"
        raise ArgumentError, err
      end

      if ( input_pattern =~ re_cut_symbol ) and !input_cut_locations.empty?
        err = "Cut symbol found in sequence, but cut locations were also supplied.  Ambiguous.\n"
        err += "pattern: #{input_pattern}\n"
        err += "symbol: #{cut_symbol}\n"
        err += "locations: #{input_cut_locations.inspect}"
        raise ArgumentError, err
      end

      input_pattern.each_byte do |c|
        c = c.chr.downcase
        unless Bio::NucleicAcid::NAMES.has_key?(c) or c == 'x' or c == 'X' or c == cut_symbol
          err = "Invalid character in pattern.\n"
          err += "Not a nucleotide or representation of possible nucleotides.  See Bio::NucleicAcid::NAMES for more information.\n"
          err += "char: #{c}\n"
          err += "input_pattern: #{input_pattern}"
          raise ArgumentError, err
        end
      end
    end

[Validate]

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