### Home Classes Methods

### In Files

- lib/bio/util/restriction_enzyme/analysis.rb
- lib/bio/util/restriction_enzyme/analysis_basic.rb

### Parent

Object

### Methods

- ::cut
- ::cut_without_permutations
- #create_enzyme_actions
- #cut
- #cut_and_return_by_permutations
- #cut_without_permutations
- #find_match_locations
- #fragments_for_display
- #permute

### 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

### Class/Module Index

Quicksearch

- Bio
- Bio::AAindex
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- Bio::Alignment::FactoryTemplate
- Bio::Alignment::FactoryTemplate::FileInFileOut
- Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
- Bio::Alignment::FactoryTemplate::FileInStdoutOut
- Bio::Alignment::FactoryTemplate::Simple
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- Bio::Alignment::GAP
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- Bio::EBI::SOAP::TCoffee
- Bio::EBI::SOAP::WUBlast
- Bio::EMBL
- Bio::EMBLDB
- Bio::EMBLDB::Common
- Bio::EMBOSS
- Bio::Ensembl
- Bio::Ensembl::Base
- Bio::Ensembl::Human
- Bio::Ensembl::Mouse
- Bio::FANTOM
- Bio::FANTOM::MaXML
- Bio::FANTOM::MaXML::Annotation
- Bio::FANTOM::MaXML::Annotation::DataSrc
- Bio::FANTOM::MaXML::Annotations
- Bio::FANTOM::MaXML::Cluster
- Bio::FANTOM::MaXML::Sequence
- Bio::FANTOM::MaXML::Sequences
- Bio::Fasta
- Bio::Fasta::Report
- Bio::Fasta::Report::FLATFILE_SPLITTER
- Bio::Fasta::Report::FastaFormat10Splitter
- Bio::Fasta::Report::Hit
- Bio::Fasta::Report::Hit::Query
- Bio::Fasta::Report::Hit::Target
- Bio::Fasta::Report::Program
- Bio::FastaDefline
- Bio::FastaFormat
- Bio::FastaNumericFormat
- Bio::Fastq
- Bio::Fastq::Error
- Bio::Fastq::Error::Diff_ids
- Bio::Fastq::Error::Long_qual
- Bio::Fastq::Error::No_atmark
- Bio::Fastq::Error::No_ids
- Bio::Fastq::Error::No_qual
- Bio::Fastq::Error::No_seq
- Bio::Fastq::Error::Qual_char
- Bio::Fastq::Error::Qual_range
- Bio::Fastq::Error::Seq_char
- Bio::Fastq::Error::Short_qual
- Bio::Fastq::Error::Skipped_unformatted_lines
- Bio::Fastq::FormatData
- Bio::Fastq::FormatData::FASTQ_ILLUMINA
- Bio::Fastq::FormatData::FASTQ_SANGER
- Bio::Fastq::FormatData::FASTQ_SOLEXA
- Bio::Feature
- Bio::Feature::Qualifier
- Bio::Features
- Bio::Fetch
- Bio::FlatFile
- Bio::FlatFile::AutoDetect
- Bio::FlatFile::AutoDetect::RuleDebug
- Bio::FlatFile::AutoDetect::RuleProc
- Bio::FlatFile::AutoDetect::RuleRegexp
- Bio::FlatFile::AutoDetect::RuleRegexp2
- Bio::FlatFile::AutoDetect::RuleSpecial
- Bio::FlatFile::AutoDetect::RuleTemplate
- Bio::FlatFile::AutoDetect::RulesArray
- Bio::FlatFile::BufferedInputStream
- Bio::FlatFile::Splitter
- Bio::FlatFile::Splitter::Default
- Bio::FlatFile::Splitter::LineOriented
- Bio::FlatFile::Splitter::Template
- Bio::FlatFile::UnknownDataFormatError
- Bio::FlatFileIndex
- Bio::FlatFileIndex::BDB_1
- Bio::FlatFileIndex::BDB_1::BDBMappingFile
- Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
- Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
- Bio::FlatFileIndex::BDBdefault
- Bio::FlatFileIndex::BDBwrapper
- Bio::FlatFileIndex::DEBUG
- Bio::FlatFileIndex::DataBank
- Bio::FlatFileIndex::FileID
- Bio::FlatFileIndex::FileIDs
- Bio::FlatFileIndex::Flat_1
- Bio::FlatFileIndex::Flat_1::FlatMappingFile
- Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
- Bio::FlatFileIndex::Flat_1::Record
- Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
- Bio::FlatFileIndex::Indexer
- Bio::FlatFileIndex::Indexer::NameSpace
- Bio::FlatFileIndex::Indexer::NameSpaces
- Bio::FlatFileIndex::Indexer::Parser
- Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
- Bio::FlatFileIndex::Indexer::Parser::EMBLParser
- Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
- Bio::FlatFileIndex::Indexer::Parser::GenBankParser
- Bio::FlatFileIndex::Indexer::Parser::GenPeptParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLClusterParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLSequenceParser
- Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
- Bio::FlatFileIndex::Indexer::Parser::SPTRParser
- Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- Bio::FlatFileIndex::NameSpaces
- Bio::FlatFileIndex::Results
- Bio::FlatFileIndex::Template
- Bio::FlatFileIndex::Template::NameSpace
- Bio::GCG
- Bio::GCG::Msf
- Bio::GCG::Seq
- Bio::GFF
- Bio::GFF::GFF2
- Bio::GFF::GFF2::Escape
- Bio::GFF::GFF2::MetaData
- Bio::GFF::GFF2::Record
- Bio::GFF::GFF2::Record::Value
- Bio::GFF::GFF3
- Bio::GFF::GFF3::Escape
- Bio::GFF::GFF3::Record
- Bio::GFF::GFF3::Record::Gap
- Bio::GFF::GFF3::Record::Gap::Code
- Bio::GFF::GFF3::Record::Target
- Bio::GFF::GFF3::RecordBoundary
- Bio::GFF::GFF3::SequenceRegion
- Bio::GFF::Record
- Bio::GO
- Bio::GO::External2go
- Bio::GO::GeneAssociation
- Bio::GO::Ontology
- Bio::GenBank
- Bio::GenBank::Locus
- Bio::GenPept
- Bio::GenPept::Locus
- Bio::Genscan
- Bio::Genscan::Report
- Bio::Genscan::Report::Exon
- Bio::Genscan::Report::Gene
- Bio::HGC
- Bio::HGC::HiGet
- Bio::HMMER
- Bio::HMMER::Report
- Bio::HMMER::Report::Hit
- Bio::HMMER::Report::Hsp
- Bio::Hinv
- Bio::Hinv::Acc2hit
- Bio::Hinv::Common
- Bio::Hinv::Hit2acc
- Bio::Hinv::HitCnt
- Bio::Hinv::HitDefinition
- Bio::Hinv::HitPubmedId
- Bio::Hinv::HitXML
- Bio::Hinv::Hix2hit
- Bio::Hinv::HixCnt
- Bio::Hinv::HixRepresent
- Bio::Hinv::HixXML
- Bio::Hinv::IdSearch
- Bio::Hinv::KeywordSearch
- Bio::Iprscan
- Bio::Iprscan::Report
- Bio::Iprscan::Report::Match
- Bio::KEGG
- Bio::KEGG::API
- Bio::KEGG::BRITE
- Bio::KEGG::COMPOUND
- Bio::KEGG::Common
- Bio::KEGG::Common::DblinksAsHash
- Bio::KEGG::Common::GenesAsHash
- Bio::KEGG::Common::ModulesAsHash
- Bio::KEGG::Common::OrthologsAsHash
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- Bio::KEGG::Common::References
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- Bio::KEGG::DRUG
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- Bio::Map::Mapping
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- Bio::Muscle
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- Bio::NCBI::REST::EFetch::Methods
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- Bio::NCBI::SOAP
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- Bio::PROSITE
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- Bio::PSORT::PSORT1::Remote
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- Bio::PhyloXML::SequenceRelation
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- Bio::PhyloXML::Tree
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- Bio::Probcons
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- Bio::Registry
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- Bio::RestrictionEnzyme
- Bio::RestrictionEnzyme::Analysis
- Bio::RestrictionEnzyme::CutSymbol
- Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
- Bio::RestrictionEnzyme::DenseIntArray
- Bio::RestrictionEnzyme::DoubleStranded
- Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
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- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::CutLocations
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::EnzymeAction
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- Bio::RestrictionEnzyme::Range
- Bio::RestrictionEnzyme::Range::CutRange
- Bio::RestrictionEnzyme::Range::CutRanges
- Bio::RestrictionEnzyme::Range::HorizontalCutRange
- Bio::RestrictionEnzyme::Range::SequenceRange
- Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
- Bio::RestrictionEnzyme::Range::VerticalCutRange
- Bio::RestrictionEnzyme::SingleStrand
- Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::SingleStrandComplement
- Bio::RestrictionEnzyme::SortedNumArray
- Bio::RestrictionEnzyme::StringFormatting
- Bio::SOAPWSDL
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- Bio::SPTR
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- Bio::SQL::Bioentry
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- Bio::SQL::BioentryReference
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- Bio::SQL::Comment
- Bio::SQL::Dbxref
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- Bio::SQL::DummyBase
- Bio::SQL::Location
- Bio::SQL::LocationQualifierValue
- Bio::SQL::Ontology
- Bio::SQL::Reference
- Bio::SQL::Seqfeature
- Bio::SQL::SeqfeatureDbxref
- Bio::SQL::SeqfeaturePath
- Bio::SQL::SeqfeatureQualifierValue
- Bio::SQL::SeqfeatureRelationship
- Bio::SQL::Sequence
- Bio::SQL::Taxon
- Bio::SQL::TaxonName
- Bio::SQL::Term
- Bio::SQL::TermDbxref
- Bio::SQL::TermPath
- Bio::SQL::TermRelationship
- Bio::SQL::TermRelationshipTerm
- Bio::SQL::TermSynonym
- Bio::SangerChromatogram
- Bio::Scf
- Bio::Sequence
- Bio::Sequence::AA
- Bio::Sequence::Adapter
- Bio::Sequence::Adapter::BioSQL
- Bio::Sequence::Adapter::EMBL
- Bio::Sequence::Adapter::FastaFormat
- Bio::Sequence::Adapter::FastaNumericFormat
- Bio::Sequence::Adapter::Fastq
- Bio::Sequence::Adapter::GenBank
- Bio::Sequence::Adapter::SangerChromatogram
- Bio::Sequence::Common
- Bio::Sequence::DBLink
- Bio::Sequence::Format
- Bio::Sequence::Format::AminoFormatter
- Bio::Sequence::Format::Formatter
- Bio::Sequence::Format::Formatter::Fasta
- Bio::Sequence::Format::Formatter::Fasta_ncbi
- Bio::Sequence::Format::Formatter::Fasta_numeric
- Bio::Sequence::Format::Formatter::Fastq
- Bio::Sequence::Format::Formatter::Fastq_illumina
- Bio::Sequence::Format::Formatter::Fastq_sanger
- Bio::Sequence::Format::Formatter::Fastq_solexa
- Bio::Sequence::Format::Formatter::Qual
- Bio::Sequence::Format::Formatter::Raw
- Bio::Sequence::Format::FormatterBase
- Bio::Sequence::Format::INSDFeatureHelper
- Bio::Sequence::Format::NucFormatter
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- Bio::Sequence::Format::NucFormatter::Genbank
- Bio::Sequence::NA
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- Bio::Sequence::QualityScore::Converter
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- Bio::Sequence::SequenceMasker
- Bio::Shell
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- Bio::Sim4
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- Bio::Sim4::Report::SegmentPair
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- Bio::Spidey
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- Bio::Spidey::Report::SeqDesc
- Bio::SwissProt
- Bio::TMHMM
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- Bio::TMHMM::TMH
- Bio::TRANSFAC
- Bio::TRANSFAC::CELL
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- Bio::TRANSFAC::GENE
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- Bio::TargetP
- Bio::TargetP::Report
- Bio::Taxonomy
- Bio::Tcoffee
- Bio::Tcoffee::DEFAULT_PARSER
- Bio::TogoWS
- Bio::TogoWS::AccessWait
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- Bio::TrEMBL
- Bio::Tree
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- Bio::Tree::NoPathError
- Bio::Tree::Node
- Bio::UniProt
- BiorubyController
- BiorubyGenerator
- BiorubyHelper
- Hash
- Object
- String

No matching classes.

# Bio::RestrictionEnzyme::Analysis

### Public Class Methods

cut( sequence, *args ) click to toggle source

See cut instance method

    # File lib/bio/util/restriction_enzyme/analysis.rb, line 23
    def self.cut( sequence, *args )
      self.new.cut( sequence, *args )
    end

cut_without_permutations( sequence, *args ) click to toggle source

See cut_without_permutations instance method

    # File lib/bio/util/restriction_enzyme/analysis_basic.rb, line 21
    def self.cut_without_permutations( sequence, *args )
      self.new.cut_without_permutations( sequence, *args )
    end

### Public Instance Methods

cut( sequence, *args ) click to toggle source

See main documentation for Bio::RestrictionEnzyme

`cut` takes into account permutations of cut variations based on competitiveness of enzymes for an enzyme cutsite or enzyme bindsite on a sequence.

Example:

FIXME add output

    Bio::RestrictionEnzyme::Analysis.cut('gaattc', 'EcoRI')

_same as:_

    Bio::RestrictionEnzyme::Analysis.cut('gaattc', 'g^aattc')

Arguments

- `sequence`: `String` kind of object that will be used as a nucleic acid sequence.

- `args`: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.

Returns | Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects. (Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments) or a `Symbol` containing an error code

    # File lib/bio/util/restriction_enzyme/analysis.rb, line 48
    def cut( sequence, *args )
      view_ranges = false

      args.select { |i| i.class == Hash }.each do |hsh|
        hsh.each do |key, value|
          if key == :view_ranges
            unless ( value.kind_of?(TrueClass) or value.kind_of?(FalseClass) )
              raise ArgumentError, "view_ranges must be set to true or false, currently #{value.inspect}."
            end
            view_ranges = value
          end
        end
      end

      res = cut_and_return_by_permutations( sequence, *args )
      return res if res.class == Symbol
      # Format the fragments for the user
      fragments_for_display( res, view_ranges )
    end

cut_without_permutations( sequence, *args ) click to toggle source

See main documentation for Bio::RestrictionEnzyme

Bio::RestrictionEnzyme.cut is preferred over this!

USE AT YOUR OWN RISK

This is a simpler version of method `cut`. `cut` takes into account permutations of cut variations based on competitiveness of enzymes for an enzyme cutsite or enzyme bindsite on a sequence. This does not take into account those possibilities and is therefore faster, but less likely to be accurate.

This code is mainly included as an academic example without having to wade through the extra layer of complexity added by the permutations.

Example:

FIXME add output

    Bio::RestrictionEnzyme::Analysis.cut_without_permutations('gaattc', 'EcoRI')

_same as:_

    Bio::RestrictionEnzyme::Analysis.cut_without_permutations('gaattc', 'g^aattc')

Arguments

- `sequence`: `String` kind of object that will be used as a nucleic acid sequence.

- `args`: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.

Returns | Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects. (Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments)

    # File lib/bio/util/restriction_enzyme/analysis_basic.rb, line 55
    def cut_without_permutations( sequence, *args )
      return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty?
      sequence = Bio::Sequence::NA.new( sequence )

      # create_enzyme_actions returns two seperate array elements, they're not
      # needed separated here so we put them into one array
      enzyme_actions = create_enzyme_actions( sequence, *args ).flatten
      return fragments_for_display( {} ) if enzyme_actions.empty?

      # Primary and complement strands are both measured from '0' to 'sequence.size-1' here
      sequence_range = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 )

      # Add the cuts to the sequence_range from each enzyme_action
      enzyme_actions.each do |enzyme_action|
        enzyme_action.cut_ranges.each do |cut_range|
          sequence_range.add_cut_range(cut_range)
        end
      end

      # Fill in the source sequence for sequence_range so it knows what bases
      # to use
      sequence_range.fragments.primary = sequence
      sequence_range.fragments.complement = sequence.forward_complement

      # Format the fragments for the user
      fragments_for_display( {0 => sequence_range} )
    end

### Protected Instance Methods

create_enzyme_actions( sequence, *args ) click to toggle source

Creates an array of EnzymeActions based on the DNA sequence and supplied enzymes.

Arguments

- `sequence`: The string of DNA to match the enzyme recognition sites against

- `args` | The enzymes to use.

Returns | `Array` with the first element being an array of EnzymeAction objects that `sometimes_cut`, and are subject to competition. The second is an array of EnzymeAction objects that `always_cut` and are not subject to competition.

    # File lib/bio/util/restriction_enzyme/analysis_basic.rb, line 120
    def create_enzyme_actions( sequence, *args )
      all_enzyme_actions = []

      args.each do |enzyme|
        enzyme = Bio::RestrictionEnzyme.new(enzyme) unless enzyme.class == Bio::RestrictionEnzyme::DoubleStranded

        # make sure pattern is the proper size
        # for more info see the internal documentation of
        # Bio::RestrictionEnzyme::DoubleStranded.create_action_at
        pattern = Bio::Sequence::NA.new(
          Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands.align(
            enzyme.primary, enzyme.complement
          ).primary
        ).to_re

        find_match_locations( sequence, pattern ).each do |offset|
          all_enzyme_actions << enzyme.create_action_at( offset )
        end
      end

      # FIXME VerticalCutRange should really be called VerticalAndHorizontalCutRange

      # * all_enzyme_actions is now full of EnzymeActions at specific locations across
      #   the sequence.
      # * all_enzyme_actions will now be examined to see if any EnzymeActions may
      #   conflict with one another, and if they do they'll be made note of in
      #   indicies_of_sometimes_cut.  They will then be remove FIXME
      # * a conflict occurs if another enzyme's bind site is compromised do due
      #   to another enzyme's cut.  Enzyme's bind sites may overlap and not be
      #   competitive, however neither bind site may be part of the other
      #   enzyme's cut or else they do become competitive.
      #
      # Take current EnzymeAction's entire bind site and compare it to all other
      # EzymeAction's cut ranges.  Only look for vertical cuts as boundaries
      # since trailing horizontal cuts would have no influence on the bind site.
      #
      # If example Enzyme A makes this cut pattern (cut range 2..5):
      #
      # 0 1 2|3 4 5 6 7
      #      +-----+
      # 0 1 2 3 4 5|6 7
      #
      # Then the bind site (and EnzymeAction range) for Enzyme B would need it's
      # right side to be at index 2 or less, or it's left side to be 6 or greater.

      competition_indexes = Set.new

      all_enzyme_actions[0..-2].each_with_index do |current_enzyme_action, i|
        next if competition_indexes.include? i
        next if current_enzyme_action.cut_ranges.empty?  # no cuts, some enzymes are like this (ex. CjuI)

        all_enzyme_actions[i+1..-1].each_with_index do |comparison_enzyme_action, j|
          j += (i + 1)
          next if competition_indexes.include? j
          next if comparison_enzyme_action.cut_ranges.empty?  # no cuts

          if (current_enzyme_action.right <= comparison_enzyme_action.cut_ranges.min_vertical) or
             (current_enzyme_action.left > comparison_enzyme_action.cut_ranges.max_vertical)
            # no conflict
          else
            competition_indexes += [i, j] # merge both indexes into the flat set
          end
        end
      end

      sometimes_cut = all_enzyme_actions.values_at( *competition_indexes )
      always_cut = all_enzyme_actions
      always_cut.delete_if {|x| sometimes_cut.include? x }

      [sometimes_cut, always_cut]
    end

cut_and_return_by_permutations( sequence, *args ) click to toggle source

See cut instance method

Arguments

- `sequence`: `String` kind of object that will be used as a nucleic acid sequence.

- `args`: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.

May also supply a `Hash` with the key ":max_permutations" to specificy how many permutations are allowed - a value of 0 indicates no permutations are allowed.

Returns | `Hash` Keys are a permutation ID, values are SequenceRange objects that have cuts applied.

also may return the `Symbol` ':sequence_empty', ':no_cuts_found', or ':too_many_permutations'

    # File lib/bio/util/restriction_enzyme/analysis.rb, line 81
    def cut_and_return_by_permutations( sequence, *args )
      my_hash = {}
      maximum_permutations = nil

      hashes_in_args = args.select { |i| i.class == Hash }
      args.delete_if { |i| i.class == Hash }
      hashes_in_args.each do |hsh|
        hsh.each do |key, value|
          case key
          when :max_permutations, 'max_permutations', :maximum_permutations, 'maximum_permutations'
            maximum_permutations = value.to_i unless value == nil
          when :view_ranges
          else
            raise ArgumentError, "Received key #{key.inspect} in argument - I only know the key ':max_permutations' and ':view_ranges' currently.  Hash passed: #{hsh.inspect}"
          end
        end
      end

      if !sequence.kind_of?(String) or sequence.empty?
        logger.warn "The supplied sequence is empty." if defined?(logger)
        return :sequence_empty
      end
      sequence = Bio::Sequence::NA.new( sequence )

      enzyme_actions, initial_cuts = create_enzyme_actions( sequence, *args )

      if enzyme_actions.empty? and initial_cuts.empty?
        logger.warn "This enzyme does not make any cuts on this sequence." if defined?(logger)
        return :no_cuts_found
      end

      # * When enzyme_actions.size is equal to '1' that means there are no permutations.
      # * If enzyme_actions.size is equal to '2' there is one
      #   permutation ("[0, 1]")
      # * If enzyme_actions.size is equal to '3' there are two
      #   permutations ("[0, 1, 2]")
      # * and so on..
      if maximum_permutations and enzyme_actions.size > 1
        if (enzyme_actions.size - 1) > maximum_permutations.to_i
          logger.warn "More permutations than maximum, skipping.  Found: #{enzyme_actions.size-1}  Max: #{maximum_permutations.to_i}" if defined?(logger)
          return :too_many_permutations
        end
      end

      if enzyme_actions.size > 1
        permutations = permute(enzyme_actions.size)

        permutations.each do |permutation|
          previous_cut_ranges = []
          # Primary and complement strands are both measured from '0' to 'sequence.size-1' here
          sequence_range = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 )

          # Add the cuts to the sequence_range from each enzyme_action contained
          # in initial_cuts.  These are the cuts that have no competition so are
          # not subject to permutations.
          initial_cuts.each do |enzyme_action|
            enzyme_action.cut_ranges.each do |cut_range|
              sequence_range.add_cut_range(cut_range)
            end
          end

          permutation.each do |id|
            enzyme_action = enzyme_actions[id]

            # conflict is false if the current enzyme action may cut in it's range.
            # conflict is true if it cannot due to a previous enzyme action making
            # a cut where this enzyme action needs a whole recognition site.
            conflict = false

            # If current size of enzyme_action overlaps with previous cut_range, don't cut
            # note that the enzyme action may fall in the middle of a previous enzyme action
            # so all cut locations must be checked that would fall underneath.
            previous_cut_ranges.each do |cut_range|
              next unless cut_range.class == Bio::RestrictionEnzyme::Range::VerticalCutRange  # we aren't concerned with horizontal cuts
              previous_cut_left = cut_range.range.first
              previous_cut_right = cut_range.range.last

              # Keep in mind:
              # * The cut location is to the immediate right of the base located at the index.
              #   ex: at^gc -- the cut location is at index 1
              # * The enzyme action location is located at the base of the index.
              #   ex: atgc -- 0 => 'a', 1 => 't', 2 => 'g', 3 => 'c'
              # method create_enzyme_actions has similar commentary if interested
              if (enzyme_action.right <= previous_cut_left) or
                 (enzyme_action.left > previous_cut_right) or
                 (enzyme_action.left > previous_cut_left and enzyme_action.right <= previous_cut_right) # in between cuts
                # no conflict
              else
                conflict = true
              end
            end

            next if conflict == true
            enzyme_action.cut_ranges.each { |cut_range| sequence_range.add_cut_range(cut_range) }
            previous_cut_ranges += enzyme_action.cut_ranges
          end # permutation.each

          # Fill in the source sequence for sequence_range so it knows what bases
          # to use
          sequence_range.fragments.primary = sequence
          sequence_range.fragments.complement = sequence.forward_complement
          my_hash[permutation] = sequence_range
        end # permutations.each

      else # if enzyme_actions.size == 1
        # no permutations, just do it
        sequence_range = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 )
        initial_cuts.each { |enzyme_action| enzyme_action.cut_ranges.each { |cut_range| sequence_range.add_cut_range(cut_range) } }
        sequence_range.fragments.primary = sequence
        sequence_range.fragments.complement = sequence.forward_complement
        my_hash[0] = sequence_range
      end

      my_hash
    end

find_match_locations( string, re ) click to toggle source

Returns an `Array` of the match indicies of a `RegExp` to a string.

Example:

    find_match_locations('abccdefeg', /[ce]/) # => [2,3,5,7]

Arguments

- `string`: The string to scan

- `re`: A RegExp to use

Returns | `Array` with indicies of match locations

    # File lib/bio/util/restriction_enzyme/analysis_basic.rb, line 203
    def find_match_locations( string, re )
      md = string.match( re )
      locations = []
      counter = 0
      while md
        # save the match index relative to the original string
        locations << (counter += md.begin(0))
        # find the next match
        md = string[ (counter += 1)..-1 ].match( re )
      end
      locations
    end

fragments_for_display( hsh, view_ranges=false ) click to toggle source

Take the fragments from SequenceRange objects generated from add_cut_range and return unique results as a Bio::RestrictionEnzyme::Analysis::Fragment object.

Arguments

- `hsh`: `Hash` Keys are a permutation ID, if any. Values are SequenceRange objects that have cuts applied.

Returns | Bio::RestrictionEnzyme::Analysis::Fragments object populated with Bio::RestrictionEnzyme::Analysis::Fragment objects.

    # File lib/bio/util/restriction_enzyme/analysis_basic.rb, line 94
    def fragments_for_display( hsh, view_ranges=false )
      ary = Fragments.new
      return ary unless hsh

      hsh.each do |permutation_id, sequence_range|
        sequence_range.fragments.for_display.each do |fragment|
          if view_ranges
            ary << Bio::RestrictionEnzyme::Fragment.new(fragment.primary, fragment.complement, fragment.p_left, fragment.p_right, fragment.c_left, fragment.c_right)
          else
            ary << Bio::RestrictionEnzyme::Fragment.new(fragment.primary, fragment.complement)
          end
        end
      end

      ary.uniq! unless view_ranges

      ary
    end

permute(count, permutations = [[0]]) click to toggle source

Returns permutation orders for a given number of elements.

Examples:

    permute(0) # => [[0]]
    permute(1) # => [[0]]
    permute(2) # => [[1, 0], [0, 1]]
    permute(3) # => [[2, 1, 0], [2, 0, 1], [1, 2, 0], [0, 2, 1], [1, 0, 2], [0, 1, 2]]
    permute(4) # => [[3, 2, 1, 0],
                     [3, 2, 0, 1],
                     [3, 1, 2, 0],
                     [3, 0, 2, 1],
                     [3, 1, 0, 2],
                     [3, 0, 1, 2],
                     [2, 3, 1, 0],
                     [2, 3, 0, 1],
                     [1, 3, 2, 0],
                     [0, 3, 2, 1],
                     [1, 3, 0, 2],
                     [0, 3, 1, 2],
                     [2, 1, 3, 0],
                     [2, 0, 3, 1],
                     [1, 2, 3, 0],
                     [0, 2, 3, 1],
                     [1, 0, 3, 2],
                     [0, 1, 3, 2],
                     [2, 1, 0, 3],
                     [2, 0, 1, 3],
                     [1, 2, 0, 3],
                     [0, 2, 1, 3],
                     [1, 0, 2, 3],
                     [0, 1, 2, 3]]

Arguments

- `count`: `Number` of different elements to be permuted

- `permutations`: ignore - for the recursive algorithm

Returns | `Array` of `Array` objects with different possible permutation orders. See examples.

    # File lib/bio/util/restriction_enzyme/analysis.rb, line 235
    def permute(count, permutations = [[0]])
      return permutations if count <= 1
      new_arrays = []
      new_array = []

      (permutations[0].size + 1).times do |n|
        new_array.clear
        permutations.each { |a| new_array << a.dup }
        new_array.each { |e| e.insert(n, permutations[0].size) }
        new_arrays += new_array
      end

      permute(count-1, new_arrays)
    end

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