burrows_wheeler 0.0.1

checksums.yaml

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data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/.travis.yml

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+language: ruby
+rvm:
+  - 2.1.0
+  - 2.0.0
+  - 1.9.3
+script: "rake test"

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in burrows_wheeler.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2014 M.Magomedov
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+[**Burrows-Wheeler transform**](http://en.wikipedia.org/wiki/Burrows%E2%80%93Wheeler_transform)
+
+[![Build Status](https://travis-ci.org/ethylamide/burrows_wheeler.svg)](https://travis-ci.org/ethylamide/burrows_wheeler)
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'burrows_wheeler'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install burrows_wheeler
+
+## Usage
+
+Typical use-case looks something like this:
+
+```ruby
+require 'burrows_wheeler/transform'
+inp = StringIO.new('ABRACADABRA!')
+File.open('/tmp/file.bwt') do |out|
+  BurrowsWheeler::Transform.encode(inp, out)
+end
+```
+
+```ruby
+File.open('/tmp/file.bwt') do |inp|
+  out = StringIO.new
+  BurrowsWheeler::Transform.decode(inp, out)
+  puts out.string
+end
+```
+
+## Contributing
+
+1. Fork it ( https://github.com/ethylamide/burrows_wheeler/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

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+require 'bundler/gem_tasks'
+require 'rake/testtask'
+
+Rake::TestTask.new do |task|
+  task.libs << %w(test lib)
+  task.pattern = 'test/test_*.rb'
+end
+
+task default: :test
+

data/burrows_wheeler.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'burrows_wheeler/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "burrows_wheeler"
+  spec.version       = BurrowsWheeler::VERSION
+  spec.authors       = ["M.Magomedov"]
+  spec.email         = ["mmagomedoff@gmail.com"]
+  spec.summary       = %q{Burrows-Wheeler transformation.}
+  spec.description   = %q{Burrows-Wheeler transformation. Encoding and decoding.}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.6"
+  spec.add_development_dependency "rake"
+end

data/lib/burrows_wheeler.rb

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+require 'burrows_wheeler/version'
+
+module BurrowsWheeler
+end

data/lib/burrows_wheeler/circular_string.rb

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+module BurrowsWheeler
+  # > CircularString.new(str, 5).to_s
+  # => "ADABRA!ABRAC",
+
+  class CircularString
+    include Comparable
+
+    attr_reader :string
+    attr_reader :shift
+
+    def initialize(string, shift)
+      @string = string
+      @shift = shift
+    end
+
+    def [](index)
+      return nil if index < 0 || index >= string.length
+      idx = (index + @shift) % @string.length
+      @string[idx]
+    end
+
+    def last
+      self[length - 1]
+    end
+
+    def subsequence(start, finish)
+      len = finish - start
+      CircularString.new(@string[start, len], @shift)
+    end
+
+    def <=>(other)
+      len = [length, other.length].min
+
+      (0..len - 1).each do |i|
+        c1, c2 = self[i], other[i]
+        return (c1 <=> c2) if c1 != c2
+      end
+
+      length <=> other.length
+    end
+
+    def length
+      @string.length
+    end
+
+    def to_s
+      (0..@string.length - 1).reduce('') do |str, idx|
+        str + self[idx]
+      end
+    end
+  end
+end

data/lib/burrows_wheeler/circular_suffix_array.rb

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+module BurrowsWheeler
+  class CircularSuffixArray
+    extend Forwardable
+
+    def initialize(string)
+      suffixes = (0..string.length - 1).map do |shift|
+        CircularString.new(string, shift)
+      end.sort
+
+      @indices = suffixes.map(&:shift)
+    end
+
+    def_delegators :@indices, :length, :[], :map, :each, :to_a
+  end
+end

data/lib/burrows_wheeler/transform.rb

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+require 'burrows_wheeler/circular_string'
+require 'burrows_wheeler/circular_suffix_array'
+
+module BurrowsWheeler
+  class Transform
+    class << self
+      def encode(inp, out)
+        str = inp.read
+        csa = CircularSuffixArray.new(str)
+        first = -1
+
+        symbols = []
+
+        (0..str.length - 1).each do |i|
+          idx = csa[i]
+          cs = CircularString.new(str, idx)
+          symbols << cs.last
+          first = i if idx == 0
+        end
+
+        # write uint64_t
+        out.write([first].pack('Q'))
+
+        symbols.each { |c| out.write(c) }
+
+        out.flush
+      end
+
+      def decode(inp, out)
+        # read uint64_t
+        first = inp.read(8).unpack('Q').first
+        data = inp.read.split('')
+        column = data.sort
+
+        length = data.length
+
+        index = {}
+        nxt = Array.new(length)
+
+        j = 0
+        while j < length
+          index[column[j]] = j
+          j += 1 while j < length - 1 && column[j] == column[j + 1]
+          j += 1
+        end
+
+        (0..length - 1).each do |i|
+          char = data[i]
+          nxt[index[char]] = i
+          index[char] += 1
+        end
+
+        (0..length - 1).each do
+          out.write(column[first])
+          first = nxt[first]
+        end
+
+        out.flush
+      end
+    end
+  end
+end

data/lib/burrows_wheeler/version.rb

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+module BurrowsWheeler
+  VERSION = "0.0.1"
+end

data/test/helper.rb

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+require 'rubygems'
+require 'bundler/setup'
+require 'minitest/autorun'
+require 'minitest/unit'

data/test/test_circular_string.rb

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+require 'helper'
+require 'burrows_wheeler/circular_string'
+
+module BurrowsWheeler
+  class TestCircularString < MiniTest::Unit::TestCase
+    def setup
+      @circular_string = CircularString.new('ABRACADABRA!', 5)
+    end
+
+    def test_indexing
+      assert_equal '!', @circular_string[6]
+    end
+
+    def test_length
+      assert_equal 12, @circular_string.length
+    end
+
+    def test_to_string_transformation
+      assert_equal 'ADABRA!ABRAC', @circular_string.to_s
+    end
+
+    def test_comparing
+      other = CircularString.new('ABRACADABRA!', 11)
+      assert_operator @circular_string, :>, other
+    end
+
+    def test_subsequence
+      sub = @circular_string.subsequence(0, 6)
+      assert_equal sub.to_s, 'AABRAC'
+    end
+  end
+end

data/test/test_circular_suffix_array.rb

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+require 'helper'
+require 'burrows_wheeler/circular_string'
+require 'burrows_wheeler/circular_suffix_array'
+
+module BurrowsWheeler
+  class TestCircularSuffixArray < MiniTest::Unit::TestCase
+    def setup
+      @circular_suffix_array = CircularSuffixArray.new('ABRACADABRA!')
+    end
+
+    def test_length
+      assert_equal 12, @circular_suffix_array.length
+    end
+
+    def test_indexing
+      assert_equal 0, @circular_suffix_array[3]
+    end
+
+    def test_array
+      assert_equal [11, 10, 7, 0, 3, 5, 8, 1, 4, 6, 9, 2], @circular_suffix_array.to_a
+    end
+  end
+end

data/test/test_transform.rb

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+require 'helper'
+require 'burrows_wheeler/transform'
+
+module BurrowsWheeler
+  class TestTransform < MiniTest::Unit::TestCase
+    def test_encode
+      inp = StringIO.new('ABRACADABRA!')
+      out = StringIO.new
+
+      BurrowsWheeler::Transform.encode(inp, out)
+
+      assert_equal "\u0003\u0000\u0000\u0000\u0000\u0000\u0000\u0000ARD!RCAAAABB", out.string
+    end
+
+    def test_decode
+      inp = StringIO.new("\u0003\u0000\u0000\u0000\u0000\u0000\u0000\u0000ARD!RCAAAABB")
+      out = StringIO.new
+
+      BurrowsWheeler::Transform.decode(inp, out)
+
+      assert_equal 'ABRACADABRA!', out.string
+    end
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: burrows_wheeler
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- M.Magomedov
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-11-17 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Burrows-Wheeler transformation. Encoding and decoding.
+email:
+- mmagomedoff@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- burrows_wheeler.gemspec
+- lib/burrows_wheeler.rb
+- lib/burrows_wheeler/circular_string.rb
+- lib/burrows_wheeler/circular_suffix_array.rb
+- lib/burrows_wheeler/transform.rb
+- lib/burrows_wheeler/version.rb
+- test/helper.rb
+- test/test_circular_string.rb
+- test/test_circular_suffix_array.rb
+- test/test_transform.rb
+homepage: ''
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Burrows-Wheeler transformation.
+test_files:
+- test/helper.rb
+- test/test_circular_string.rb
+- test/test_circular_suffix_array.rb
+- test/test_transform.rb