bioinform 0.1.11 → 0.1.12

data/lib/bioinform/support/third_part/active_support/hash_with_indifferent_access.rb

@@ -0,0 +1,178 @@
+require_relative 'core_ext/hash/keys'
+
+# This class has dubious semantics and we only have it so that
+# people can write <tt>params[:key]</tt> instead of <tt>params['key']</tt>
+# and they get the same value for both keys.
+
+module ActiveSupport
+  class HashWithIndifferentAccess < Hash
+
+    # Always returns true, so that <tt>Array#extract_options!</tt> finds members of this class.
+    def extractable_options?
+      true
+    end
+
+    def with_indifferent_access
+      dup
+    end
+
+    def nested_under_indifferent_access
+      self
+    end
+
+    def initialize(constructor = {})
+      if constructor.is_a?(Hash)
+        super()
+        update(constructor)
+      else
+        super(constructor)
+      end
+    end
+
+    def default(key = nil)
+      if key.is_a?(Symbol) && include?(key = key.to_s)
+        self[key]
+      else
+        super
+      end
+    end
+
+    def self.new_from_hash_copying_default(hash)
+      new(hash).tap do |new_hash|
+        new_hash.default = hash.default
+      end
+    end
+
+    alias_method :regular_writer, :[]= unless method_defined?(:regular_writer)
+    alias_method :regular_update, :update unless method_defined?(:regular_update)
+
+    # Assigns a new value to the hash:
+    #
+    #   hash = HashWithIndifferentAccess.new
+    #   hash[:key] = "value"
+    #
+    def []=(key, value)
+      regular_writer(convert_key(key), convert_value(value))
+    end
+
+    alias_method :store, :[]=
+
+    # Updates the instantized hash with values from the second:
+    #
+    #   hash_1 = HashWithIndifferentAccess.new
+    #   hash_1[:key] = "value"
+    #
+    #   hash_2 = HashWithIndifferentAccess.new
+    #   hash_2[:key] = "New Value!"
+    #
+    #   hash_1.update(hash_2) # => {"key"=>"New Value!"}
+    #
+    def update(other_hash)
+      if other_hash.is_a? HashWithIndifferentAccess
+        super(other_hash)
+      else
+        other_hash.each_pair { |key, value| regular_writer(convert_key(key), convert_value(value)) }
+        self
+      end
+    end
+
+    alias_method :merge!, :update
+
+    # Checks the hash for a key matching the argument passed in:
+    #
+    #   hash = HashWithIndifferentAccess.new
+    #   hash["key"] = "value"
+    #   hash.key? :key  # => true
+    #   hash.key? "key" # => true
+    #
+    def key?(key)
+      super(convert_key(key))
+    end
+
+    alias_method :include?, :key?
+    alias_method :has_key?, :key?
+    alias_method :member?, :key?
+
+    # Same as <tt>Hash#fetch</tt> where the key passed as argument can be
+    # either a string or a symbol:
+    #
+    #   counters = HashWithIndifferentAccess.new
+    #   counters[:foo] = 1
+    #
+    #   counters.fetch("foo")          # => 1
+    #   counters.fetch(:bar, 0)        # => 0
+    #   counters.fetch(:bar) {|key| 0} # => 0
+    #   counters.fetch(:zoo)           # => KeyError: key not found: "zoo"
+    #
+    def fetch(key, *extras)
+      super(convert_key(key), *extras)
+    end
+
+    # Returns an array of the values at the specified indices:
+    #
+    #   hash = HashWithIndifferentAccess.new
+    #   hash[:a] = "x"
+    #   hash[:b] = "y"
+    #   hash.values_at("a", "b") # => ["x", "y"]
+    #
+    def values_at(*indices)
+      indices.collect {|key| self[convert_key(key)]}
+    end
+
+    # Returns an exact copy of the hash.
+    def dup
+      self.class.new(self).tap do |new_hash|
+        new_hash.default = default
+      end
+    end
+
+    # Merges the instantized and the specified hashes together, giving precedence to the values from the second hash.
+    # Does not overwrite the existing hash.
+    def merge(hash)
+      self.dup.update(hash)
+    end
+
+    # Performs the opposite of merge, with the keys and values from the first hash taking precedence over the second.
+    # This overloaded definition prevents returning a regular hash, if reverse_merge is called on a <tt>HashWithDifferentAccess</tt>.
+    def reverse_merge(other_hash)
+      super self.class.new_from_hash_copying_default(other_hash)
+    end
+
+    def reverse_merge!(other_hash)
+      replace(reverse_merge( other_hash ))
+    end
+
+    # Removes a specified key from the hash.
+    def delete(key)
+      super(convert_key(key))
+    end
+
+    def stringify_keys!; self end
+    def stringify_keys; dup end
+    undef :symbolize_keys!
+    def symbolize_keys; to_hash.symbolize_keys end
+    def to_options!; self end
+
+    # Convert to a Hash with String keys.
+    def to_hash
+      Hash.new(default).merge!(self)
+    end
+
+    protected
+      def convert_key(key)
+        key.kind_of?(Symbol) ? key.to_s : key
+      end
+
+      def convert_value(value)
+        if value.is_a? Hash
+          value.nested_under_indifferent_access
+        elsif value.is_a?(Array)
+          value.dup.replace(value.map { |e| convert_value(e) })
+        else
+          value
+        end
+      end
+  end
+end
+
+HashWithIndifferentAccess = ActiveSupport::HashWithIndifferentAccess

data/lib/bioinform/support/third_part/active_support/multibyte/chars.rb

@@ -0,0 +1,476 @@
+# encoding: utf-8
+require_relative '../core_ext/string/access'
+require_relative '../core_ext/string/behavior'
+
+module ActiveSupport #:nodoc:
+  module Multibyte #:nodoc:
+    # Chars enables you to work transparently with UTF-8 encoding in the Ruby String class without having extensive
+    # knowledge about the encoding. A Chars object accepts a string upon initialization and proxies String methods in an
+    # encoding safe manner. All the normal String methods are also implemented on the proxy.
+    #
+    # String methods are proxied through the Chars object, and can be accessed through the +mb_chars+ method. Methods
+    # which would normally return a String object now return a Chars object so methods can be chained.
+    #
+    #   "The Perfect String  ".mb_chars.downcase.strip.normalize # => "the perfect string"
+    #
+    # Chars objects are perfectly interchangeable with String objects as long as no explicit class checks are made.
+    # If certain methods do explicitly check the class, call +to_s+ before you pass chars objects to them.
+    #
+    #   bad.explicit_checking_method "T".mb_chars.downcase.to_s
+    #
+    # The default Chars implementation assumes that the encoding of the string is UTF-8, if you want to handle different
+    # encodings you can write your own multibyte string handler and configure it through
+    # ActiveSupport::Multibyte.proxy_class.
+    #
+    #   class CharsForUTF32
+    #     def size
+    #       @wrapped_string.size / 4
+    #     end
+    #
+    #     def self.accepts?(string)
+    #       string.length % 4 == 0
+    #     end
+    #   end
+    #
+    #   ActiveSupport::Multibyte.proxy_class = CharsForUTF32
+    class Chars
+      attr_reader :wrapped_string
+      alias to_s wrapped_string
+      alias to_str wrapped_string
+
+      if RUBY_VERSION >= "1.9"
+        # Creates a new Chars instance by wrapping _string_.
+        def initialize(string)
+          @wrapped_string = string
+          @wrapped_string.force_encoding(Encoding::UTF_8) unless @wrapped_string.frozen?
+        end
+      else
+        def initialize(string) #:nodoc:
+          @wrapped_string = string
+        end
+      end
+
+      # Forward all undefined methods to the wrapped string.
+      def method_missing(method, *args, &block)
+        if method.to_s =~ /!$/
+          @wrapped_string.__send__(method, *args, &block)
+          self
+        else
+          result = @wrapped_string.__send__(method, *args, &block)
+          result.kind_of?(String) ? chars(result) : result
+        end
+      end
+
+      # Returns +true+ if _obj_ responds to the given method. Private methods are included in the search
+      # only if the optional second parameter evaluates to +true+.
+      def respond_to?(method, include_private=false)
+        super || @wrapped_string.respond_to?(method, include_private)
+      end
+
+      # Enable more predictable duck-typing on String-like classes. See Object#acts_like?.
+      def acts_like_string?
+        true
+      end
+
+      # Returns +true+ when the proxy class can handle the string. Returns +false+ otherwise.
+      def self.consumes?(string)
+        # Unpack is a little bit faster than regular expressions.
+        string.unpack('U*')
+        true
+      rescue ArgumentError
+        false
+      end
+
+      include Comparable
+
+      # Returns -1, 0, or 1, depending on whether the Chars object is to be sorted before,
+      # equal or after the object on the right side of the operation. It accepts any object
+      # that implements +to_s+:
+      #
+      #   'é'.mb_chars <=> 'ü'.mb_chars # => -1
+      #
+      # See <tt>String#<=></tt> for more details.
+      def <=>(other)
+        @wrapped_string <=> other.to_s
+      end
+
+      if RUBY_VERSION < "1.9"
+        # Returns +true+ if the Chars class can and should act as a proxy for the string _string_. Returns
+        # +false+ otherwise.
+        def self.wants?(string)
+          $KCODE == 'UTF8' && consumes?(string)
+        end
+
+        # Returns a new Chars object containing the _other_ object concatenated to the string.
+        #
+        # Example:
+        #   ('Café'.mb_chars + ' périferôl').to_s # => "Café périferôl"
+        def +(other)
+          chars(@wrapped_string + other)
+        end
+
+        # Like <tt>String#=~</tt> only it returns the character offset (in codepoints) instead of the byte offset.
+        #
+        # Example:
+        #   'Café périferôl'.mb_chars =~ /ô/ # => 12
+        def =~(other)
+          translate_offset(@wrapped_string =~ other)
+        end
+
+        # Inserts the passed string at specified codepoint offsets.
+        #
+        # Example:
+        #   'Café'.mb_chars.insert(4, ' périferôl').to_s # => "Café périferôl"
+        def insert(offset, fragment)
+          unpacked = Unicode.u_unpack(@wrapped_string)
+          unless offset > unpacked.length
+            @wrapped_string.replace(
+              Unicode.u_unpack(@wrapped_string).insert(offset, *Unicode.u_unpack(fragment)).pack('U*')
+            )
+          else
+            raise IndexError, "index #{offset} out of string"
+          end
+          self
+        end
+
+        # Returns +true+ if contained string contains _other_. Returns +false+ otherwise.
+        #
+        # Example:
+        #   'Café'.mb_chars.include?('é') # => true
+        def include?(other)
+          # We have to redefine this method because Enumerable defines it.
+          @wrapped_string.include?(other)
+        end
+
+        # Returns the position _needle_ in the string, counting in codepoints. Returns +nil+ if _needle_ isn't found.
+        #
+        # Example:
+        #   'Café périferôl'.mb_chars.index('ô')   # => 12
+        #   'Café périferôl'.mb_chars.index(/\w/u) # => 0
+        def index(needle, offset=0)
+          wrapped_offset = first(offset).wrapped_string.length
+          index = @wrapped_string.index(needle, wrapped_offset)
+          index ? (Unicode.u_unpack(@wrapped_string.slice(0...index)).size) : nil
+        end
+
+        # Returns the position _needle_ in the string, counting in
+        # codepoints, searching backward from _offset_ or the end of the
+        # string. Returns +nil+ if _needle_ isn't found.
+        #
+        # Example:
+        #   'Café périferôl'.mb_chars.rindex('é')   # => 6
+        #   'Café périferôl'.mb_chars.rindex(/\w/u) # => 13
+        def rindex(needle, offset=nil)
+          offset ||= length
+          wrapped_offset = first(offset).wrapped_string.length
+          index = @wrapped_string.rindex(needle, wrapped_offset)
+          index ? (Unicode.u_unpack(@wrapped_string.slice(0...index)).size) : nil
+        end
+
+        # Returns the number of codepoints in the string
+        def size
+          Unicode.u_unpack(@wrapped_string).size
+        end
+        alias_method :length, :size
+
+        # Strips entire range of Unicode whitespace from the right of the string.
+        def rstrip
+          chars(@wrapped_string.gsub(Unicode::TRAILERS_PAT, ''))
+        end
+
+        # Strips entire range of Unicode whitespace from the left of the string.
+        def lstrip
+          chars(@wrapped_string.gsub(Unicode::LEADERS_PAT, ''))
+        end
+
+        # Strips entire range of Unicode whitespace from the right and left of the string.
+        def strip
+          rstrip.lstrip
+        end
+
+        # Returns the codepoint of the first character in the string.
+        #
+        # Example:
+        #   'こんにちは'.mb_chars.ord # => 12371
+        def ord
+          Unicode.u_unpack(@wrapped_string)[0]
+        end
+
+        # Works just like <tt>String#rjust</tt>, only integer specifies characters instead of bytes.
+        #
+        # Example:
+        #
+        #   "¾ cup".mb_chars.rjust(8).to_s
+        #   # => "   ¾ cup"
+        #
+        #   "¾ cup".mb_chars.rjust(8, " ").to_s # Use non-breaking whitespace
+        #   # => "   ¾ cup"
+        def rjust(integer, padstr=' ')
+          justify(integer, :right, padstr)
+        end
+
+        # Works just like <tt>String#ljust</tt>, only integer specifies characters instead of bytes.
+        #
+        # Example:
+        #
+        #   "¾ cup".mb_chars.rjust(8).to_s
+        #   # => "¾ cup   "
+        #
+        #   "¾ cup".mb_chars.rjust(8, " ").to_s # Use non-breaking whitespace
+        #   # => "¾ cup   "
+        def ljust(integer, padstr=' ')
+          justify(integer, :left, padstr)
+        end
+
+        # Works just like <tt>String#center</tt>, only integer specifies characters instead of bytes.
+        #
+        # Example:
+        #
+        #   "¾ cup".mb_chars.center(8).to_s
+        #   # => " ¾ cup  "
+        #
+        #   "¾ cup".mb_chars.center(8, " ").to_s # Use non-breaking whitespace
+        #   # => " ¾ cup  "
+        def center(integer, padstr=' ')
+          justify(integer, :center, padstr)
+        end
+
+      else
+        def =~(other)
+          @wrapped_string =~ other
+        end
+      end
+
+      # Works just like <tt>String#split</tt>, with the exception that the items in the resulting list are Chars
+      # instances instead of String. This makes chaining methods easier.
+      #
+      # Example:
+      #   'Café périferôl'.mb_chars.split(/é/).map { |part| part.upcase.to_s } # => ["CAF", " P", "RIFERÔL"]
+      def split(*args)
+        @wrapped_string.split(*args).map { |i| i.mb_chars }
+      end
+
+      # Like <tt>String#[]=</tt>, except instead of byte offsets you specify character offsets.
+      #
+      # Example:
+      #
+      #   s = "Müller"
+      #   s.mb_chars[2] = "e" # Replace character with offset 2
+      #   s
+      #   # => "Müeler"
+      #
+      #   s = "Müller"
+      #   s.mb_chars[1, 2] = "ö" # Replace 2 characters at character offset 1
+      #   s
+      #   # => "Möler"
+      def []=(*args)
+        replace_by = args.pop
+        # Indexed replace with regular expressions already works
+        if args.first.is_a?(Regexp)
+          @wrapped_string[*args] = replace_by
+        else
+          result = Unicode.u_unpack(@wrapped_string)
+          case args.first
+          when Fixnum
+            raise IndexError, "index #{args[0]} out of string" if args[0] >= result.length
+            min = args[0]
+            max = args[1].nil? ? min : (min + args[1] - 1)
+            range = Range.new(min, max)
+            replace_by = [replace_by].pack('U') if replace_by.is_a?(Fixnum)
+          when Range
+            raise RangeError, "#{args[0]} out of range" if args[0].min >= result.length
+            range = args[0]
+          else
+            needle = args[0].to_s
+            min = index(needle)
+            max = min + Unicode.u_unpack(needle).length - 1
+            range = Range.new(min, max)
+          end
+          result[range] = Unicode.u_unpack(replace_by)
+          @wrapped_string.replace(result.pack('U*'))
+        end
+      end
+
+      # Reverses all characters in the string.
+      #
+      # Example:
+      #   'Café'.mb_chars.reverse.to_s # => 'éfaC'
+      def reverse
+        chars(Unicode.g_unpack(@wrapped_string).reverse.flatten.pack('U*'))
+      end
+
+      # Implements Unicode-aware slice with codepoints. Slicing on one point returns the codepoints for that
+      # character.
+      #
+      # Example:
+      #   'こんにちは'.mb_chars.slice(2..3).to_s # => "にち"
+      def slice(*args)
+        if args.size > 2
+          raise ArgumentError, "wrong number of arguments (#{args.size} for 1)" # Do as if we were native
+        elsif (args.size == 2 && !(args.first.is_a?(Numeric) || args.first.is_a?(Regexp)))
+          raise TypeError, "cannot convert #{args.first.class} into Integer" # Do as if we were native
+        elsif (args.size == 2 && !args[1].is_a?(Numeric))
+          raise TypeError, "cannot convert #{args[1].class} into Integer" # Do as if we were native
+        elsif args[0].kind_of? Range
+          cps = Unicode.u_unpack(@wrapped_string).slice(*args)
+          result = cps.nil? ? nil : cps.pack('U*')
+        elsif args[0].kind_of? Regexp
+          result = @wrapped_string.slice(*args)
+        elsif args.size == 1 && args[0].kind_of?(Numeric)
+          character = Unicode.u_unpack(@wrapped_string)[args[0]]
+          result = character && [character].pack('U')
+        else
+          cps = Unicode.u_unpack(@wrapped_string).slice(*args)
+          result = cps && cps.pack('U*')
+        end
+        result && chars(result)
+      end
+      alias_method :[], :slice
+
+      # Limit the byte size of the string to a number of bytes without breaking characters. Usable
+      # when the storage for a string is limited for some reason.
+      #
+      # Example:
+      #   'こんにちは'.mb_chars.limit(7).to_s # => "こん"
+      def limit(limit)
+        slice(0...translate_offset(limit))
+      end
+
+      # Convert characters in the string to uppercase.
+      #
+      # Example:
+      #   'Laurent, où sont les tests ?'.mb_chars.upcase.to_s # => "LAURENT, OÙ SONT LES TESTS ?"
+      def upcase
+        chars(Unicode.apply_mapping @wrapped_string, :uppercase_mapping)
+      end
+
+      # Convert characters in the string to lowercase.
+      #
+      # Example:
+      #   'VĚDA A VÝZKUM'.mb_chars.downcase.to_s # => "věda a výzkum"
+      def downcase
+        chars(Unicode.apply_mapping @wrapped_string, :lowercase_mapping)
+      end
+
+      # Converts the first character to uppercase and the remainder to lowercase.
+      #
+      # Example:
+      #  'über'.mb_chars.capitalize.to_s # => "Über"
+      def capitalize
+        (slice(0) || chars('')).upcase + (slice(1..-1) || chars('')).downcase
+      end
+
+      # Capitalizes the first letter of every word, when possible.
+      #
+      # Example:
+      #   "ÉL QUE SE ENTERÓ".mb_chars.titleize    # => "Él Que Se Enteró"
+      #   "日本語".mb_chars.titleize                 # => "日本語"
+      def titleize
+        chars(downcase.to_s.gsub(/\b('?[\S])/u) { Unicode.apply_mapping $1, :uppercase_mapping })
+      end
+      alias_method :titlecase, :titleize
+
+      # Returns the KC normalization of the string by default. NFKC is considered the best normalization form for
+      # passing strings to databases and validations.
+      #
+      # * <tt>form</tt> - The form you want to normalize in. Should be one of the following:
+      #   <tt>:c</tt>, <tt>:kc</tt>, <tt>:d</tt>, or <tt>:kd</tt>. Default is
+      #   ActiveSupport::Multibyte::Unicode.default_normalization_form
+      def normalize(form = nil)
+        chars(Unicode.normalize(@wrapped_string, form))
+      end
+
+      # Performs canonical decomposition on all the characters.
+      #
+      # Example:
+      #   'é'.length                         # => 2
+      #   'é'.mb_chars.decompose.to_s.length # => 3
+      def decompose
+        chars(Unicode.decompose_codepoints(:canonical, Unicode.u_unpack(@wrapped_string)).pack('U*'))
+      end
+
+      # Performs composition on all the characters.
+      #
+      # Example:
+      #   'é'.length                       # => 3
+      #   'é'.mb_chars.compose.to_s.length # => 2
+      def compose
+        chars(Unicode.compose_codepoints(Unicode.u_unpack(@wrapped_string)).pack('U*'))
+      end
+
+      # Returns the number of grapheme clusters in the string.
+      #
+      # Example:
+      #   'क्षि'.mb_chars.length   # => 4
+      #   'क्षि'.mb_chars.g_length # => 3
+      def g_length
+        Unicode.g_unpack(@wrapped_string).length
+      end
+
+      # Replaces all ISO-8859-1 or CP1252 characters by their UTF-8 equivalent resulting in a valid UTF-8 string.
+      #
+      # Passing +true+ will forcibly tidy all bytes, assuming that the string's encoding is entirely CP1252 or ISO-8859-1.
+      def tidy_bytes(force = false)
+        chars(Unicode.tidy_bytes(@wrapped_string, force))
+      end
+
+       %w(capitalize downcase lstrip reverse rstrip slice strip tidy_bytes upcase).each do |method|
+        # Only define a corresponding bang method for methods defined in the proxy; On 1.9 the proxy will
+        # exclude lstrip!, rstrip! and strip! because they are already work as expected on multibyte strings.
+        if public_method_defined?(method)
+          define_method("#{method}!") do |*args|
+            @wrapped_string = send(args.nil? ? method : method, *args).to_s
+            self
+          end
+        end
+      end
+
+      protected
+
+        def translate_offset(byte_offset) #:nodoc:
+          return nil if byte_offset.nil?
+          return 0   if @wrapped_string == ''
+
+          if @wrapped_string.respond_to?(:force_encoding)
+            @wrapped_string = @wrapped_string.dup.force_encoding(Encoding::ASCII_8BIT)
+          end
+
+          begin
+            @wrapped_string[0...byte_offset].unpack('U*').length
+          rescue ArgumentError
+            byte_offset -= 1
+            retry
+          end
+        end
+
+        def justify(integer, way, padstr=' ') #:nodoc:
+          raise ArgumentError, "zero width padding" if padstr.length == 0
+          padsize = integer - size
+          padsize = padsize > 0 ? padsize : 0
+          case way
+          when :right
+            result = @wrapped_string.dup.insert(0, padding(padsize, padstr))
+          when :left
+            result = @wrapped_string.dup.insert(-1, padding(padsize, padstr))
+          when :center
+            lpad = padding((padsize / 2.0).floor, padstr)
+            rpad = padding((padsize / 2.0).ceil, padstr)
+            result = @wrapped_string.dup.insert(0, lpad).insert(-1, rpad)
+          end
+          chars(result)
+        end
+
+        def padding(padsize, padstr=' ') #:nodoc:
+          if padsize != 0
+            chars(padstr * ((padsize / Unicode.u_unpack(padstr).size) + 1)).slice(0, padsize)
+          else
+            ''
+          end
+        end
+
+        def chars(string) #:nodoc:
+          self.class.new(string)
+        end
+    end
+  end
+end

data/lib/bioinform/support/third_part/active_support/multibyte/exceptions.rb

@@ -0,0 +1,8 @@
+# encoding: utf-8
+
+module ActiveSupport #:nodoc:
+  module Multibyte #:nodoc:
+    # Raised when a problem with the encoding was found.
+    class EncodingError < StandardError; end
+  end
+end