bioinform 0.1.17 → 0.2.0

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

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

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

@@ -1,393 +0,0 @@
-# encoding: utf-8
-module ActiveSupport
-  module Multibyte
-    module Unicode
-
-      extend self
-
-      # A list of all available normalization forms. See http://www.unicode.org/reports/tr15/tr15-29.html for more
-      # information about normalization.
-      NORMALIZATION_FORMS = [:c, :kc, :d, :kd]
-
-      # The Unicode version that is supported by the implementation
-      UNICODE_VERSION = '5.2.0'
-
-      # The default normalization used for operations that require normalization. It can be set to any of the
-      # normalizations in NORMALIZATION_FORMS.
-      #
-      # Example:
-      #   ActiveSupport::Multibyte::Unicode.default_normalization_form = :c
-      attr_accessor :default_normalization_form
-      @default_normalization_form = :kc
-
-      # Hangul character boundaries and properties
-      HANGUL_SBASE = 0xAC00
-      HANGUL_LBASE = 0x1100
-      HANGUL_VBASE = 0x1161
-      HANGUL_TBASE = 0x11A7
-      HANGUL_LCOUNT = 19
-      HANGUL_VCOUNT = 21
-      HANGUL_TCOUNT = 28
-      HANGUL_NCOUNT = HANGUL_VCOUNT * HANGUL_TCOUNT
-      HANGUL_SCOUNT = 11172
-      HANGUL_SLAST = HANGUL_SBASE + HANGUL_SCOUNT
-      HANGUL_JAMO_FIRST = 0x1100
-      HANGUL_JAMO_LAST = 0x11FF
-
-      # All the unicode whitespace
-      WHITESPACE = [
-        (0x0009..0x000D).to_a, # White_Space # Cc   [5] <control-0009>..<control-000D>
-        0x0020,                # White_Space # Zs       SPACE
-        0x0085,                # White_Space # Cc       <control-0085>
-        0x00A0,                # White_Space # Zs       NO-BREAK SPACE
-        0x1680,                # White_Space # Zs       OGHAM SPACE MARK
-        0x180E,                # White_Space # Zs       MONGOLIAN VOWEL SEPARATOR
-        (0x2000..0x200A).to_a, # White_Space # Zs  [11] EN QUAD..HAIR SPACE
-        0x2028,                # White_Space # Zl       LINE SEPARATOR
-        0x2029,                # White_Space # Zp       PARAGRAPH SEPARATOR
-        0x202F,                # White_Space # Zs       NARROW NO-BREAK SPACE
-        0x205F,                # White_Space # Zs       MEDIUM MATHEMATICAL SPACE
-        0x3000,                # White_Space # Zs       IDEOGRAPHIC SPACE
-      ].flatten.freeze
-
-      # BOM (byte order mark) can also be seen as whitespace, it's a non-rendering character used to distinguish
-      # between little and big endian. This is not an issue in utf-8, so it must be ignored.
-      LEADERS_AND_TRAILERS = WHITESPACE + [65279] # ZERO-WIDTH NO-BREAK SPACE aka BOM
-
-      # Returns a regular expression pattern that matches the passed Unicode codepoints
-      def self.codepoints_to_pattern(array_of_codepoints) #:nodoc:
-        array_of_codepoints.collect{ |e| [e].pack 'U*' }.join('|')
-      end
-      TRAILERS_PAT = /(#{codepoints_to_pattern(LEADERS_AND_TRAILERS)})+\Z/u
-      LEADERS_PAT = /\A(#{codepoints_to_pattern(LEADERS_AND_TRAILERS)})+/u
-
-      # Unpack the string at codepoints boundaries. Raises an EncodingError when the encoding of the string isn't
-      # valid UTF-8.
-      #
-      # Example:
-      #   Unicode.u_unpack('Café') # => [67, 97, 102, 233]
-      def u_unpack(string)
-        begin
-          string.unpack 'U*'
-        rescue ArgumentError
-          raise EncodingError, 'malformed UTF-8 character'
-        end
-      end
-
-      # Detect whether the codepoint is in a certain character class. Returns +true+ when it's in the specified
-      # character class and +false+ otherwise. Valid character classes are: <tt>:cr</tt>, <tt>:lf</tt>, <tt>:l</tt>,
-      # <tt>:v</tt>, <tt>:lv</tt>, <tt>:lvt</tt> and <tt>:t</tt>.
-      #
-      # Primarily used by the grapheme cluster support.
-      def in_char_class?(codepoint, classes)
-        classes.detect { |c| database.boundary[c] === codepoint } ? true : false
-      end
-
-      # Unpack the string at grapheme boundaries. Returns a list of character lists.
-      #
-      # Example:
-      #   Unicode.g_unpack('क्षि') # => [[2325, 2381], [2359], [2367]]
-      #   Unicode.g_unpack('Café') # => [[67], [97], [102], [233]]
-      def g_unpack(string)
-        codepoints = u_unpack(string)
-        unpacked = []
-        pos = 0
-        marker = 0
-        eoc = codepoints.length
-        while(pos < eoc)
-          pos += 1
-          previous = codepoints[pos-1]
-          current = codepoints[pos]
-          if (
-              # CR X LF
-              ( previous == database.boundary[:cr] and current == database.boundary[:lf] ) or
-              # L X (L|V|LV|LVT)
-              ( database.boundary[:l] === previous and in_char_class?(current, [:l,:v,:lv,:lvt]) ) or
-              # (LV|V) X (V|T)
-              ( in_char_class?(previous, [:lv,:v]) and in_char_class?(current, [:v,:t]) ) or
-              # (LVT|T) X (T)
-              ( in_char_class?(previous, [:lvt,:t]) and database.boundary[:t] === current ) or
-              # X Extend
-              (database.boundary[:extend] === current)
-            )
-          else
-            unpacked << codepoints[marker..pos-1]
-            marker = pos
-          end
-        end
-        unpacked
-      end
-
-      # Reverse operation of g_unpack.
-      #
-      # Example:
-      #   Unicode.g_pack(Unicode.g_unpack('क्षि')) # => 'क्षि'
-      def g_pack(unpacked)
-        (unpacked.flatten).pack('U*')
-      end
-
-      # Re-order codepoints so the string becomes canonical.
-      def reorder_characters(codepoints)
-        length = codepoints.length- 1
-        pos = 0
-        while pos < length do
-          cp1, cp2 = database.codepoints[codepoints[pos]], database.codepoints[codepoints[pos+1]]
-          if (cp1.combining_class > cp2.combining_class) && (cp2.combining_class > 0)
-            codepoints[pos..pos+1] = cp2.code, cp1.code
-            pos += (pos > 0 ? -1 : 1)
-          else
-            pos += 1
-          end
-        end
-        codepoints
-      end
-
-      # Decompose composed characters to the decomposed form.
-      def decompose_codepoints(type, codepoints)
-        codepoints.inject([]) do |decomposed, cp|
-          # if it's a hangul syllable starter character
-          if HANGUL_SBASE <= cp and cp < HANGUL_SLAST
-            sindex = cp - HANGUL_SBASE
-            ncp = [] # new codepoints
-            ncp << HANGUL_LBASE + sindex / HANGUL_NCOUNT
-            ncp << HANGUL_VBASE + (sindex % HANGUL_NCOUNT) / HANGUL_TCOUNT
-            tindex = sindex % HANGUL_TCOUNT
-            ncp << (HANGUL_TBASE + tindex) unless tindex == 0
-            decomposed.concat ncp
-          # if the codepoint is decomposable in with the current decomposition type
-          elsif (ncp = database.codepoints[cp].decomp_mapping) and (!database.codepoints[cp].decomp_type || type == :compatability)
-            decomposed.concat decompose_codepoints(type, ncp.dup)
-          else
-            decomposed << cp
-          end
-        end
-      end
-
-      # Compose decomposed characters to the composed form.
-      def compose_codepoints(codepoints)
-        pos = 0
-        eoa = codepoints.length - 1
-        starter_pos = 0
-        starter_char = codepoints[0]
-        previous_combining_class = -1
-        while pos < eoa
-          pos += 1
-          lindex = starter_char - HANGUL_LBASE
-          # -- Hangul
-          if 0 <= lindex and lindex < HANGUL_LCOUNT
-            vindex = codepoints[starter_pos+1] - HANGUL_VBASE rescue vindex = -1
-            if 0 <= vindex and vindex < HANGUL_VCOUNT
-              tindex = codepoints[starter_pos+2] - HANGUL_TBASE rescue tindex = -1
-              if 0 <= tindex and tindex < HANGUL_TCOUNT
-                j = starter_pos + 2
-                eoa -= 2
-              else
-                tindex = 0
-                j = starter_pos + 1
-                eoa -= 1
-              end
-              codepoints[starter_pos..j] = (lindex * HANGUL_VCOUNT + vindex) * HANGUL_TCOUNT + tindex + HANGUL_SBASE
-            end
-            starter_pos += 1
-            starter_char = codepoints[starter_pos]
-          # -- Other characters
-          else
-            current_char = codepoints[pos]
-            current = database.codepoints[current_char]
-            if current.combining_class > previous_combining_class
-              if ref = database.composition_map[starter_char]
-                composition = ref[current_char]
-              else
-                composition = nil
-              end
-              unless composition.nil?
-                codepoints[starter_pos] = composition
-                starter_char = composition
-                codepoints.delete_at pos
-                eoa -= 1
-                pos -= 1
-                previous_combining_class = -1
-              else
-                previous_combining_class = current.combining_class
-              end
-            else
-              previous_combining_class = current.combining_class
-            end
-            if current.combining_class == 0
-              starter_pos = pos
-              starter_char = codepoints[pos]
-            end
-          end
-        end
-        codepoints
-      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(string, force = false)
-        if force
-          return string.unpack("C*").map do |b|
-            tidy_byte(b)
-          end.flatten.compact.pack("C*").unpack("U*").pack("U*")
-        end
-
-        bytes = string.unpack("C*")
-        conts_expected = 0
-        last_lead = 0
-
-        bytes.each_index do |i|
-
-          byte          = bytes[i]
-          is_cont       = byte > 127 && byte < 192
-          is_lead       = byte > 191 && byte < 245
-          is_unused     = byte > 240
-          is_restricted = byte > 244
-
-          # Impossible or highly unlikely byte? Clean it.
-          if is_unused || is_restricted
-            bytes[i] = tidy_byte(byte)
-          elsif is_cont
-            # Not expecting continuation byte? Clean up. Otherwise, now expect one less.
-            conts_expected == 0 ? bytes[i] = tidy_byte(byte) : conts_expected -= 1
-          else
-            if conts_expected > 0
-              # Expected continuation, but got ASCII or leading? Clean backwards up to
-              # the leading byte.
-              (1..(i - last_lead)).each {|j| bytes[i - j] = tidy_byte(bytes[i - j])}
-              conts_expected = 0
-            end
-            if is_lead
-              # Final byte is leading? Clean it.
-              if i == bytes.length - 1
-                bytes[i] = tidy_byte(bytes.last)
-              else
-                # Valid leading byte? Expect continuations determined by position of
-                # first zero bit, with max of 3.
-                conts_expected = byte < 224 ? 1 : byte < 240 ? 2 : 3
-                last_lead = i
-              end
-            end
-          end
-        end
-        bytes.empty? ? "" : bytes.flatten.compact.pack("C*").unpack("U*").pack("U*")
-      end
-
-      # Returns the KC normalization of the string by default. NFKC is considered the best normalization form for
-      # passing strings to databases and validations.
-      #
-      # * <tt>string</tt> - The string to perform normalization on.
-      # * <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.default_normalization_form
-      def normalize(string, form=nil)
-        form ||= @default_normalization_form
-        # See http://www.unicode.org/reports/tr15, Table 1
-        codepoints = u_unpack(string)
-        case form
-          when :d
-            reorder_characters(decompose_codepoints(:canonical, codepoints))
-          when :c
-            compose_codepoints(reorder_characters(decompose_codepoints(:canonical, codepoints)))
-          when :kd
-            reorder_characters(decompose_codepoints(:compatability, codepoints))
-          when :kc
-            compose_codepoints(reorder_characters(decompose_codepoints(:compatability, codepoints)))
-          else
-            raise ArgumentError, "#{form} is not a valid normalization variant", caller
-        end.pack('U*')
-      end
-
-      def apply_mapping(string, mapping) #:nodoc:
-        u_unpack(string).map do |codepoint|
-          cp = database.codepoints[codepoint]
-          if cp and (ncp = cp.send(mapping)) and ncp > 0
-            ncp
-          else
-            codepoint
-          end
-        end.pack('U*')
-      end
-
-      # Holds data about a codepoint in the Unicode database
-      class Codepoint
-        attr_accessor :code, :combining_class, :decomp_type, :decomp_mapping, :uppercase_mapping, :lowercase_mapping
-      end
-
-      # Holds static data from the Unicode database
-      class UnicodeDatabase
-        ATTRIBUTES = :codepoints, :composition_exclusion, :composition_map, :boundary, :cp1252
-
-        attr_writer(*ATTRIBUTES)
-
-        def initialize
-          @codepoints = Hash.new(Codepoint.new)
-          @composition_exclusion = []
-          @composition_map = {}
-          @boundary = {}
-          @cp1252 = {}
-        end
-
-        # Lazy load the Unicode database so it's only loaded when it's actually used
-        ATTRIBUTES.each do |attr_name|
-          class_eval(<<-EOS, __FILE__, __LINE__ + 1)
-            def #{attr_name}     # def codepoints
-              load               #   load
-              @#{attr_name}      #   @codepoints
-            end                  # end
-          EOS
-        end
-
-        # Loads the Unicode database and returns all the internal objects of UnicodeDatabase.
-        def load
-          begin
-            @codepoints, @composition_exclusion, @composition_map, @boundary, @cp1252 = File.open(self.class.filename, 'rb') { |f| Marshal.load f.read }
-          rescue Exception => e
-              raise IOError.new("Couldn't load the Unicode tables for UTF8Handler (#{e.message}), ActiveSupport::Multibyte is unusable")
-          end
-
-          # Redefine the === method so we can write shorter rules for grapheme cluster breaks
-          @boundary.each do |k,_|
-            @boundary[k].instance_eval do
-              def ===(other)
-                detect { |i| i === other } ? true : false
-              end
-            end if @boundary[k].kind_of?(Array)
-          end
-
-          # define attr_reader methods for the instance variables
-          class << self
-            attr_reader(*ATTRIBUTES)
-          end
-        end
-
-        # Returns the directory in which the data files are stored
-        def self.dirname
-          File.dirname(__FILE__) + '/../values/'
-        end
-
-        # Returns the filename for the data file for this version
-        def self.filename
-          File.expand_path File.join(dirname, "unicode_tables.dat")
-        end
-      end
-
-      private
-
-      def tidy_byte(byte)
-        if byte < 160
-          [database.cp1252[byte] || byte].pack("U").unpack("C*")
-        elsif byte < 192
-          [194, byte]
-        else
-          [195, byte - 64]
-        end
-      end
-
-      def database
-        @database ||= UnicodeDatabase.new
-      end
-
-    end
-  end
-end

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

@@ -1,60 +0,0 @@
-# encoding: utf-8
-
-module ActiveSupport #:nodoc:
-  module Multibyte #:nodoc:
-    if Kernel.const_defined?(:Encoding)
-      # Returns a regular expression that matches valid characters in the current encoding
-      def self.valid_character
-        VALID_CHARACTER[Encoding.default_external.to_s]
-      end
-    else
-      def self.valid_character
-        case $KCODE
-        when 'UTF8'
-          VALID_CHARACTER['UTF-8']
-        when 'SJIS'
-          VALID_CHARACTER['Shift_JIS']
-        end
-      end
-    end
-
-    if 'string'.respond_to?(:valid_encoding?)
-      # Verifies the encoding of a string
-      def self.verify(string)
-        string.valid_encoding?
-      end
-    else
-      def self.verify(string)
-        if expression = valid_character
-          # Splits the string on character boundaries, which are determined based on $KCODE.
-          string.split(//).all? { |c| expression =~ c }
-        else
-          true
-        end
-      end
-    end
-
-    # Verifies the encoding of the string and raises an exception when it's not valid
-    def self.verify!(string)
-      raise EncodingError.new("Found characters with invalid encoding") unless verify(string)
-    end
-
-    if 'string'.respond_to?(:force_encoding)
-      # Removes all invalid characters from the string.
-      #
-      # Note: this method is a no-op in Ruby 1.9
-      def self.clean(string)
-        string
-      end
-    else
-      def self.clean(string)
-        if expression = valid_character
-          # Splits the string on character boundaries, which are determined based on $KCODE.
-          string.split(//).grep(expression).join
-        else
-          string
-        end
-      end
-    end
-  end
-end