From 2c9dd1b59c45c91c9d28b9ad295bac42ca04d06b Mon Sep 17 00:00:00 2001 From: martinahansen Date: Sat, 19 Mar 2011 20:40:01 +0000 Subject: [PATCH] added rdoc stuff git-svn-id: http://biopieces.googlecode.com/svn/trunk@1302 74ccb610-7750-0410-82ae-013aeee3265d --- code_ruby/Maasha/lib/doc/Base36.html | 316 +++ code_ruby/Maasha/lib/doc/Base36Error.html | 200 ++ code_ruby/Maasha/lib/doc/Biopieces.html | 562 +++++ code_ruby/Maasha/lib/doc/BitArray.html | 869 ++++++++ code_ruby/Maasha/lib/doc/BitArrayError.html | 201 ++ code_ruby/Maasha/lib/doc/Boulder.html | 361 ++++ code_ruby/Maasha/lib/doc/BoulderError.html | 201 ++ code_ruby/Maasha/lib/doc/CastError.html | 200 ++ code_ruby/Maasha/lib/doc/Casts.html | 823 ++++++++ code_ruby/Maasha/lib/doc/Digest.html | 416 ++++ code_ruby/Maasha/lib/doc/DigestError.html | 200 ++ code_ruby/Maasha/lib/doc/Fasta.html | 308 +++ code_ruby/Maasha/lib/doc/FastaError.html | 200 ++ code_ruby/Maasha/lib/doc/Fastq.html | 306 +++ code_ruby/Maasha/lib/doc/FastqError.html | 200 ++ code_ruby/Maasha/lib/doc/Filesys.html | 452 ++++ code_ruby/Maasha/lib/doc/FilesysError.html | 201 ++ code_ruby/Maasha/lib/doc/Genbank.html | 521 +++++ code_ruby/Maasha/lib/doc/GenbankError.html | 201 ++ code_ruby/Maasha/lib/doc/GenbankFeatures.html | 473 +++++ code_ruby/Maasha/lib/doc/Locator.html | 586 ++++++ code_ruby/Maasha/lib/doc/LocatorError.html | 201 ++ code_ruby/Maasha/lib/doc/OptionHandler.html | 1028 ++++++++++ code_ruby/Maasha/lib/doc/Read.html | 646 ++++++ code_ruby/Maasha/lib/doc/SFF.html | 712 +++++++ code_ruby/Maasha/lib/doc/SFFError.html | 200 ++ code_ruby/Maasha/lib/doc/Seq.html | 1825 +++++++++++++++++ code_ruby/Maasha/lib/doc/SeqError.html | 200 ++ code_ruby/Maasha/lib/doc/Status.html | 524 +++++ code_ruby/Maasha/lib/doc/Stream.html | 557 +++++ code_ruby/Maasha/lib/doc/String.html | 408 ++++ code_ruby/Maasha/lib/doc/StringError.html | 200 ++ code_ruby/Maasha/lib/doc/base36_rb.html | 55 + 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code_ruby/Maasha/lib/doc/sff_rb.html | 57 + 69 files changed, 15967 insertions(+) create mode 100644 code_ruby/Maasha/lib/doc/Base36.html create mode 100644 code_ruby/Maasha/lib/doc/Base36Error.html create mode 100644 code_ruby/Maasha/lib/doc/Biopieces.html create mode 100644 code_ruby/Maasha/lib/doc/BitArray.html create mode 100644 code_ruby/Maasha/lib/doc/BitArrayError.html create mode 100644 code_ruby/Maasha/lib/doc/Boulder.html create mode 100644 code_ruby/Maasha/lib/doc/BoulderError.html create mode 100644 code_ruby/Maasha/lib/doc/CastError.html create mode 100644 code_ruby/Maasha/lib/doc/Casts.html create mode 100644 code_ruby/Maasha/lib/doc/Digest.html create mode 100644 code_ruby/Maasha/lib/doc/DigestError.html create mode 100644 code_ruby/Maasha/lib/doc/Fasta.html create mode 100644 code_ruby/Maasha/lib/doc/FastaError.html create mode 100644 code_ruby/Maasha/lib/doc/Fastq.html create mode 100644 code_ruby/Maasha/lib/doc/FastqError.html create mode 100644 code_ruby/Maasha/lib/doc/Filesys.html create mode 100644 code_ruby/Maasha/lib/doc/FilesysError.html create mode 100644 code_ruby/Maasha/lib/doc/Genbank.html create mode 100644 code_ruby/Maasha/lib/doc/GenbankError.html create mode 100644 code_ruby/Maasha/lib/doc/GenbankFeatures.html create mode 100644 code_ruby/Maasha/lib/doc/Locator.html create mode 100644 code_ruby/Maasha/lib/doc/LocatorError.html create mode 100644 code_ruby/Maasha/lib/doc/OptionHandler.html create mode 100644 code_ruby/Maasha/lib/doc/Read.html create mode 100644 code_ruby/Maasha/lib/doc/SFF.html create mode 100644 code_ruby/Maasha/lib/doc/SFFError.html create mode 100644 code_ruby/Maasha/lib/doc/Seq.html create mode 100644 code_ruby/Maasha/lib/doc/SeqError.html create mode 100644 code_ruby/Maasha/lib/doc/Status.html create mode 100644 code_ruby/Maasha/lib/doc/Stream.html create mode 100644 code_ruby/Maasha/lib/doc/String.html create mode 100644 code_ruby/Maasha/lib/doc/StringError.html create mode 100644 code_ruby/Maasha/lib/doc/base36_rb.html create mode 100644 code_ruby/Maasha/lib/doc/biopieces_rb.html create mode 100644 code_ruby/Maasha/lib/doc/bitarray_rb.html create mode 100644 code_ruby/Maasha/lib/doc/bits_rb.html create mode 100644 code_ruby/Maasha/lib/doc/boulder_rb.html create mode 100644 code_ruby/Maasha/lib/doc/digest_rb.html create mode 100644 code_ruby/Maasha/lib/doc/fasta_rb.html create mode 100644 code_ruby/Maasha/lib/doc/fastq_rb.html create mode 100644 code_ruby/Maasha/lib/doc/filesys_rb.html create mode 100644 code_ruby/Maasha/lib/doc/genbank_rb.html create mode 100644 code_ruby/Maasha/lib/doc/images/brick.png create mode 100644 code_ruby/Maasha/lib/doc/images/brick_link.png create mode 100644 code_ruby/Maasha/lib/doc/images/bug.png create mode 100644 code_ruby/Maasha/lib/doc/images/bullet_black.png create mode 100644 code_ruby/Maasha/lib/doc/images/bullet_toggle_minus.png create mode 100644 code_ruby/Maasha/lib/doc/images/bullet_toggle_plus.png create mode 100644 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code_ruby/Maasha/lib/doc/js/jquery.js create mode 100644 code_ruby/Maasha/lib/doc/js/quicksearch.js create mode 100644 code_ruby/Maasha/lib/doc/js/thickbox-compressed.js create mode 100644 code_ruby/Maasha/lib/doc/rdoc.css create mode 100644 code_ruby/Maasha/lib/doc/seq_rb.html create mode 100644 code_ruby/Maasha/lib/doc/sff_rb.html diff --git a/code_ruby/Maasha/lib/doc/Base36.html b/code_ruby/Maasha/lib/doc/Base36.html new file mode 100644 index 0000000..c1078ec --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Base36.html @@ -0,0 +1,316 @@ + + + + + + + Class: Base36 + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

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+ +
+ + + + + + + +
+

Methods

+ +
+ + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Base36

+ +
+

+Class containing methods to encode and decode Base 36. Note that the ALPH +is [alph + num] and not [num + alph] which prevents us from simply using +.to_i(36) and .to_s(36). +

+

+en.wikipedia.org/wiki/Base_36 +

+ +
+ + + + + + + + + +
+

Public Class Methods

+ + +
+ + +
+ + decode(base36) + click to toggle source + +
+ +
+ +

+Method that decodes a base36 string and returns an integer. +

+ + + +
+
+    # File base36.rb, line 55
+55:   def self.decode(base36)
+56:     raise Base36Error if base36.empty?
+57: 
+58:     result = 0
+59:     pos    = 0
+60: 
+61:     base36.upcase.reverse.each_char do |char|
+62:       result += ALPH.index(char) * (BASE36 ** pos)
+63:       pos    += 1
+64:     end
+65: 
+66:     return result;
+67:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + encode(num) + click to toggle source + +
+ +
+ +

+Method that encodes an integer into a base36 string that is returned. +

+ + + +
+
+    # File base36.rb, line 39
+39:   def self.encode(num)
+40:     raise Base36Error unless num.is_a? Fixnum
+41: 
+42:     base36 = ""
+43: 
+44:     while num > 0
+45:       base36 << ALPH[(num % BASE36)]
+46:       num /= BASE36
+47:     end
+48: 
+49:     base36 << ALPH[0] if num == 0
+50: 
+51:     base36.reverse
+52:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Base36Error.html b/code_ruby/Maasha/lib/doc/Base36Error.html new file mode 100644 index 0000000..2e2be76 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Base36Error.html @@ -0,0 +1,200 @@ + + + + + + + Class: Base36Error + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

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+
+ +
+
+ + +
+ +
+ + + +
+

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+ +

StandardError

+ +
+ + + + + + + + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Base36Error

+ +
+

+Error class for all exceptions to do with Base36. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Biopieces.html b/code_ruby/Maasha/lib/doc/Biopieces.html new file mode 100644 index 0000000..3cacc08 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Biopieces.html @@ -0,0 +1,562 @@ + + + + + + + Class: Biopieces + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

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+
+ +
+
+ + +
+ +
+ + + +
+

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+ +

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+ +
+ + + + + + + +
+

Methods

+ +
+ + + + +
+

Included Modules

+
    + + +
  • Enumerable
    • + + +
+
+ +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Biopieces

+ +
+

+Biopieces are command line scripts and uses +OptionParser to parse command line options according to a list of casts. +Each cast prescribes the long and short name of the option, the type, if it +is mandatory, the default value, and allowed and disallowed values. An +optional list of extra casts can be supplied, and the integrity of the +casts are checked. Following the command line parsing, the options are +checked according to the casts. Methods are also included for handling the +parsing and emitting of Biopiece records, which are ASCII text records +consisting of lines with a key/value pair separated by a colon and a white +space ’: ’. Each record is separated by a line with three +dashes ’—’. +

+ +
+ + + + + + +
+

Attributes

+ + +
+ + + + +
+ out[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+

Public Class Methods

+ + +
+ + +
+ + new(test=nil, input=STDIN, output=STDOUT) + click to toggle source + +
+ +
+ +

+Initialize a Biopiece and write the status to file. Options are for testing +purposes only. +

+ + + +
+
+    # File biopieces.rb, line 49
+49:   def initialize(test=nil, input=STDIN, output=STDOUT)
+50:     @test   = test
+51:     @input  = input
+52:     @output = output
+53:   end
+
+ +
+ + + + +
+ + +
+ +
+

Public Instance Methods

+ + +
+ + +
+ + each() + click to toggle source + +
+ +
+ + + + + +
+ + + + +
+ Alias for: each_record +
+ +
+ + +
+ + +
+ + each_record() + click to toggle source + +
+ +
+ +

+Open Biopiece input stream if not open and iterate over all Biopiece +records in the stream. +

+ + + +
+
+    # File biopieces.rb, line 66
+66:   def each_record
+67:     @in = Stream::open(@options, mode="r", @input) unless @in.is_a? IO
+68:     return if @in.nil?
+69: 
+70:     record = {}
+71: 
+72:     @in.each_line do |line|
+73:       case line
+74:       when /^([^:]+): (.*)$/
+75:         record[$1.to_sym] = $2
+76:       when /^---$/
+77:         yield record unless record.empty?
+78:         record = {}
+79:       else
+80:         raise "Bad record format: #{line}"
+81:       end
+82:     end
+83: 
+84:     yield record unless record.empty?
+85: 
+86:     self # conventionally
+87:   end
+
+ +
+ + +
+ Also aliased as: each +
+ + + +
+ + +
+ + +
+ + mktmpdir() + click to toggle source + +
+ +
+ +

+Create a temporary directory inside the ENV[“BP_TMP“] dir. +

+ + + +
+
+     # File biopieces.rb, line 106
+106:   def mktmpdir
+107:     time = Time.now.to_i
+108:     user = ENV["USER"]
+109:     pid  = $$
+110:     path = ENV["BP_TMP"] + "/" + [user, time + pid, pid, "bp_tmp"].join("_")
+111:     Dir.mkdir(path)
+112:     Status.new.set_tmpdir(path)
+113:     path
+114:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + parse(argv, cast_list=[], script_path=$0) + click to toggle source + +
+ +
+ +

+Check the integrity of a list of casts, followed by parsion options from +argv and finally checking the options according to the casts. Returns nil +if argv is empty, otherwise an options hash. +

+ + + +
+
+    # File biopieces.rb, line 58
+58:   def parse(argv, cast_list=[], script_path=$0)
+59:     casts          = Casts.new(cast_list)
+60:     option_handler = OptionHandler.new(argv, casts, script_path, @test)
+61:     @options       = option_handler.options_parse
+62:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + puts(record) + click to toggle source + +
+ +
+ +

+Open Biopiece output stream if not open and puts record to the stream. +

+ + + +
+
+     # File biopieces.rb, line 92
+ 92:   def puts(record)
+ 93:     @out = Stream::open(@options, mode="w", @output) unless @out.is_a? IO
+ 94: 
+ 95:     record.each do |key,value|
+ 96:       @out.print "#{key.to_s}: #{value}\n"
+ 97:     end
+ 98: 
+ 99:     @out.print "---\n"
+100:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + to_s() + click to toggle source + +
+ +
+ + + + + +
+
+     # File biopieces.rb, line 102
+102:   def to_s
+103:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/BitArray.html b/code_ruby/Maasha/lib/doc/BitArray.html new file mode 100644 index 0000000..44a12d4 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/BitArray.html @@ -0,0 +1,869 @@ + + + + + + + Class: BitArray + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

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+ +
+ + + + + + + +
+

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+ +
+ + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

BitArray

+ +
+

+Class containing methods for creating and manipulating a bit array. +

+ +
+ + + + + + +
+

Attributes

+ + +
+ + +
+ size[R] +
+ +
+ + + +
+
+ +
+ + +
+ byte_array[R] +
+ +
+ + + +
+
+ +
+ + + + +
+

Public Class Methods

+ + +
+ + +
+ + new(size) + click to toggle source + +
+ +
+ +

+Method to initialize a new bit array of a given size. +

+ + + +
+
+    # File bitarray.rb, line 35
+35:   def initialize(size)
+36:     @size        = size
+37:     @byte_array  = init_byte_array
+38:     @count_array = init_count_array
+39:   end
+
+ +
+ + + + +
+ + +
+ +
+

Public Instance Methods

+ + +
+ + +
+ + &(ba) + click to toggle source + +
+ +
+ +

+Method to run bitwise AND (&) on two bit arrays and return the result +in a new bit array. Bits are copied if they exists in BOTH operands. +00111100 & 00001101 = 00001100 +

+ + + +
+
+    # File bitarray.rb, line 76
+76:   def &(ba)
+77:     raise BitArrayError, "uneven size of bit arrays: #{self.size} != #{ba.size}" if self.size != ba.size
+78: 
+79:     result = BitArray.new(ba.size)
+80: 
+81:     (0 ... ba.byte_array.size).each do |byte|
+82:       result.byte_array[byte] = (self.byte_array[byte].ord & ba.byte_array[byte].ord).chr
+83:     end
+84: 
+85:     result
+86:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + ^(ba) + click to toggle source + +
+ +
+ +

+Method to run bitwise XOR (^) on two bit arrays and return the result in a +new bit array. Bits are copied if they exists in ONE BUT NOT BOTH operands. +00111100 ^ 00001101 = 00110001 +

+ + + +
+
+     # File bitarray.rb, line 106
+106:   def ^(ba)
+107:     raise BitArrayError, "uneven size of bit arrays: #{self.size} != #{ba.size}" if self.size != ba.size
+108: 
+109:     result = BitArray.new(ba.size)
+110: 
+111:     (0 ... ba.byte_array.size).each do |byte|
+112:       result.byte_array[byte] = (self.byte_array[byte].ord ^ ba.byte_array[byte].ord).chr
+113:     end
+114: 
+115:     result
+116:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + bit_set(pos) + click to toggle source + +
+ +
+ +

+Method to set a bit to 1 at a given position in the bit array. +

+ + + +
+
+    # File bitarray.rb, line 42
+42:   def bit_set(pos)
+43:     raise BitArrayError, "Position #{pos} must be an integer."              unless pos.is_a? Fixnum
+44:     raise BitArrayError, "Position #{pos} outside of range: 0 ... #{@size}" unless (0 ... @size ).include? pos
+45: 
+46:     @byte_array[byte_pos(pos)] = (@byte_array[byte_pos(pos)].ord | bit_pos(pos)).chr
+47:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + bit_set?(pos) + click to toggle source + +
+ +
+ +

+Method to check if a bit at a given position in the bit array is set. +

+ + + +
+
+    # File bitarray.rb, line 50
+50:   def bit_set?(pos)
+51:     raise BitArrayError, "Position #{pos} must be an integer."              unless pos.is_a? Fixnum
+52:     raise BitArrayError, "Position #{pos} outside of range: 0 ... #{@size}" unless (0 ... @size ).include? pos
+53: 
+54:     (@byte_array[byte_pos(pos)].ord & bit_pos(pos)) != 0
+55:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + bits_off() + click to toggle source + +
+ +
+ +

+Method that returns the number of bits set “off” in a bit +array. +

+ + + +
+
+    # File bitarray.rb, line 69
+69:   def bits_off
+70:     @size - bits_on
+71:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + bits_on() + click to toggle source + +
+ +
+ +

+Method that returns the number of bits set “on” in a bit array. +

+ + + +
+
+    # File bitarray.rb, line 58
+58:   def bits_on 
+59:     bits_on = 0
+60: 
+61:     (0 ... self.byte_array.size).each do |byte|
+62:       bits_on += @count_array[self.byte_array[byte].ord]
+63:     end
+64: 
+65:     bits_on
+66:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + to_s() + click to toggle source + +
+ +
+ +

+Method to convert a bit array to a string. +

+ + + +
+
+     # File bitarray.rb, line 119
+119:   def to_s
+120:     string = ""
+121: 
+122:     (0 ... @size).each do |pos|
+123:       if self.bit_set? pos 
+124:         string << "1"
+125:       else
+126:         string << "0"
+127:       end
+128:     end
+129: 
+130:     string
+131:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + |(ba) + click to toggle source + +
+ +
+ +

+Method to run bitwise OR (|) on two bit arrays and return the result in a +new bit array. Bits are copied if they exists in EITHER operands. 00111100 +| 00001101 = 00111101 +

+ + + +
+
+     # File bitarray.rb, line 91
+ 91:   def |(ba)
+ 92:     raise BitArrayError, "uneven size of bit arrays: #{self.size} != #{ba.size}" if self.size != ba.size
+ 93: 
+ 94:     result = BitArray.new(ba.size)
+ 95: 
+ 96:     (0 ... ba.byte_array.size).each do |byte|
+ 97:       result.byte_array[byte] = (self.byte_array[byte].ord | ba.byte_array[byte].ord).chr
+ 98:     end
+ 99: 
+100:     result
+101:   end
+
+ +
+ + + + +
+ + +
+ +
+

Private Instance Methods

+ + +
+ + +
+ + bit_pos(pos) + click to toggle source + +
+ +
+ +

+Method that returns the bit position in a byte. +

+ + + +
+
+     # File bitarray.rb, line 177
+177:   def bit_pos(pos)
+178:     1 << (BitsInChar - 1 - (pos % BitsInChar))
+179:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + bits_in_char(char) + click to toggle source + +
+ +
+ +

+Method that returns the number of set bits in a char. +

+ + + +
+
+     # File bitarray.rb, line 161
+161:   def bits_in_char(char)
+162:     bits = 0
+163: 
+164:     (0 ... BitsInChar).each do |pos|
+165:       bits += 1 if ((char & bit_pos(pos)) != 0)
+166:     end
+167: 
+168:     bits
+169:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + byte_pos(pos) + click to toggle source + +
+ +
+ +

+Method that returns the byte position in the byte array for a given bit +position. +

+ + + +
+
+     # File bitarray.rb, line 172
+172:   def byte_pos(pos)
+173:     pos / BitsInChar
+174:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + init_byte_array() + click to toggle source + +
+ +
+ +

+Method to initialize the byte array (string) that constitutes the bit +array. +

+ + + +
+
+     # File bitarray.rb, line 138
+138:   def init_byte_array
+139:     raise BitArrayError, "Size must be an integer, not #{@size}" unless @size.is_a? Fixnum
+140:     raise BitArrayError, "Size must be positive, not #{@size}"   unless @size > 0
+141: 
+142:     byte_array = ""
+143:     byte_array << 0.chr * (((@size - 1) / BitsInChar) + 1)
+144: 
+145:     byte_array
+146:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + init_count_array() + click to toggle source + +
+ +
+ +

+Method that returns an array where the element index value is the number of +bits set for that index value. +

+ + + +
+
+     # File bitarray.rb, line 150
+150:   def init_count_array
+151:     count_array = []
+152: 
+153:     (0 ... (2 ** BitsInChar)).each do |i|
+154:       count_array << bits_in_char(i)
+155:     end
+156: 
+157:     count_array
+158:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/BitArrayError.html b/code_ruby/Maasha/lib/doc/BitArrayError.html new file mode 100644 index 0000000..6b352ae --- /dev/null +++ b/code_ruby/Maasha/lib/doc/BitArrayError.html @@ -0,0 +1,201 @@ + + + + + + + Class: BitArrayError + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
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+
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+ +
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+

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+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

BitArrayError

+ +
+

+Error class for all exceptions to do with BitArray. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Boulder.html b/code_ruby/Maasha/lib/doc/Boulder.html new file mode 100644 index 0000000..b1af1ca --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Boulder.html @@ -0,0 +1,361 @@ + + + + + + + Class: Boulder + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
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+
+ +
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+ +
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+

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+ +
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+ +
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+

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+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Boulder

+ +
+

+Class to manipulate boulder records - Lincoln Steins own YAML like format: +stein.cshl.org/boulder/docs/Boulder.html +

+ +
+ + + + + + + + + +
+

Public Class Methods

+ + +
+ + +
+ + new(input=STDIN, output=STDOUT) + click to toggle source + +
+ +
+ +

+Initialize a Boulder object. Options are for +testing purposes only. +

+ + + +
+
+    # File boulder.rb, line 39
+39:   def initialize(input=STDIN, output=STDOUT)
+40:     @input  = input
+41:     @output = output
+42:   end
+
+ +
+ + + + +
+ + +
+ +
+

Public Instance Methods

+ + +
+ + +
+ + each() + click to toggle source + +
+ +
+ + + + + +
+
+    # File boulder.rb, line 44
+44:   def each
+45:     while not @input.eof? do
+46:       block = @input.gets(SEP)
+47:       raise BoulderError, "Missing record seperator" unless block =~ /#{SEP}$/
+48: 
+49:       record = {}
+50: 
+51:       block.chomp(SEP).each_line do |line|
+52:         key, val = line.chomp.split('=', 2)
+53: 
+54:         raise BoulderError, "Missing key/value seperator" if val.nil?
+55:         raise BoulderError, "Missing key"                 if key.empty?
+56:         raise BoulderError, "Missing value"               if val.empty?
+57: 
+58:         record[key.to_sym] = val
+59:       end
+60: 
+61:       yield record
+62:     end
+63:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + to_boulder(record) + click to toggle source + +
+ +
+ +

+Method that converts and returns a hash record as a Boulder string. +

+ + + +
+
+    # File boulder.rb, line 67
+67:   def to_boulder(record)
+68:     str = ""
+69: 
+70:     record.each_pair do |key, val|
+71:       str << "#{key}=#{val}\n"
+72:     end
+73: 
+74:     str << "=\n"
+75: 
+76:     str
+77:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/BoulderError.html b/code_ruby/Maasha/lib/doc/BoulderError.html new file mode 100644 index 0000000..ded84e1 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/BoulderError.html @@ -0,0 +1,201 @@ + + + + + + + Class: BoulderError + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

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+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

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+ +
+ + + + + + + + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

BoulderError

+ +
+

+Error class for all exceptions to do with Boulder. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/CastError.html b/code_ruby/Maasha/lib/doc/CastError.html new file mode 100644 index 0000000..3689d7c --- /dev/null +++ b/code_ruby/Maasha/lib/doc/CastError.html @@ -0,0 +1,200 @@ + + + + + + + Class: CastError + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

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+
+ +
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+ + +
+ +
+ + + +
+

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+ +

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+ +
+ + + + + + + + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

CastError

+ +
+

+Error class for all exceptions to do with option casts. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Casts.html b/code_ruby/Maasha/lib/doc/Casts.html new file mode 100644 index 0000000..8892aa8 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Casts.html @@ -0,0 +1,823 @@ + + + + + + + Class: Casts + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

Array

+ +
+ + + + + + + + + + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Casts

+ +
+

+Class to handle casts of command line options. Each cast prescribes the +long and short name of the option, the type, if it is mandatory, the +default value, and allowed and disallowed values. An optional list of extra +casts can be supplied, and the integrity of the casts are checked. +

+ +
+ + + +
+

Constants

+
+ +
TYPES
+ +
+ + +
MANDATORY
+ +
+ + +
+
+ + + + + + + +
+

Public Class Methods

+ + +
+ + +
+ + new(cast_list=[]) + click to toggle source + +
+ +
+ +

+Initialize cast object with an optional options cast list to which +ubiquitous casts are added after which all casts are checked. +

+ + + +
+
+     # File biopieces.rb, line 132
+132:   def initialize(cast_list=[])
+133:     @cast_list = cast_list
+134:     ubiquitous
+135:     check
+136:     long_to_sym
+137:     self.push *@cast_list
+138:   end
+
+ +
+ + + + +
+ + +
+ +
+

Private Instance Methods

+ + +
+ + +
+ + check() + click to toggle source + +
+ +
+ +

+Check integrity of the casts. +

+ + + +
+
+     # File biopieces.rb, line 151
+151:   def check
+152:     check_keys
+153:     check_values
+154:     check_duplicates
+155:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + check_duplicates() + click to toggle source + +
+ +
+ +

+Check cast for duplicate long or short options names. +

+ + + +
+
+     # File biopieces.rb, line 237
+237:   def check_duplicates
+238:     check_hash = {}
+239:     @cast_list.each do |cast|
+240:       raise CastError, "Duplicate argument: '--#{cast[:long]}'" if check_hash.has_key? cast[:long]
+241:       raise CastError, "Duplicate argument: '-#{cast[:short]}'" if check_hash.has_key? cast[:short]
+242:       check_hash[cast[:long]]  = true
+243:       check_hash[cast[:short]] = true
+244:     end
+245:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + check_keys() + click to toggle source + +
+ +
+ +

+Check if all mandatory keys are present in casts and raise if not. +

+ + + +
+
+     # File biopieces.rb, line 158
+158:   def check_keys
+159:     @cast_list.each do |cast|
+160:       MANDATORY.each do |mandatory|
+161:         raise CastError, "Missing symbol in cast: '#{mandatory.to_sym}'" unless cast.has_key? mandatory.to_sym
+162:       end
+163:     end
+164:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + check_val_allowed(cast) + click to toggle source + +
+ +
+ +

+Check if values to allowed are legal and raise if not. +

+ + + +
+
+     # File biopieces.rb, line 223
+223:   def check_val_allowed(cast)
+224:     unless cast[:allowed].is_a? String or cast[:allowed].nil?
+225:       raise CastError, "Illegal cast of allowed: '#{cast[:allowed]}'"
+226:     end
+227:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + check_val_default(cast) + click to toggle source + +
+ +
+ +

+Check if values to default are legal and raise if not. +

+ + + +
+
+     # File biopieces.rb, line 213
+213:   def check_val_default(cast)
+214:     unless cast[:default].nil?          or
+215:            cast[:default].is_a? String  or
+216:            cast[:default].is_a? Integer or
+217:            cast[:default].is_a? Float
+218:       raise CastError, "Illegal cast of default: '#{cast[:default]}'"
+219:     end
+220:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + check_val_disallowed(cast) + click to toggle source + +
+ +
+ +

+Check if values to disallowed are legal and raise if not. +

+ + + +
+
+     # File biopieces.rb, line 230
+230:   def check_val_disallowed(cast)
+231:     unless cast[:disallowed].is_a? String or cast[:disallowed].nil?
+232:       raise CastError, "Illegal cast of disallowed: '#{cast[:disallowed]}'"
+233:     end
+234:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + check_val_long(cast) + click to toggle source + +
+ +
+ +

+Check if the values to long are legal and raise if not. +

+ + + +
+
+     # File biopieces.rb, line 180
+180:   def check_val_long(cast)
+181:     unless cast[:long].is_a? String and cast[:long].length > 1
+182:       raise CastError, "Illegal cast of long: '#{cast[:long]}'"
+183:     end
+184:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + check_val_mandatory(cast) + click to toggle source + +
+ +
+ +

+Check if values to mandatory are legal and raise if not. +

+ + + +
+
+     # File biopieces.rb, line 206
+206:   def check_val_mandatory(cast)
+207:     unless cast[:mandatory] == true or cast[:mandatory] == false
+208:       raise CastError, "Illegal cast of mandatory: '#{cast[:mandatory]}'"
+209:     end
+210:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + check_val_short(cast) + click to toggle source + +
+ +
+ +

+Check if the values to short are legal and raise if not. +

+ + + +
+
+     # File biopieces.rb, line 187
+187:   def check_val_short(cast)
+188:     unless cast[:short].is_a? String and cast[:short].length == 1
+189:       raise CastError, "Illegal cast of short: '#{cast[:short]}'"
+190:     end
+191:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + check_val_type(cast) + click to toggle source + +
+ +
+ +

+Check if values to type are legal and raise if not. +

+ + + +
+
+     # File biopieces.rb, line 194
+194:   def check_val_type(cast)
+195:     type_hash = {}
+196:     TYPES.each do |type|
+197:       type_hash[type] = true
+198:     end
+199: 
+200:     unless type_hash.has_key? cast[:type]
+201:       raise CastError, "Illegal cast of type: '#{cast[:type]}'"
+202:     end
+203:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + check_values() + click to toggle source + +
+ +
+ +

+Check if all values in casts are valid. +

+ + + +
+
+     # File biopieces.rb, line 167
+167:   def check_values
+168:     @cast_list.each do |cast|
+169:       check_val_long(cast)
+170:       check_val_short(cast)
+171:       check_val_type(cast)
+172:       check_val_mandatory(cast)
+173:       check_val_default(cast)
+174:       check_val_allowed(cast)
+175:       check_val_disallowed(cast)
+176:     end
+177:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + long_to_sym() + click to toggle source + +
+ +
+ +

+Convert values to :long keys to symbols for all casts. +

+ + + +
+
+     # File biopieces.rb, line 248
+248:   def long_to_sym
+249:     @cast_list.each do |cast|
+250:       cast[:long] = cast[:long].to_sym
+251:     end
+252:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + ubiquitous() + click to toggle source + +
+ +
+ +

+Add ubiquitous options casts. +

+ + + +
+
+     # File biopieces.rb, line 143
+143:   def ubiquitous
+144:     @cast_list << {:long=>'help',       :short=>'?', :type=>'flag',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+145:     @cast_list << {:long=>'stream_in',  :short=>'I', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+146:     @cast_list << {:long=>'stream_out', :short=>'O', :type=>'file',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+147:     @cast_list << {:long=>'verbose',    :short=>'v', :type=>'flag',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+148:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Digest.html b/code_ruby/Maasha/lib/doc/Digest.html new file mode 100644 index 0000000..b25354f --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Digest.html @@ -0,0 +1,416 @@ + + + + + + + Class: Digest + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

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+
+ +
+
+ + +
+ +
+ + + +
+

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+ +

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+ +
+ + + + + + + +
+

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+ +
+ + + + +
+

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+
    + + +
  • Enumerable
    • + + +
+
+ +
+ +
+ + + +
+

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+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Digest

+ +
+ +
+ + + + + + + + + +
+

Public Class Methods

+ + +
+ + +
+ + new(seq, pattern, cut_pos) + click to toggle source + +
+ +
+ +

+Initialize a digest object with the following arguments: +

+
    +

  • +seq: A sequence object. +

    +
    • +

  • +pattern: A restriction enzyme recognition pattern. +

    +
    • +

  • +cut_pos: Offset from match position where the enzyme cuts. +

    +
    • +
+ + + +
+
+    # File digest.rb, line 37
+37:   def initialize(seq, pattern, cut_pos)
+38:     @seq     = seq
+39:     @pattern = disambiguate(pattern)
+40:     @cut_pos = cut_pos
+41:     @offset  = 0
+42:   end
+
+ +
+ + + + +
+ + +
+ +
+

Public Instance Methods

+ + +
+ + +
+ + each() + click to toggle source + +
+ +
+ +

+Method to get the next digestion product from a sequence. +

+ + + +
+
+    # File digest.rb, line 45
+45:   def each
+46:     @seq.seq.upcase.scan @pattern do
+47:       pos = $`.length + @cut_pos - 1
+48:      
+49:       if pos >= 0 and pos < @seq.length - 2
+50:         seq = Seq.new("#{@seq.seq_name}[#{@offset}-#{pos}]", @seq.seq[@offset .. pos], @seq.type)
+51: 
+52:         yield seq
+53:       end
+54: 
+55:       @offset = pos + 1
+56:     end
+57: 
+58:     if @offset < 0
+59:       @offset = 0
+60:     elsif @offset > @seq.length
+61:       @offset = 0
+62:     end
+63: 
+64:     seq = Seq.new("#{@seq.seq_name}[#{@offset}-#{@seq.length - 1}]", @seq.seq[@offset .. @seq.length], @seq.type)
+65: 
+66:     yield seq
+67: 
+68:     self # conventionally
+69:   end
+
+ +
+ + + + +
+ + +
+ +
+

Private Instance Methods

+ + +
+ + +
+ + disambiguate(pattern) + click to toggle source + +
+ +
+ +

+Method that returns a regexp object with a restriction enzyme pattern with +ambiguity codes substituted to the appropriate regexp. +

+ + + +
+
+     # File digest.rb, line 76
+ 76:   def disambiguate(pattern)
+ 77:     ambiguity = {
+ 78:       'A' => "A",
+ 79:       'T' => "T",
+ 80:       'U' => "T",
+ 81:       'C' => "C",
+ 82:       'G' => "G",
+ 83:       'M' => "[AC]",
+ 84:       'R' => "[AG]",
+ 85:       'W' => "[AT]",
+ 86:       'S' => "[CG]",
+ 87:       'Y' => "[CT]",
+ 88:       'K' => "[GT]",
+ 89:       'V' => "[ACG]",
+ 90:       'H' => "[ACT]",
+ 91:       'D' => "[AGT]",
+ 92:       'B' => "[CGT]",
+ 93:       'N' => "[GATC]"
+ 94:     }
+ 95: 
+ 96:     new_pattern = ""
+ 97: 
+ 98:     pattern.upcase.each_char do |char|
+ 99:       if ambiguity.has_key? char
+100:         new_pattern << ambiguity[char]
+101:       else
+102:         raise DigestError, "Could not disambiguate residue: #{char}"
+103:       end
+104:     end
+105: 
+106:     Regexp.new(new_pattern)
+107:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/DigestError.html b/code_ruby/Maasha/lib/doc/DigestError.html new file mode 100644 index 0000000..6176583 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/DigestError.html @@ -0,0 +1,200 @@ + + + + + + + Class: DigestError + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

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+ +
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+

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+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

DigestError

+ +
+

+Error class for all exceptions to do with Digest. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Fasta.html b/code_ruby/Maasha/lib/doc/Fasta.html new file mode 100644 index 0000000..65ce1bb --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Fasta.html @@ -0,0 +1,308 @@ + + + + + + + Class: Fasta + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

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+
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+ + +
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+

Fasta

+ +
+ +
+ + + + + + + + + +
+

Public Instance Methods

+ + +
+ + +
+ + get_entry() + click to toggle source + +
+ +
+ +

+Method to get the next FASTA entry form an ios and return this as a Seq object. If no entry is found or eof then nil is +returned. +

+ + + +
+
+    # File fasta.rb, line 34
+34:   def get_entry
+35:     block = @io.gets($/ + '>')
+36:     return nil if block.nil?
+37: 
+38:     block.chomp!($/ + '>')
+39: 
+40:     (seq_name, seq) = block.split($/, 2)
+41: 
+42:     raise FastaError, "Bad FASTA format" if seq_name.nil? or seq.nil?
+43: 
+44:     entry          = Seq.new
+45:     entry.type     = @type.nil? ? nil : @type.downcase
+46:     entry.seq      = seq.gsub(/\s/, '')
+47:     entry.seq_name = seq_name.sub(/^>/, '').rstrip
+48: 
+49:     raise FastaError, "Bad FASTA format" if entry.seq_name.empty?
+50:     raise FastaError, "Bad FASTA format" if entry.seq.empty?
+51: 
+52:     entry
+53:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + puts(record) + click to toggle source + +
+ +
+ +

+TODO - this should be some custom to_s method instead. +

+ + + +
+
+    # File fasta.rb, line 56
+56:   def puts(record)
+57:     if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+58:       @io.print ">#{record[:SEQ_NAME]}\n"
+59:       @io.print "#{record[:SEQ]}\n"
+60:     end
+61:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/FastaError.html b/code_ruby/Maasha/lib/doc/FastaError.html new file mode 100644 index 0000000..a5ec5a1 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/FastaError.html @@ -0,0 +1,200 @@ + + + + + + + Class: FastaError + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

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+ +
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+

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+ +
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+

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+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

FastaError

+ +
+

+Error class for all exceptions to do with FASTA. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Fastq.html b/code_ruby/Maasha/lib/doc/Fastq.html new file mode 100644 index 0000000..5152dcf --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Fastq.html @@ -0,0 +1,306 @@ + + + + + + + Class: Fastq + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

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+

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+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Fastq

+ +
+ +
+ + + + + + + + + +
+

Public Instance Methods

+ + +
+ + +
+ + get_entry() + click to toggle source + +
+ +
+ +

+Method to get the next FASTQ entry form an ios and return this as a Seq object. If no entry is found or eof then nil is +returned. +

+ + + +
+
+    # File fastq.rb, line 34
+34:   def get_entry
+35:     begin
+36:       seq_name       = @io.gets.chomp!
+37:       seq            = @io.gets.chomp!
+38:       qual_name      = @io.gets.chomp!
+39:       qual           = @io.gets.chomp!
+40: 
+41:       entry          = Seq.new
+42:       entry.type     = @type.nil? ? nil : @type.downcase
+43:       entry.seq      = seq
+44:       entry.seq_name = seq_name[1 .. seq_name.length]
+45:       entry.qual     = qual
+46: 
+47:       entry
+48:     rescue
+49:       nil
+50:     end
+51:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + puts(record) + click to toggle source + +
+ +
+ +

+TODO - this should be some custom to_s method instead. +

+ + + +
+
+    # File fastq.rb, line 54
+54:   def puts(record)
+55:     if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+56:       @io.print ">#{record[:SEQ_NAME]}\n"
+57:       @io.print "#{record[:SEQ]}\n"
+58:     end
+59:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/FastqError.html b/code_ruby/Maasha/lib/doc/FastqError.html new file mode 100644 index 0000000..0ec36b4 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/FastqError.html @@ -0,0 +1,200 @@ + + + + + + + Class: FastqError + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

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+ +
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+

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+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

FastqError

+ +
+

+Error class for all exceptions to do with FASTQ. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Filesys.html b/code_ruby/Maasha/lib/doc/Filesys.html new file mode 100644 index 0000000..4c874ae --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Filesys.html @@ -0,0 +1,452 @@ + + + + + + + Class: Filesys + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
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+
+

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+
+ +
+
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+

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+ +

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+ +
+ + + + + + + +
+

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+ +
+ + + + +
+

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+
    + + +
  • Enumerable
    • + + +
+
+ +
+ +
+ + + +
+

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+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Filesys

+ +
+ +
+ + + + + + + + + +
+

Public Class Methods

+ + +
+ + +
+ + new(io, type=nil) + click to toggle source + +
+ +
+ + + + + +
+
+    # File filesys.rb, line 58
+58:   def initialize(io, type=nil)
+59:     @io   = io
+60:     @type = type
+61:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + open(*args) + click to toggle source + +
+ +
+ +

+Class method allowing open to be used on (zipped) files. See File.open. +

+ + + +
+
+    # File filesys.rb, line 35
+35:   def self.open(*args)
+36:     args = *args
+37:     file = args.first
+38: 
+39:     if file == "-"
+40:       ios = self.new(STDIN)
+41:     elsif File.pipe? file
+42:       ios = self.new(File.open(*args))
+43:     else
+44:       ios = self.zopen(*args)
+45:     end
+46: 
+47:     if block_given?
+48:       begin
+49:         yield ios
+50:       ensure
+51:         ios.close
+52:       end
+53:     else
+54:       return ios
+55:     end
+56:   end
+
+ +
+ + + + +
+ + +
+ +
+

Private Class Methods

+ + +
+ + +
+ + zopen(*args) + click to toggle source + +
+ +
+ +

+Helper method to return an ios to a file that may be zipped in which case +the ios is unzipped on the fly. See File.open. +

+ + + +
+
+    # File filesys.rb, line 79
+79:   def self.zopen(*args)
+80:     ios = File.open(*args)
+81: 
+82:     begin
+83:       ios = Zlib::GzipReader.new(ios)
+84:     rescue
+85:       ios.rewind
+86:     end
+87: 
+88:     self.new(ios)
+89:   end
+
+ +
+ + + + +
+ + +
+ +
+

Public Instance Methods

+ + +
+ + +
+ + close() + click to toggle source + +
+ +
+ +

+Method to close ios. +

+ + + +
+
+    # File filesys.rb, line 64
+64:   def close
+65:     @io.close
+66:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + each() + click to toggle source + +
+ +
+ +

+Iterator method for parsing entries. +

+ + + +
+
+    # File filesys.rb, line 69
+69:   def each
+70:     while entry = get_entry do
+71:       yield entry
+72:     end
+73:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/FilesysError.html b/code_ruby/Maasha/lib/doc/FilesysError.html new file mode 100644 index 0000000..3a6624d --- /dev/null +++ b/code_ruby/Maasha/lib/doc/FilesysError.html @@ -0,0 +1,201 @@ + + + + + + + Class: FilesysError + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
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+
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+

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+

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+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

FilesysError

+ +
+

+Error class for all exceptions to do with Filesys. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Genbank.html b/code_ruby/Maasha/lib/doc/Genbank.html new file mode 100644 index 0000000..ed25065 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Genbank.html @@ -0,0 +1,521 @@ + + + + + + + Class: Genbank + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
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+
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+

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+ +

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+ +
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+ +
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+ +
+ + + +
+

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+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Genbank

+ +
+ +
+ + + + + + + + + +
+

Public Class Methods

+ + +
+ + +
+ + new(io) + click to toggle source + +
+ +
+ + + + + +
+
+    # File genbank.rb, line 32
+32:   def initialize(io)
+33:     @io      = io
+34:     @entry   = []
+35:   end
+
+ +
+ + + + +
+ + +
+ +
+

Public Instance Methods

+ + +
+ + +
+ + each(hash_keys, hash_feats, hash_quals) + click to toggle source + +
+ +
+ +

+Iterator method for parsing Genbank entries. +

+ + + +
+
+    # File genbank.rb, line 38
+38:   def each(hash_keys, hash_feats, hash_quals)
+39:     while @entry = get_entry do
+40:       keys = get_keys(hash_keys)
+41:       seq  = get_seq
+42: 
+43:       features = GenbankFeatures.new(@entry, hash_feats, hash_quals)
+44: 
+45:       features.each do |record|
+46:         keys.each_pair { |key,val| record[key] = val }
+47: 
+48:                                 loc = Locator.new(record[:LOCATOR], seq)
+49:                                 record[:SEQ]     = loc.subseq.seq
+50:         record[:SEQ_LEN] = loc.subseq.length
+51:                                 record[:STRAND]  = loc.strand
+52:                                 record[:S_BEG]   = loc.s_beg
+53:                                 record[:S_END]   = loc.s_end
+54: 
+55:         yield record
+56:       end
+57:     end
+58:   end
+
+ +
+ + + + +
+ + +
+ +
+

Private Instance Methods

+ + +
+ + +
+ + get_entry() + click to toggle source + +
+ +
+ +

+Method to get the next Genbank entry form an ios +and return this. +

+ + + +
+
+    # File genbank.rb, line 63
+63:   def get_entry
+64:     block = @io.gets("//" + $/)
+65:     return nil if block.nil?
+66: 
+67:     block.chomp!("//" + $/ )
+68: 
+69:     entry = block.split $/
+70: 
+71:     return nil if entry.empty?
+72: 
+73:     entry
+74:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + get_keys(hash_keys) + click to toggle source + +
+ +
+ +

+Method to get the base keys from Genbank entry +and return these in a hash. +

+ + + +
+
+     # File genbank.rb, line 93
+ 93:   def get_keys(hash_keys)
+ 94:     keys = {}
+ 95:     i    = 0
+ 96:     j    = 0
+ 97: 
+ 98:     while @entry[i] and @entry[i] !~ /^FEATURES/
+ 99:       if @entry[i] =~ /^\s{0,3}([A-Z]{2})/
+100:         if want_key?(hash_keys, $1)
+101:           j = i + 1
+102: 
+103:           key, val = @entry[i].lstrip.split(/\s+/, 2)
+104: 
+105:           while @entry[j] and @entry[j] !~ /^\s{0,3}[A-Z]/
+106:             val << @entry[j].lstrip
+107:             j += 1
+108:           end
+109: 
+110:           if keys[key.to_sym]
+111:             keys[key.to_sym] << ";" + val
+112:           else
+113:             keys[key.to_sym] = val
+114:           end
+115:         end
+116:       end
+117: 
+118:       j > i ? i = j : i += 1
+119:     end
+120: 
+121:     keys
+122:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + get_seq() + click to toggle source + +
+ +
+ +

+Method to get the DNA sequence from a Genbank +entry and return this as a Seq object. +

+ + + +
+
+    # File genbank.rb, line 78
+78:   def get_seq
+79:     i = @entry.size
+80:     j = i - 1
+81: 
+82:     while @entry[j] and @entry[j] !~ /^[A-Z]/
+83:       j -= 1
+84:     end
+85: 
+86:     seq = @entry[j + 1 .. i].join.delete(" 0123456789")
+87: 
+88:     Seq.new(nil, seq, "dna") if seq
+89:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + want_key?(hash_keys, key) + click to toggle source + +
+ +
+ + + + + +
+
+     # File genbank.rb, line 124
+124:   def want_key?(hash_keys, key)
+125:     if hash_keys
+126:       if hash_keys[key.to_sym]
+127:         return true
+128:       else
+129:         return false
+130:       end
+131:     else
+132:       return true
+133:     end
+134:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/GenbankError.html b/code_ruby/Maasha/lib/doc/GenbankError.html new file mode 100644 index 0000000..5c0f160 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/GenbankError.html @@ -0,0 +1,201 @@ + + + + + + + Class: GenbankError + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

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+
+ +
+
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+ +
+ + + +
+

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+ +

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+ +
+ + + + + + + + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

GenbankError

+ +
+

+Error class for all exceptions to do with Genbank. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/GenbankFeatures.html b/code_ruby/Maasha/lib/doc/GenbankFeatures.html new file mode 100644 index 0000000..ac47161 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/GenbankFeatures.html @@ -0,0 +1,473 @@ + + + + + + + Class: GenbankFeatures + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

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+
+ +
+
+ + +
+ +
+ + + +
+

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+ +

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+ +
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+

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+ +
+ + + + +
+ +
+ + + +
+

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+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

GenbankFeatures

+ +
+ +
+ + + + + + + + + +
+

Public Class Methods

+ + +
+ + +
+ + new(entry, hash_feats, hash_quals) + click to toggle source + +
+ +
+ + + + + +
+
+     # File genbank.rb, line 141
+141:   def initialize(entry, hash_feats, hash_quals)
+142:     @entry      = entry
+143:     @hash_feats = hash_feats
+144:     @hash_quals = hash_quals
+145:   end
+
+ +
+ + + + +
+ + +
+ +
+

Public Instance Methods

+ + +
+ + +
+ + each() + click to toggle source + +
+ +
+ + + + + +
+
+     # File genbank.rb, line 147
+147:   def each
+148:     while @entry[@@i] and @entry[@@i] !~ /^ORIGIN/
+149:       if @entry[@@i] =~ /^\s{5}([A-Za-z_-]+)/
+150:         if want_feat? $1
+151:           record = {}
+152: 
+153:           feat, loc = @entry[@@i].lstrip.split(/\s+/, 2)
+154: 
+155:           @@j = @@i + 1
+156: 
+157:           while @entry[@@j] and @entry[@@j] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
+158:             loc << @entry[@@j].lstrip
+159:             @@j += 1
+160:           end
+161: 
+162:           get_quals.each_pair { |k,v|
+163:             record[k.upcase.to_sym] = v
+164:           }
+165: 
+166:           record[:FEATURE] = feat
+167:           record[:LOCATOR] = loc
+168: 
+169:           yield record
+170:         end
+171:       end
+172: 
+173:       @@j > @@i ? @@i = @@j : @@i += 1
+174:     end
+175:   end
+
+ +
+ + + + +
+ + +
+ +
+

Private Instance Methods

+ + +
+ + +
+ + get_quals() + click to toggle source + +
+ +
+ + + + + +
+
+     # File genbank.rb, line 179
+179:   def get_quals
+180:     quals = {}
+181:     k     = 0
+182: 
+183:     while @entry[@@j] and @entry[@@j] !~ /^\s{5}[A-Za-z_-]|^[A-Z]/
+184:       if @entry[@@j] =~ /^\s{21}\/([^=]+)="([^"]+)/
+185:         qual = $1
+186:         val  = $2
+187: 
+188:         if want_qual? qual
+189:           k = @@j + 1
+190: 
+191:           while @entry[k] and @entry[k] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
+192:             val << @entry[k].lstrip.chomp('"')
+193:             k += 1
+194:           end
+195: 
+196:           if quals[qual]
+197:             quals[qual] << ";" + val
+198:           else
+199:             quals[qual] = val
+200:           end
+201:         end
+202:       end
+203: 
+204:       k > @@j ? @@j = k : @@j += 1
+205:     end
+206: 
+207:     quals
+208:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + want_feat?(feat) + click to toggle source + +
+ +
+ + + + + +
+
+     # File genbank.rb, line 210
+210:   def want_feat?(feat)
+211:     if @hash_feats
+212:       if @hash_feats[feat.upcase.to_sym]
+213:         return true
+214:       else
+215:         return false
+216:       end
+217:     else
+218:       return true
+219:     end
+220:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + want_qual?(qual) + click to toggle source + +
+ +
+ + + + + +
+
+     # File genbank.rb, line 222
+222:   def want_qual?(qual)
+223:     if @hash_quals
+224:       if @hash_quals[qual.upcase.to_sym]
+225:         return true
+226:       else
+227:         return false
+228:       end
+229:     else
+230:       return true
+231:     end
+232:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Locator.html b/code_ruby/Maasha/lib/doc/Locator.html new file mode 100644 index 0000000..95dadba --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Locator.html @@ -0,0 +1,586 @@ + + + + + + + Class: Locator + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

Object

+ +
+ + + + + + + +
+

Methods

+ +
+ + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Locator

+ +
+ +
+ + + + + + +
+

Attributes

+ + +
+ + + + +
+ locator[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ seq[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ subseq[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+

Public Class Methods

+ + +
+ + +
+ + new(locator, seq) + click to toggle source + +
+ +
+ + + + + +
+
+     # File genbank.rb, line 242
+242:   def initialize(locator, seq)
+243:     @locator = locator
+244:     @seq     = seq
+245:     @subseq  = Seq.new(nil, "", "dna")
+246:     parse_locator(locator)
+247:   end
+
+ +
+ + + + +
+ + +
+ +
+

Public Instance Methods

+ + +
+ + +
+ + s_beg() + click to toggle source + +
+ +
+ + + + + +
+
+     # File genbank.rb, line 257
+257:   def s_beg
+258:     if @locator =~ /(\d+)/
+259:       return $1.to_i - 1
+260:     end
+261:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + s_end() + click to toggle source + +
+ +
+ + + + + +
+
+     # File genbank.rb, line 263
+263:   def s_end
+264:     if @locator.reverse =~ /(\d+)/
+265:       return $1.reverse.to_i - 1
+266:     end
+267:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + strand() + click to toggle source + +
+ +
+ + + + + +
+
+     # File genbank.rb, line 249
+249:   def strand
+250:     if @locator.match("complement")
+251:       return "-"
+252:     else
+253:       return "+"
+254:     end
+255:   end
+
+ +
+ + + + +
+ + +
+ +
+

Private Instance Methods

+ + +
+ + +
+ + balance_parens?(locator) + click to toggle source + +
+ +
+ + + + + +
+
+     # File genbank.rb, line 342
+342:   def balance_parens?(locator)
+343:     parens = 0
+344: 
+345:     locator.each_char do |char|
+346:       case char
+347:       when '(' then parens += 1
+348:       when ')' then parens -= 1
+349:       end
+350:     end
+351: 
+352:     if parens == 0
+353:       return true
+354:     else
+355:       return false
+356:     end
+357:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + parse_locator(locator, join = nil, comp = nil, order = nil) + click to toggle source + +
+ +
+ +

+Method that uses recursion to parse a locator string from a feature table +and fetches the appropriate subsequence. the operators join(), +complement(), and order() are handled. the locator string is broken into a +comma separated lists, and modified if the parens donnot balance. otherwise +the comma separated list of ranges are stripped from operators, and the +subsequence are fetched and handled according to the operators. SNP +locators are also dealt with (single positions). +

+ + + +
+
+     # File genbank.rb, line 279
+279:   def parse_locator(locator, join = nil, comp = nil, order = nil)
+280:     intervals = locator.split(",")
+281: 
+282:     unless balance_parens?(intervals.first)   # locator includes a join/comp/order of several ranges
+283:       case locator
+284:       when /^join\((.*)\)$/
+285:         locator = $1
+286:         join     = true
+287:       when /^complement\((.*)\)$/
+288:         locator = $1
+289:         comp     = true
+290:       when /^order\((.*)\)$/
+291:         locator = $1
+292:         order    = true
+293:       end
+294: 
+295:       parse_locator(locator, join, comp, order)
+296:     else
+297:       intervals.each do |interval|
+298:         case interval
+299:         when /^join\((.*)\)$/
+300:           locator = $1
+301:           join    = true
+302:           parse_locator(locator, join, comp, order)
+303:         when /^complement\((.*)\)$/
+304:           locator = $1
+305:           comp    = true
+306:           parse_locator(locator, join, comp, order)
+307:         when /^order\((.*)\)$/
+308:           locator = $1
+309:           order   = true
+310:           parse_locator(locator, join, comp, order)
+311:         when /^[<>]?(\d+)[^\d]+(\d+)$/
+312:           int_beg = $1.to_i - 1
+313:           int_end = $2.to_i - 1
+314: 
+315:           newseq = Seq.new(nil, @seq.seq[int_beg...int_end], "dna")
+316: 
+317:                                         unless newseq.seq.nil?
+318:                                                 newseq.revcomp if comp
+319: 
+320:                                                 @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
+321:                                         end
+322:         when /^(\d+)$/
+323:           pos = $1.to_i - 1
+324: 
+325:           newseq = Seq.new(nil, @seq.seq[pos], "dna")
+326: 
+327:                                         unless newseq.seq.nil?
+328:                 newseq.revcomp if comp 
+329: 
+330:                 @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
+331:                                         end
+332:         else
+333:           $stderr.puts "WARNING: Could not match locator -> #{locator}";
+334:           @subseq.seq << ""
+335:         end
+336:       end
+337:     end
+338: 
+339:     return @subseq
+340:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/LocatorError.html b/code_ruby/Maasha/lib/doc/LocatorError.html new file mode 100644 index 0000000..6cf4391 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/LocatorError.html @@ -0,0 +1,201 @@ + + + + + + + Class: LocatorError + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

StandardError

+ +
+ + + + + + + + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

LocatorError

+ +
+

+Error class for all exceptions to do with Genbank/EMBL/DDBJ feature table +locators. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/OptionHandler.html b/code_ruby/Maasha/lib/doc/OptionHandler.html new file mode 100644 index 0000000..d9bc163 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/OptionHandler.html @@ -0,0 +1,1028 @@ + + + + + + + Class: OptionHandler + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ + + +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

OptionHandler

+ +
+

+Class for parsing argv using OptionParser according to given casts. Default +options are set, file glob expressions expanded, and options are checked +according to the casts. Usage information is printed and exit called if +required. +

+ +
+ + + +
+

Constants

+
+ +
REGEX_LIST
+ +
+ + +
REGEX_INT
+ +
+ + +
REGEX_STRING
+ +
+ + +
+
+ + + + + + + +
+

Public Class Methods

+ + +
+ + +
+ + new(argv, casts, script_path, test=nil) + click to toggle source + +
+ +
+ + + + + +
+
+     # File biopieces.rb, line 266
+266:   def initialize(argv, casts, script_path, test=nil)
+267:     @argv        = argv
+268:     @casts       = casts
+269:     @script_path = script_path
+270:     @test        = test
+271:   end
+
+ +
+ + + + +
+ + +
+ +
+

Public Instance Methods

+ + +
+ + +
+ + options_check() + click to toggle source + +
+ +
+ +

+Check all options according to casts. +

+ + + +
+
+     # File biopieces.rb, line 407
+407:   def options_check
+408:     @casts.each do |cast|
+409:       options_check_mandatory(cast)
+410:       options_check_int(cast)
+411:       options_check_uint(cast)
+412:       options_check_file(cast)
+413:       options_check_files(cast)
+414:       options_check_dir(cast)
+415:       options_check_allowed(cast)
+416:       options_check_disallowed(cast)
+417:     end
+418:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + options_check_allowed(cast) + click to toggle source + +
+ +
+ +

+Check options and raise unless allowed. +

+ + + +
+
+     # File biopieces.rb, line 470
+470:   def options_check_allowed(cast)
+471:     if cast[:allowed] and @options.has_key? cast[:long]
+472:       allowed_hash = {}
+473:       cast[:allowed].split(',').each { |a| allowed_hash[a.to_s] = 1 }
+474:   
+475:       raise ArgumentError, "Argument '#{@options[cast[:long]]}' to --#{cast[:long]} not allowed" unless allowed_hash.has_key? @options[cast[:long]].to_s
+476:     end
+477:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + options_check_dir(cast) + click to toggle source + +
+ +
+ +

+Check dir! type argument and raise if directory don’t exist. +

+ + + +
+
+     # File biopieces.rb, line 463
+463:   def options_check_dir(cast)
+464:     if cast[:type] == 'dir!' and @options.has_key? cast[:long]
+465:       raise ArgumentError, "No such directory: '#{@options[cast[:long]]}'" unless File.directory? @options[cast[:long]]
+466:     end
+467:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + options_check_disallowed(cast) + click to toggle source + +
+ +
+ +

+Check disallowed argument values and raise if disallowed. +

+ + + +
+
+     # File biopieces.rb, line 480
+480:   def options_check_disallowed(cast)
+481:     if cast[:disallowed] and @options.has_key? cast[:long]
+482:       cast[:disallowed].split(',').each do |val|
+483:         raise ArgumentError, "Argument '#{@options[cast[:long]]}' to --#{cast[:long]} is disallowed" if val.to_s == @options[cast[:long]].to_s
+484:       end
+485:     end
+486:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + options_check_file(cast) + click to toggle source + +
+ +
+ +

+Check file! type argument and raise if file don’t exists. +

+ + + +
+
+     # File biopieces.rb, line 446
+446:   def options_check_file(cast)
+447:     if cast[:type] == 'file!' and @options.has_key? cast[:long]
+448:       raise ArgumentError, "No such file: '#{@options[cast[:long]]}'" unless File.file? @options[cast[:long]]
+449:     end
+450:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + options_check_files(cast) + click to toggle source + +
+ +
+ +

+Check files! type argument and raise if files don’t exists. +

+ + + +
+
+     # File biopieces.rb, line 453
+453:   def options_check_files(cast)
+454:     if cast[:type] == 'files!' and @options.has_key? cast[:long]
+455:       @options[cast[:long]].each do |path|
+456:         next if path == "-"
+457:         raise ArgumentError, "File not readable: '#{path}'" unless File.readable? path
+458:       end
+459:     end
+460:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + options_check_int(cast) + click to toggle source + +
+ +
+ +

+Check int type option and raise if not an integer. +

+ + + +
+
+     # File biopieces.rb, line 428
+428:   def options_check_int(cast)
+429:     if cast[:type] == 'int' and @options.has_key? cast[:long]
+430:       unless @options[cast[:long]].is_a? Integer
+431:         raise ArgumentError, "Argument to --#{cast[:long]} must be an integer, not '#{@options[cast[:long]]}'"
+432:       end
+433:     end
+434:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + options_check_mandatory(cast) + click to toggle source + +
+ +
+ +

+Check if a mandatory option is set and raise if it isn’t. +

+ + + +
+
+     # File biopieces.rb, line 421
+421:   def options_check_mandatory(cast)
+422:     if cast[:mandatory]
+423:       raise ArgumentError, "Mandatory argument: --#{cast[:long]}" unless @options.has_key? cast[:long]
+424:     end
+425:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + options_check_uint(cast) + click to toggle source + +
+ +
+ +

+Check uint type option and raise if not an unsinged integer. +

+ + + +
+
+     # File biopieces.rb, line 437
+437:   def options_check_uint(cast)
+438:     if cast[:type] == 'uint' and @options.has_key? cast[:long]
+439:       unless @options[cast[:long]].is_a? Integer and @options[cast[:long]] >= 0
+440:         raise ArgumentError, "Argument to --#{cast[:long]} must be an unsigned integer, not '#{@options[cast[:long]]}'"
+441:       end
+442:     end
+443:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + options_default() + click to toggle source + +
+ +
+ +

+Set default options value from cast unless a value is set. +

+ + + +
+
+     # File biopieces.rb, line 374
+374:   def options_default
+375:     @casts.each do |cast|
+376:       if cast[:default]
+377:         @options[cast[:long]] = cast[:default] unless @options.has_key? cast[:long]
+378:       end
+379:     end
+380:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + options_glob() + click to toggle source + +
+ +
+ +

+Expands glob expressions to a full list of paths. Examples: +“*.fna” or “foo.fna,*.fna” or +“foo.fna,/bar/*.fna“ +

+ + + +
+
+     # File biopieces.rb, line 384
+384:   def options_glob
+385:     @casts.each do |cast|
+386:       if cast[:type] == 'files' or cast[:type] == 'files!'
+387:         if @options.has_key? cast[:long]
+388:           files = []
+389:         
+390:           @options[cast[:long]].each do |path|
+391:             if path.include? "*"
+392:               Dir.glob(path).each do |file|
+393:                 files << file if File.file? file
+394:               end
+395:             else
+396:               files << path
+397:             end
+398:           end
+399: 
+400:           @options[cast[:long]] = files
+401:         end
+402:       end
+403:     end
+404:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + options_parse() + click to toggle source + +
+ +
+ +

+Parse options from argv using OptionParser and casts denoting long and +short option names. Usage information is printed and exit called. A hash +with options is returned. +

+ + + +
+
+     # File biopieces.rb, line 276
+276:   def options_parse
+277:     @options = {}
+278: 
+279:     option_parser = OptionParser.new do |option|
+280:       @casts.each do |cast|
+281:         case cast[:type]
+282:         when 'flag'
+283:           option.on("-#{cast[:short]}", "--#{cast[:long]}") do |o|
+284:             @options[cast[:long]] = o
+285:           end
+286:         when 'float'
+287:           option.on("-#{cast[:short]}", "--#{cast[:long]} F", Float) do |f|
+288:             @options[cast[:long]] = f
+289:           end
+290:         when 'string'
+291:           option.on("-#{cast[:short]}", "--#{cast[:long]} S", String) do |s|
+292:             @options[cast[:long]] = s.to_sym
+293:           end
+294:         when REGEX_LIST
+295:           option.on( "-#{cast[:short]}", "--#{cast[:long]} A", Array) do |a|
+296:             @options[cast[:long]] = a
+297:           end
+298:         when REGEX_INT
+299:           option.on("-#{cast[:short]}", "--#{cast[:long]} I", Integer) do |i|
+300:             @options[cast[:long]] = i
+301:           end
+302:         when REGEX_STRING
+303:           option.on("-#{cast[:short]}", "--#{cast[:long]} S", String) do |s|
+304:             @options[cast[:long]] = s
+305:           end
+306:         else
+307:           raise ArgumentError, "Unknown option type: '#{cast[:type]}'"
+308:         end
+309:       end
+310:     end
+311: 
+312:     option_parser.parse!(@argv)
+313: 
+314:     if print_usage_full?
+315:       print_usage_and_exit(true)
+316:     elsif print_usage_short?
+317:       print_usage_and_exit
+318:     end
+319: 
+320:     options_default
+321:     options_glob
+322:     options_check
+323: 
+324:     @options
+325:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + print_usage_and_exit(full=nil) + click to toggle source + +
+ +
+ +

+Print usage info by Calling an external script ‘print_wiki’ +using a system() call and exit. An optional ‘full’ flag outputs +the full usage info. +

+ + + + + +
+ + + + +
+ + +
+ + +
+ + print_usage_full?() + click to toggle source + +
+ +
+ +

+Check if full “usage info” should be printed. +

+ + + +
+
+     # File biopieces.rb, line 335
+335:   def print_usage_full?
+336:     @options[:help]
+337:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + print_usage_short?() + click to toggle source + +
+ +
+ +

+Check if short “usage info” should be printed. +

+ + + +
+
+     # File biopieces.rb, line 340
+340:   def print_usage_short?
+341:     if not $stdin.tty?
+342:       return false
+343:     elsif @options[:stream_in]
+344:       return false
+345:     elsif @options[:data_in]
+346:       return false
+347:     elsif wiki_path =~ /^(list_biopieces|list_genomes|list_mysql_databases|biostat)$/  # TODO get rid of this!
+348:       return false
+349:     else
+350:       return true
+351:     end
+352:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + wiki_path() + click to toggle source + +
+ +
+ +

+Given the script name determine the path of the wiki file with the usage +info. +

+ + + +
+
+     # File biopieces.rb, line 328
+328:   def wiki_path
+329:     path = ENV["BP_DIR"] + "/bp_usage/" + File.basename(@script_path) + ".wiki"
+330:     raise "No such wiki file: #{path}" unless File.file? path
+331:     path
+332:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Read.html b/code_ruby/Maasha/lib/doc/Read.html new file mode 100644 index 0000000..32cd91e --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Read.html @@ -0,0 +1,646 @@ + + + + + + + Class: Read + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

Object

+ +
+ + + + + + + +
+

Methods

+ +
+ + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Read

+ +
+

+Class containing data accessor methods for an SFF +entry and methods for manipulating this entry. +

+ +
+ + + + + + +
+

Attributes

+ + +
+ + + + +
+ read_header_length[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ name_length[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ number_of_bases[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ clip_qual_left[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ clip_qual_right[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ clip_adapter_left[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ clip_adaptor_right[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ name[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ flowgram_values[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ flow_index_per_base[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ bases[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ quality_scores[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ x_pos[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ y_pos[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+

Public Instance Methods

+ + +
+ + +
+ + clip() + click to toggle source + +
+ +
+ +

+Method that clips sequence (i.e. trims) according to clip_qual_left and clip_qual_right information. +

+ + + +
+
+     # File sff.rb, line 228
+228:   def clip
+229:     self.bases          = self.bases[self.clip_qual_left - 1 ... self.clip_qual_right]
+230:     self.quality_scores = self.quality_scores[self.clip_qual_left - 1 ... self.clip_qual_right]
+231:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + mask() + click to toggle source + +
+ +
+ +

+Method that soft masks the sequence (i.e. lowercases sequence) according to +clip_qual_left and clip_qual_right information. +

+ + + +
+
+     # File sff.rb, line 218
+218:   def mask
+219:     left   = self.bases[0 ... self.clip_qual_left - 1].downcase
+220:     middle = self.bases[self.clip_qual_left - 1 ... self.clip_qual_right]
+221:     right  = self.bases[self.clip_qual_right ... self.bases.length].downcase
+222: 
+223:     self.bases = left + middle + right
+224:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + to_bp() + click to toggle source + +
+ +
+ +

+Method that converts a Read object’s data to +a Biopiece record (a hash). +

+ + + +
+
+     # File sff.rb, line 197
+197:   def to_bp
+198:     coordinates_get
+199: 
+200:     hash = {}
+201: 
+202:     hash[:SEQ_NAME]           = self.name
+203:     hash[:SEQ]                = self.bases
+204:     hash[:SEQ_LEN]            = self.bases.length
+205:     hash[:CLIP_QUAL_LEFT]     = self.clip_qual_left     - 1
+206:     hash[:CLIP_QUAL_RIGHT]    = self.clip_qual_right    - 1
+207:     hash[:CLIP_ADAPTOR_LEFT]  = self.clip_adapter_left  - 1
+208:     hash[:CLIP_ADAPTOR_RIGHT] = self.clip_adaptor_right - 1
+209:     hash[:SCORES]             = self.quality_scores.map { |i| (i += 64).chr }.join ""
+210:     hash[:X_POS]              = self.x_pos
+211:     hash[:Y_POS]              = self.y_pos
+212: 
+213:     hash
+214:   end
+
+ +
+ + + + +
+ + +
+ +
+

Private Instance Methods

+ + +
+ + +
+ + coordinates_get() + click to toggle source + +
+ +
+ +

+Method that extracts the X/Y coordinates from an SFF +read name encoded with base36. +

+ + + +
+
+     # File sff.rb, line 237
+237:   def coordinates_get
+238:     base36 = self.name[5, 5]
+239:     num    = Base36.decode(base36)
+240: 
+241:     self.x_pos = num >> BIT_SHIFT
+242:     self.y_pos = num &  BIT_MASK
+243:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/SFF.html b/code_ruby/Maasha/lib/doc/SFF.html new file mode 100644 index 0000000..f3497f6 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/SFF.html @@ -0,0 +1,712 @@ + + + + + + + Class: SFF + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

Object

+ +
+ + + + + + + + + + + + +
+

Included Modules

+
    + + +
  • Enumerable
    • + + +
+
+ +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

SFF

+ +
+

+Class containing methods to parse SFF files: www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff +

+ +
+ + + + + + + + + +
+

Public Class Methods

+ + +
+ + +
+ + new(io) + click to toggle source + +
+ +
+ +

+Method to initialize an SFF object along with +instance variables pertaining to the SFF header +section. +

+ + + +
+
+    # File sff.rb, line 58
+58:   def initialize(io)
+59:     @io                       = io
+60:     @magic_number             = 0
+61:     @version                  = ""
+62:     @index_offset             = 0
+63:     @index_length             = 0
+64:     @number_of_reads          = 0
+65:     @header_length            = 0
+66:     @key_length               = 0
+67:     @number_of_flows_per_read = 0
+68:     @flowgram_format_code     = 0
+69:     @flow_chars               = ""
+70:     @key_sequence             = ""
+71:     @eight_byte_padding       = 0
+72: 
+73:     header_parse
+74:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + open(*args) + click to toggle source + +
+ +
+ +

+Class method for opening SFF files. +

+ + + +
+
+    # File sff.rb, line 41
+41:   def self.open(*args)
+42:     ios = File.open(*args)
+43: 
+44:     if block_given?
+45:       begin
+46:         yield self.new(ios)
+47:       ensure
+48:         ios.close
+49:       end
+50:     else
+51:       return self.new(ios)
+52:     end
+53:   end
+
+ +
+ + + + +
+ + +
+ +
+

Public Instance Methods

+ + +
+ + +
+ + close() + click to toggle source + +
+ +
+ +

+Method to close ios. +

+ + + +
+
+    # File sff.rb, line 77
+77:   def close
+78:     @io.close
+79:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + each() + click to toggle source + +
+ +
+ +

+Method to iterate over each SFF entry. +

+ + + +
+
+    # File sff.rb, line 82
+82:   def each
+83:     while (read = read_parse) do
+84:       yield read
+85:     end
+86: 
+87:     self   # conventionally
+88:   end
+
+ +
+ + + + +
+ + +
+ +
+

Private Instance Methods

+ + +
+ + +
+ + check_header_length() + click to toggle source + +
+ +
+ +

+Method to check the header length of an SFF file. +Raises an error if the header length don’t match the file position +after reading the header section. +

+ + + +
+
+     # File sff.rb, line 183
+183:   def check_header_length
+184:     raise SFFError, "Bad header length: #{header_length}" unless @io.pos == @header_length
+185:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + check_magic_number() + click to toggle source + +
+ +
+ +

+Method to check the magic number of an SFF file. +Raises an error if the magic number don’t match. +

+ + + +
+
+     # File sff.rb, line 170
+170:   def check_magic_number
+171:     raise SFFError, "Badly formatted SFF file." unless @magic_number == 779314790
+172:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + check_version() + click to toggle source + +
+ +
+ +

+Method to check the version number of an SFF file. +Raises an error if the version don’t match. +

+ + + +
+
+     # File sff.rb, line 176
+176:   def check_version
+177:     raise SFFError, "Wrong version: #{@version}" unless @version.to_i == 1
+178:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + fast_forward() + click to toggle source + +
+ +
+ +

+Method that reads the eight_byte_padding field found at the end of the data +section and fast forwards, i.e. move the file read pointer, so that the +length of the section is divisible by 8. +

+ + + +
+
+     # File sff.rb, line 122
+122:   def fast_forward
+123:     eight_byte_padding = 8 - (@io.pos % 8)
+124: 
+125:     @io.read(eight_byte_padding) unless eight_byte_padding == 8
+126:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + header_parse() + click to toggle source + +
+ +
+ +

+Method to parse the SFF file’s header section +and load the information into the instance variables. +

+ + + +
+
+     # File sff.rb, line 94
+ 94:   def header_parse
+ 95:     template     = "NC4N2NNnnnC"
+ 96:     bits_in_uint = 32
+ 97: 
+ 98:     data = @io.read(31).unpack(template)
+ 99:     
+100:     @magic_number             = data[0]
+101:     @version                  = data[1 .. 4].join ""
+102:     @index_offset             = (data[5] << bits_in_uint) | data[6]
+103:     @index_length             = data[7]
+104:     @number_of_reads          = data[8]
+105:     @header_length            = data[9]
+106:     @key_length               = data[10]
+107:     @number_of_flows_per_read = data[11]
+108:     @flowgram_format_code     = data[12]
+109:     @flow_chars               = @io.read(@number_of_flows_per_read).unpack("A*").join ""
+110:     @key_sequence             = @io.read(@key_length).unpack("A*").join ""
+111: 
+112:     fast_forward
+113: 
+114:     check_magic_number
+115:     check_version
+116:     check_header_length
+117:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + read_parse() + click to toggle source + +
+ +
+ +

+Method to parse a read section of an SFF file. +

+ + + +
+
+     # File sff.rb, line 129
+129:   def read_parse
+130:     return nil if @number_of_reads == @@count
+131: 
+132:     template = "nnNnnnn"
+133: 
+134:     read = Read.new()
+135: 
+136:     data = @io.read(16).unpack(template)
+137: 
+138:     read.read_header_length  = data[0]
+139:     read.name_length         = data[1]
+140:     read.number_of_bases     = data[2]
+141:     read.clip_qual_left      = data[3]
+142:     read.clip_qual_right     = data[4]
+143:     read.clip_adapter_left   = data[5]
+144:     read.clip_adaptor_right  = data[6]
+145:     read.name                = @io.read(read.name_length).unpack("A*").join ""
+146: 
+147:     fast_forward
+148: 
+149:     @io.read(2 * @number_of_flows_per_read) # skip through flowgram_values
+150:     @io.read(read.number_of_bases)          # skip through flow_index_per_base
+151: 
+152:     # NB! Parsing of flowgram_values and flow_index_per_base is currently disabled since these are not needed.
+153:     # read.flowgram_values     = @io.read(2 * @number_of_flows_per_read).unpack("n*").map { |val| val = sprintf("%.2f", val * 0.01) }
+154:     # flow_index_per_base      = @io.read(read.number_of_bases).unpack("C*")
+155:     # (1 ... flow_index_per_base.length).each { |i| flow_index_per_base[i] += flow_index_per_base[i - 1] }
+156:     # read.flow_index_per_base = flow_index_per_base
+157: 
+158:     read.bases               = @io.read(read.number_of_bases).unpack("A*").join ""
+159:     read.quality_scores      = @io.read(read.number_of_bases).unpack("C*")
+160: 
+161:     fast_forward
+162: 
+163:     @@count += 1
+164: 
+165:     read
+166:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/SFFError.html b/code_ruby/Maasha/lib/doc/SFFError.html new file mode 100644 index 0000000..5ce72a1 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/SFFError.html @@ -0,0 +1,200 @@ + + + + + + + Class: SFFError + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

StandardError

+ +
+ + + + + + + + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

SFFError

+ +
+

+Error class for all exceptions to do with SFF. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Seq.html b/code_ruby/Maasha/lib/doc/Seq.html new file mode 100644 index 0000000..b458f01 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Seq.html @@ -0,0 +1,1825 @@ + + + + + + + Class: Seq + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

Object

+ +
+ + + + + + + + + + + + +
+

Included Modules

+
    + + +
  • Amatch
    • + + +
+
+ +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Seq

+ +
+ +
+ + + + + + +
+

Attributes

+ + +
+ + + + +
+ seq_name[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ seq[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ type[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+ qual[RW] +
+ +
+ + + +
+
+ +
+ + + + +
+

Public Class Methods

+ + +
+ + +
+ + generate_oligos(length, type) + click to toggle source + +
+ +
+ +

+Method that generates all possible oligos of a specifed length and type. +

+ + + +
+
+    # File seq.rb, line 47
+47:   def self.generate_oligos(length, type)
+48:     raise SeqError, "Cannot generate negative oligo length: #{length}" if length <= 0
+49: 
+50:     case type.downcase
+51:     when /dna/     then alph = DNA
+52:     when /rna/     then alph = RNA
+53:     when /protein/ then alph = PROTEIN
+54:     else
+55:       raise SeqError, "Unknown sequence type: #{type}"
+56:     end
+57: 
+58:     oligos = [""]
+59: 
+60:     (1 .. length).each do
+61:       list = []
+62: 
+63:       oligos.each do |oligo|
+64:         alph.each do |char|
+65:           list << oligo + char
+66:         end
+67:       end
+68: 
+69:       oligos = list
+70:     end
+71: 
+72:     oligos
+73:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + new(seq_name = nil, seq = nil, type = nil, qual = nil) + click to toggle source + +
+ +
+ +

+Initialize a sequence object with the following arguments: +

+
    +

  • +seq_name: Name of the sequence. +

    +
    • +

  • +seq: The sequence. +

    +
    • +

  • +type: The sequence type - DNA, RNA, or protein +

    +
    • +

  • +qual: An Illumina type quality scores string. +

    +
    • +
+ + + +
+
+    # File seq.rb, line 80
+80:   def initialize(seq_name = nil, seq = nil, type = nil, qual = nil)
+81:     @seq_name = seq_name
+82:     @seq      = seq
+83:     @type     = type
+84:     @qual     = qual
+85:   end
+
+ +
+ + + + +
+ + +
+ +
+

Public Instance Methods

+ + +
+ + +
+ + adaptor_clip_left(adaptor, hd_percent = 0) + click to toggle source + +
+ +
+ +

+Method that locates an adaptor or part thereof in the sequence of a Seq object beginning from the left and removes the +adaptor sequence if found. The hd_percent is used to calculate the maximum +hamming distance allowed for all possible overlaps. +

+ + + +
+
+     # File seq.rb, line 377
+377:   def adaptor_clip_left(adaptor, hd_percent = 0)
+378:     pos = self.adaptor_locate_left(adaptor, hd_percent)
+379: 
+380:     if pos > 0
+381:       self.seq  = self.seq[pos + 1 ... self.length]
+382:       self.qual = self.qual[pos + 1 ... self.qual.length] unless self.qual.nil?
+383:     end
+384:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + adaptor_clip_right(adaptor, hd_percent = 0) + click to toggle source + +
+ +
+ +

+Method that locates an adaptor or part thereof in the sequence of a Seq object beginning from the right and removes the +adaptor sequence if found. The hd_percent is used to calculate the maximum +hamming distance allowed for all possible overlaps. +

+ + + +
+
+     # File seq.rb, line 364
+364:   def adaptor_clip_right(adaptor, hd_percent = 0)
+365:     pos = self.adaptor_locate_right(adaptor, hd_percent)
+366: 
+367:     if pos > 0
+368:       self.seq  = self.seq[0 ... pos]
+369:       self.qual = self.qual[0 ... pos] unless self.qual.nil?
+370:     end
+371:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + adaptor_locate_left(adaptor, hd_percent = 0) + click to toggle source + +
+ +
+ +

+Method that locates an adaptor or part thereof in the sequence of a Seq object beginning from the left. Returns the +location in the sequence that overlaps with the adaptor or -1 if the +adaptor was not found. The hd_percent is used to calculate the maximum +hamming distance allowed for all possible overlaps. +

+ + + +
+
+     # File seq.rb, line 340
+340:   def adaptor_locate_left(adaptor, hd_percent = 0)
+341:     raise SeqError, "Hamming distance percent out of range #{hd_percent}" unless (0 .. 100).include? hd_percent
+342:     pos = adaptor.length
+343: 
+344:     while pos > 0
+345:       len          = pos
+346:       subseq       = self.seq[0 ... len].upcase
+347:       subadaptor   = adaptor[adaptor.length - len ... adaptor.length].upcase
+348:       m            = Hamming.new(subseq)
+349:       hamming_dist = m.match(subadaptor)
+350:       hamming_max  = (len * hd_percent * 0.01).round
+351: 
+352:       pos -= 1
+353: 
+354:       return pos if hamming_dist <= hamming_max
+355:     end
+356:     
+357:     1
+358:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + adaptor_locate_right(adaptor, hd_percent = 0) + click to toggle source + +
+ +
+ +

+Method that locates an adaptor or part thereof in the sequence of a Seq object beginning from the right. Returns the +location in the sequence that overlaps with the adaptor or -1 if the +adaptor was not found. The hd_percent is used to calculate the maximum +hamming distance allowed for all possible overlaps. +

+ + + +
+
+     # File seq.rb, line 316
+316:   def adaptor_locate_right(adaptor, hd_percent = 0)
+317:     raise SeqError, "Hamming distance percent out of range #{hd_percent}" unless (0 .. 100).include? hd_percent
+318:     pos = self.length - adaptor.length
+319: 
+320:     while pos < self.length
+321:       len          = self.length - pos
+322:       subseq       = self.seq[pos ... pos + len].upcase
+323:       subadaptor   = adaptor[0 ... len].upcase
+324:       m            = Hamming.new(subseq)
+325:       hamming_dist = m.match(subadaptor)
+326:       hamming_max  = (len * hd_percent * 0.01).round
+327:       return pos if hamming_dist <= hamming_max
+328: 
+329:       pos += 1
+330:     end
+331: 
+332:     1
+333:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + complement() + click to toggle source + +
+ +
+ +

+Method that complements sequence including ambiguity codes. +

+ + + +
+
+     # File seq.rb, line 196
+196:   def complement
+197:     raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
+198: 
+199:     if self.is_dna?
+200:       self.seq.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn' )
+201:     elsif self.is_rna?
+202:       self.seq.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn' )
+203:     else
+204:       raise SeqError, "Cannot complement sequence type: #{self.type}"
+205:     end
+206:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + composition() + click to toggle source + +
+ +
+ +

+Method that returns the residue compositions of a sequence in a hash where +the key is the residue and the value is the residue count. +

+ + + +
+
+     # File seq.rb, line 272
+272:   def composition
+273:     comp = Hash.new(0);
+274: 
+275:     self.seq.upcase.each_char do |char|
+276:       comp[char] += 1
+277:     end
+278: 
+279:     comp
+280:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + convert_phred2illumina!() + click to toggle source + +
+ +
+ +

+Method to convert the quality scores from a specified base to another base. +

+ + + +
+
+     # File seq.rb, line 388
+388:   def convert_phred2illumina!
+389:     self.qual.gsub! /./ do |score|
+390:       score_phred  = score.ord - SCORE_PHRED
+391:       raise SeqError, "Bad Phred score: #{score} (#{score_phred})" unless (0 .. 40).include? score_phred
+392:       score_illumina = score_phred + SCORE_ILLUMINA
+393:       score          = score_illumina.chr
+394:     end
+395:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + convert_solexa2illumina!() + click to toggle source + +
+ +
+ +

+Method to convert the quality scores from Solexa odd/ratio to Illumina +format. +

+ + + +
+
+     # File seq.rb, line 399
+399:   def convert_solexa2illumina!
+400:     self.qual.gsub! /./ do |score|
+401:       score = solexa_char2illumina_char(score)
+402:     end
+403:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + generate(length, type) + click to toggle source + +
+ +
+ +

+Method that generates a random sequence of a given length and type. +

+ + + +
+
+     # File seq.rb, line 209
+209:   def generate(length, type)
+210:     raise SeqError, "Cannot generate sequence length < 1: #{length}" if length <= 0
+211: 
+212:     case type.downcase
+213:     when "dna"
+214:       alph = DNA
+215:     when "rna"
+216:       alph = RNA
+217:     when "protein"
+218:       alph = PROTEIN
+219:     else
+220:       raise SeqError, "Unknown sequence type: #{type}"
+221:     end
+222: 
+223:     seq_new   = Array.new(length) { alph[rand(alph.size)] }.join("")
+224:     self.seq  = seq_new
+225:     self.type = type.downcase
+226:     seq_new
+227:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + hard_mask() + click to toggle source + +
+ +
+ +

+Method that returns the percentage of hard masked residues or N’s in +a sequence. +

+ + + +
+
+     # File seq.rb, line 301
+301:   def hard_mask
+302:     ((self.seq.upcase.scan("N").size.to_f / (self.len - self.indels).to_f) * 100).round(2)
+303:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + homopol_max(min = 1) + click to toggle source + +
+ +
+ +

+Method that returns the length of the longest homopolymeric stretch found +in a sequence. +

+ + + +
+
+     # File seq.rb, line 284
+284:   def homopol_max(min = 1)
+285:     return 0 if self.seq.nil? or self.seq.empty?
+286: 
+287:     found = false
+288: 
+289:     self.seq.upcase.scan(/A{#{min},}|T{#{min},}|G{#{min},}|C{#{min},}|N{#{min},}/) do |match|
+290:       found = true
+291:       min   = match.size > min ? match.size : min
+292:     end
+293: 
+294:     return 0 unless found
+295:  
+296:     min
+297:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + indels() + click to toggle source + +
+ +
+ +

+Return the number indels in a sequence. +

+ + + +
+
+    # File seq.rb, line 95
+95:   def indels
+96:     regex = Regexp.new(/[#{Regexp.escape(INDELS.join(""))}]/)
+97:     self.seq.scan(regex).size
+98:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + is_dna?() + click to toggle source + +
+ +
+ +

+Method that returns true is a given sequence type is DNA. +

+ + + +
+
+     # File seq.rb, line 101
+101:   def is_dna?
+102:     self.type == 'dna'
+103:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + is_protein?() + click to toggle source + +
+ +
+ +

+Method that returns true is a given sequence type is protein. +

+ + + +
+
+     # File seq.rb, line 111
+111:   def is_protein?
+112:     self.type == 'protein'
+113:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + is_rna?() + click to toggle source + +
+ +
+ +

+Method that returns true is a given sequence type is RNA. +

+ + + +
+
+     # File seq.rb, line 106
+106:   def is_rna?
+107:     self.type == 'rna'
+108:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + len() + click to toggle source + +
+ +
+ + + + + +
+ + + + +
+ Alias for: length +
+ +
+ + +
+ + +
+ + length() + click to toggle source + +
+ +
+ +

+Returns the length of a sequence. +

+ + + +
+
+    # File seq.rb, line 88
+88:   def length
+89:     self.seq.nil? ? 0 : self.seq.length
+90:   end
+
+ +
+ + +
+ Also aliased as: len +
+ + + +
+ + +
+ + +
+ + match(patter, pos) + click to toggle source + +
+ +
+ + 
+  seq.match(pattern[, pos ] [, hd=max] [, ed=max]) -> matchdata or nil
+
+

+Method to locate a pattern in a sequence and return the position of the +match or nil if no match was found. Optional maximum Hamming and Edit +distance can be specified. +

+ + + +
+
+     # File seq.rb, line 411
+411:   def match(patter, pos)
+412:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + revcomp() + click to toggle source + +
+ +
+ + + + + +
+ + + + +
+ Alias for: reverse_complement +
+ +
+ + +
+ + +
+ + reverse() + click to toggle source + +
+ +
+ +

+Method to reverse the sequence. +

+ + + +
+
+     # File seq.rb, line 191
+191:   def reverse
+192:     self.seq.reverse!
+193:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + reverse_complement() + click to toggle source + +
+ +
+ +

+Method to reverse complement sequence. +

+ + + +
+
+     # File seq.rb, line 183
+183:   def reverse_complement
+184:     self.reverse
+185:     self.complement
+186:   end
+
+ +
+ + +
+ Also aliased as: revcomp +
+ + + +
+ + +
+ + +
+ + soft_mask() + click to toggle source + +
+ +
+ +

+Method that returns the percentage of soft masked residues or lower cased +residues in a sequence. +

+ + + +
+
+     # File seq.rb, line 307
+307:   def soft_mask
+308:     ((self.seq.scan(/[a-z]/).size.to_f / (self.len - self.indels).to_f) * 100).round(2)
+309:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + subseq(start, length = self.length - start) + click to toggle source + +
+ +
+ +

+Method that returns a subsequence of from a given start position and of a +given length. +

+ + + +
+
+     # File seq.rb, line 231
+231:   def subseq(start, length = self.length - start)
+232:     raise SeqError, "subsequence start: #{start} < 0"                                                if start  < 0
+233:     raise SeqError, "subsequence length: #{length} < 1"                                              if length <= 0
+234:     raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
+235: 
+236:     stop = start + length - 1
+237: 
+238:     seq  = self.seq[start .. stop]
+239:     qual = self.qual[start .. stop] unless self.qual.nil?
+240: 
+241:     Seq.new(self.seq_name, seq, self.type, qual)
+242:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + subseq!(start, length = self.length - start) + click to toggle source + +
+ +
+ +

+Method that replaces a sequence with a subsequence from a given start +position and of a given length. +

+ + + +
+
+     # File seq.rb, line 246
+246:   def subseq!(start, length = self.length - start)
+247:     raise SeqError, "subsequence start: #{start} < 0"                                                if start  < 0
+248:     raise SeqError, "subsequence length: #{length} < 1"                                              if length <= 0
+249:     raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
+250: 
+251:     stop = start + length - 1
+252: 
+253:     self.seq  = self.seq[start .. stop]
+254:     self.qual = self.qual[start .. stop] unless self.qual.nil?
+255:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + subseq_rand(length) + click to toggle source + +
+ +
+ +

+Method that returns a subsequence of a given length beginning at a random +position. +

+ + + +
+
+     # File seq.rb, line 259
+259:   def subseq_rand(length)
+260:     if self.length - length + 1 == 0
+261:       start = 0
+262:     else
+263:       start = rand(self.length - length + 1)
+264:     end
+265: 
+266:     self.subseq(start, length)
+267:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + to_bp() + click to toggle source + +
+ +
+ +

+Method that given a Seq entry returns a Biopieces record (a hash). +

+ + + +
+
+     # File seq.rb, line 132
+132:   def to_bp
+133:     raise SeqError, "Missing seq_name" if self.seq_name.nil?
+134:     raise SeqError, "Missing seq"      if self.seq.nil?
+135:     record             = {}
+136:     record[:SEQ_NAME] = self.seq_name
+137:     record[:SEQ]      = self.seq
+138:     record[:SEQ_LEN]  = self.length
+139:     record[:SCORES]   = self.qual if self.qual
+140:     record
+141:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + to_dna() + click to toggle source + +
+ +
+ +

+Method to reverse-transcribe RNA to DNA. +

+ + + +
+
+     # File seq.rb, line 124
+124:   def to_dna
+125:     raise SeqError, "Cannot reverse-transcribe 0 length sequence" if self.length == 0
+126:     raise SeqError, "Cannot reverse-transcribe sequence type: #{self.type}" unless self.is_rna?
+127:     self.type = 'dna'
+128:     self.seq.tr!('Uu','Tt')
+129:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + to_fasta(wrap = nil) + click to toggle source + +
+ +
+ +

+Method that given a Seq entry returns a FASTA entry +(a string). +

+ + + +
+
+     # File seq.rb, line 144
+144:   def to_fasta(wrap = nil)
+145:     raise SeqError, "Missing seq_name" if self.seq_name.nil?
+146:     raise SeqError, "Missing seq"      if self.seq.nil?
+147: 
+148:     seq_name = self.seq_name
+149:     seq      = self.seq
+150: 
+151:     unless wrap.nil?
+152:       seq.gsub! /(.{#{wrap}})/ do |match|
+153:         match << "\n"
+154:       end
+155: 
+156:       seq.chomp!
+157:     end
+158: 
+159:     ">#{seq_name}\n#{seq}\n"
+160:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + to_key() + click to toggle source + +
+ +
+ +

+Method that generates a unique key for a DNA sequence and return this key +as a Fixnum. +

+ + + +
+
+     # File seq.rb, line 164
+164:   def to_key
+165:     key = 0
+166:     
+167:     self.seq.upcase.each_char do |char|
+168:       key <<= 2
+169:       
+170:       case char
+171:       when 'A' then key |= 0
+172:       when 'C' then key |= 1
+173:       when 'G' then key |= 2
+174:       when 'T' then key |= 3
+175:       else raise SeqError, "Bad residue: #{char}"
+176:       end
+177:     end
+178:     
+179:     key
+180:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + to_rna() + click to toggle source + +
+ +
+ +

+Method to transcribe DNA to RNA. +

+ + + +
+
+     # File seq.rb, line 116
+116:   def to_rna
+117:     raise SeqError, "Cannot transcribe 0 length sequence" if self.length == 0
+118:     raise SeqError, "Cannot transcribe sequence type: #{self.type}" unless self.is_dna?
+119:     self.type = 'rna'
+120:     self.seq.tr!('Tt','Uu')
+121:   end
+
+ +
+ + + + +
+ + +
+ +
+

Private Instance Methods

+ + +
+ + +
+ + solexa2phred(score) + click to toggle source + +
+ +
+ +

+Method to convert a Solexa score (odd ratio) to a phred (probability) +integer score. +

+ + + +
+
+     # File seq.rb, line 418
+418:   def solexa2phred(score)
+419:     (10.0 * Math.log(10.0 ** (score / 10.0) + 1.0, 10)).to_i
+420:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + solexa_char2illumina_char(char) + click to toggle source + +
+ +
+ +

+Method to convert a Solexa score encoded using base 64 ASCII to a Phred +score encoded using base 64 ASCII. +

+ + + +
+
+     # File seq.rb, line 424
+424:   def solexa_char2illumina_char(char)
+425:     score_solexa = char.ord - 64
+426:     score_phred  = solexa2phred(score_solexa)
+427:     (score_phred + 64).chr
+428:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/SeqError.html b/code_ruby/Maasha/lib/doc/SeqError.html new file mode 100644 index 0000000..16dca69 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/SeqError.html @@ -0,0 +1,200 @@ + + + + + + + Class: SeqError + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

StandardError

+ +
+ + + + + + + + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

SeqError

+ +
+

+Error class for all exceptions to do with Seq. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Status.html b/code_ruby/Maasha/lib/doc/Status.html new file mode 100644 index 0000000..a06e728 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Status.html @@ -0,0 +1,524 @@ + + + + + + + Class: Status + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

Object

+ +
+ + + + + + + +
+

Methods

+ +
+ + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Status

+ +
+

+Class for manipulating the execution status of Biopieces by setting a status file with a time +stamp, process id, and command arguments. The status file is used for +creating log entries and for displaying the runtime status of Biopieces. +

+ +
+ + + + + + + + + +
+

Public Instance Methods

+ + +
+ + +
+ + delete() + click to toggle source + +
+ +
+ +

+Delete status file. +

+ + + +
+
+     # File biopieces.rb, line 547
+547:   def delete
+548:     File.delete(path)
+549:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + get_tmpdir() + click to toggle source + +
+ +
+ +

+Extract the temporary directory path from the status file, and return this +or nil if not found. +

+ + + +
+
+     # File biopieces.rb, line 520
+520:   def get_tmpdir
+521:     File.open(path, mode="r") do |fh|
+522:       tmpdir_path = fh.read.chomp.split(";").last
+523:       return tmpdir_path if File.directory?(tmpdir_path)
+524:     end
+525: 
+526:     nil
+527:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + log(exit_status) + click to toggle source + +
+ +
+ +

+Write the Biopiece status to the log file. +

+ + + +
+
+     # File biopieces.rb, line 530
+530:   def log(exit_status)
+531:     time1   = Time.new.strftime("%Y-%m-%d %X")
+532:     user    = ENV["USER"]
+533:     script  = File.basename($0)
+534: 
+535:     stream = File.open(path)
+536:     time0, args, tmp_dir = stream.first.split(";")
+537:     stream.close
+538: 
+539:     elap     = time_diff(time0, time1)
+540:     command  = [script, args].join(" ") 
+541:     log_file = ENV["BP_LOG"] + "/biopieces.log"
+542: 
+543:     File.open(log_file, mode = "a") { |file| file.puts [time0, time1, elap, user, exit_status, command].join("\t") }
+544:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + set() + click to toggle source + +
+ +
+ +

+Write the status to a status file. +

+ + + +
+
+     # File biopieces.rb, line 495
+495:   def set
+496:     time0  = Time.new.strftime("%Y-%m-%d %X")
+497: 
+498:     File.open(path, mode="w") do |fh|
+499:       fh.puts [time0, ARGV.join(" ")].join(";")
+500:     end
+501:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + set_tmpdir(tmpdir_path) + click to toggle source + +
+ +
+ +

+Append the a temporary directory path to the status file. +

+ + + +
+
+     # File biopieces.rb, line 504
+504:   def set_tmpdir(tmpdir_path)
+505:     status = ""
+506: 
+507:     File.open(path, mode="r") do |fh|
+508:       status = fh.read.chomp
+509:     end
+510: 
+511:     status = "#{status};#{tmpdir_path}\n"
+512: 
+513:     File.open(path, mode="w") do |fh|
+514:       fh << status
+515:     end
+516:   end
+
+ +
+ + + + +
+ + +
+ +
+

Private Instance Methods

+ + +
+ + +
+ + path() + click to toggle source + +
+ +
+ +

+Path to status file +

+ + + +
+
+     # File biopieces.rb, line 554
+554:   def path
+555:     user   = ENV["USER"]
+556:     script = File.basename($0)
+557:     pid    = $$
+558:     path   = ENV["BP_TMP"] + "/" + [user, script, pid, "status"].join(".")
+559:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + time_diff(t0, t1) + click to toggle source + +
+ +
+ +

+Get the elapsed time from the difference between two time stamps. +

+ + + +
+
+     # File biopieces.rb, line 562
+562:   def time_diff(t0, t1)
+563:     Time.at((DateTime.parse(t1).to_time - DateTime.parse(t0).to_time).to_i).gmtime.strftime('%X')
+564:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/Stream.html b/code_ruby/Maasha/lib/doc/Stream.html new file mode 100644 index 0000000..24d3772 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/Stream.html @@ -0,0 +1,557 @@ + + + + + + + Class: Stream + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

In Files

+
+ +
+
+ + +
+ +
+ + + +
+

Parent

+ +

IO

+ +
+ + + + + + + +
+

Methods

+ +
+ + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

Stream

+ +
+ +
+ + + + + + + + + +
+

Public Class Methods

+ + +
+ + +
+ + open(options, mode, stdio) + click to toggle source + +
+ +
+ +

+Open Biopieces output data stream for reading +from stdin or a file specified in options[:stream_in] OR writing to stdout +or a file specified in options[:stream_out] or options[:data_out]. +

+ + + +
+
+     # File biopieces.rb, line 572
+572:   def self.open(options, mode, stdio)
+573:     if mode == "r"
+574:       if options[:data_in] and options[:data_in].first == "-"
+575:         self.nread(["-"])
+576:       else
+577:         $stdin.tty? ? read(options[:stream_in]) : stdio
+578:       end
+579:     elsif mode == "w"
+580:       options[:stream_out] ? self.write(options[:stream_out], options[:compress]) : stdio
+581:     else
+582:       raise "Bad mode #{mode}"
+583:     end
+584:   end
+
+ +
+ + + + +
+ + +
+ +
+

Private Class Methods

+ + +
+ + +
+ + nread(files) + click to toggle source + +
+ +
+ +

+Opens a list of files for reading and return an io object. +

+ + + +
+
+     # File biopieces.rb, line 616
+616:   def self.nread(files)
+617:     stdin, stdout, stderr = Open3.popen3("cat " + files.join(' '));
+618:     stdin.close
+619:     stderr.close
+620:     stdout
+621:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + nwrite(file) + click to toggle source + +
+ +
+ +

+Opens a file for writing and return an io object. +

+ + + +
+
+     # File biopieces.rb, line 624
+624:   def self.nwrite(file)
+625:     File.open(file, mode="w")
+626:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + read(files) + click to toggle source + +
+ +
+ +

+Opens a reads stream to a list of files. +

+ + + +
+
+     # File biopieces.rb, line 589
+589:   def self.read(files)
+590:     return if files.nil? #TODO case/when
+591:     self.zipped?(files) ? self.zread(files) : self.nread(files)
+592:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + write(file, zip=nil) + click to toggle source + +
+ +
+ +

+Opens a write stream to a file and returns a io object. +

+ + + +
+
+     # File biopieces.rb, line 595
+595:   def self.write(file, zip=nil)
+596:     zip ? self.zwrite(file) : self.nwrite(file)
+597:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + zipped?(files) + click to toggle source + +
+ +
+ +

+Test if a list of files are gzipped or not. Raises if files are mixed +zipped and unzipped. +

+ + + +
+
+     # File biopieces.rb, line 630
+630:   def self.zipped?(files)
+631:     type_hash = {}
+632: 
+633:     files.each do |file|
+634:       type = `file #{file}`
+635: 
+636:       if type =~ /gzip compressed/
+637:         type_hash[:gzip] = true
+638:       else
+639:         type_hash[:ascii] = true
+640:       end
+641:     end
+642: 
+643:     raise "Mixture of zipped and unzipped files" if type_hash.size == 2
+644: 
+645:     type_hash[:gzip]
+646:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + zread(files) + click to toggle source + +
+ +
+ +

+Opens a list of gzipped files for reading and return an io object. +

+ + + +
+
+     # File biopieces.rb, line 600
+600:   def self.zread(files)
+601:     stdin, stdout, stderr = Open3.popen3("zcat " + files.join(' '));
+602:     stdin.close
+603:     stderr.close
+604:     stdout
+605:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + zwrite(file) + click to toggle source + +
+ +
+ +

+Opens a file for gzipped writing and return an io object. +

+ + + +
+
+     # File biopieces.rb, line 608
+608:   def self.zwrite(file)
+609:     stdin, stdout, stderr = Open3.popen3("gzip -f > #{file}")
+610:     stderr.close
+611:     stdout.close
+612:     stdin
+613:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/String.html b/code_ruby/Maasha/lib/doc/String.html new file mode 100644 index 0000000..61c0653 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/String.html @@ -0,0 +1,408 @@ + + + + + + + Class: String + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
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+

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+
+ +
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+ + +
+ +
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+

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+ +

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+ +
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+

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+ +
+ + + + +
+ +
+ + + +
+

Class Index + [+]

+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

String

+ +
+

+Monkey patching Class String to add bitwise +operators. Behaviour matching Perl’s: perldoc.perl.org/perlop.html#Bitwise-String-Operators +

+ +
+ + + + + + + + + +
+

Public Class Methods

+ + +
+ + +
+ + hamming_dist(str1, str2) + click to toggle source + +
+ +
+ +

+Method to that returns the case senstive Hamming Distance between two +strings. en.wikipedia.org/wiki/Hamming_distance +

+ + + +
+
+    # File bits.rb, line 34
+34:   def self.hamming_dist(str1, str2)
+35:     raise StringError, "Uneven string lengths: #{str1.length} != #{str2.length}" if str1.length != str2.length
+36:     (str1 ^ str2 ).count("\x01-\xff")
+37:   end
+
+ +
+ + + + +
+ + +
+ +
+

Public Instance Methods

+ + +
+ + +
+ + &(str) + click to toggle source + +
+ +
+ +

+Method that performs bitwise AND operation where bits are copied if they +exists in BOTH operands. If the operand sizes are different, the & +operator methods acts as though the longer operand were truncated to the +length of the shorter. +

+ + + +
+
+    # File bits.rb, line 43
+43:   def &(str)
+44:     new = ""
+45: 
+46:     (0 ... [self.length, str.length].min).each do |i|
+47:       new << (self[i].ord & str[i].ord)
+48:     end
+49: 
+50:     new
+51:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + ^(str) + click to toggle source + +
+ +
+ +

+Method that performs bitwise XOR operation where bits are copied if they +exists in ONE BUT NOT BOTH operands. +

+ + + +
+
+    # File bits.rb, line 77
+77:   def ^(str)
+78:     new = ""
+79: 
+80:     (0 ... [self.length, str.length].min).each do |i|
+81:       new << (self[i].ord ^ str[i].ord)
+82:     end
+83: 
+84:     new
+85:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + |(str) + click to toggle source + +
+ +
+ +

+Method that performs bitwise OR operation where bits are copied if they +exists in EITHER operands. If the operand sizes differ, the shorter operand +is extended with the terminal part of the longer operand. +

+ + + +
+
+    # File bits.rb, line 57
+57:   def |(str)
+58:     new = ""
+59: 
+60:     min = [self.length, str.length].min
+61: 
+62:     (0 ... min).each do |i|
+63:       new << (self[i].ord | str[i].ord)
+64:     end
+65: 
+66:     if self.length > str.length
+67:       new << self[min ... self.length]
+68:     elsif self.length < str.length
+69:       new << str[min ... str.length]
+70:     end
+71: 
+72:     new
+73:   end
+
+ +
+ + + + +
+ + +
+ + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/StringError.html b/code_ruby/Maasha/lib/doc/StringError.html new file mode 100644 index 0000000..2151699 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/StringError.html @@ -0,0 +1,200 @@ + + + + + + + Class: StringError + + + + + + + + + + + +
+
+
+

+ Home + Classes + Methods +

+
+
+ +
+
+

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+
+ +
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+ +
+ + + +
+

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+ +

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+ +
+ + + + + + + + + + +
+ +
+ + + +
+

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+
+
+ Quicksearch + +
+
+ + + +
+ + +
+
+ +
+

StringError

+ +
+

+Error class for all exceptions to do with String. +

+ +
+ + + + + + + + + + +
+ + +
+ +

Disabled; run with --debug to generate this.

+ +
+ +
+

[Validate]

+

Generated with the Darkfish + Rdoc Generator 1.1.6.

+
+ + + + diff --git a/code_ruby/Maasha/lib/doc/base36_rb.html b/code_ruby/Maasha/lib/doc/base36_rb.html new file mode 100644 index 0000000..5b15245 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/base36_rb.html @@ -0,0 +1,55 @@ + + + + + + + + File: base36.rb [RDoc Documentation] + + + + + + + + + + +
+
+
Last Modified
+
2011-02-11 19:42:32 +0100
+ + +
Requires
+
+
    + +
+
+ + + +
+
+ +
+ +
+

Description

+

+Copyright (C) 2011 Martin A. Hansen. +

+ +
+ +
+ + + diff --git a/code_ruby/Maasha/lib/doc/biopieces_rb.html b/code_ruby/Maasha/lib/doc/biopieces_rb.html new file mode 100644 index 0000000..9757f4c --- /dev/null +++ b/code_ruby/Maasha/lib/doc/biopieces_rb.html @@ -0,0 +1,62 @@ + + + + + + + + File: biopieces.rb [RDoc Documentation] + + + + + + + + + + +
+
+
Last Modified
+
2011-03-19 09:14:44 +0100
+ + +
Requires
+
+
    + +
  • fileutils
    • + +
  • date
    • + +
  • optparse
    • + +
  • open3
    • + +
  • pp
    • + +
+
+ + + +
+
+ +
+ +
+

Description

+ +
+ +
+ + + diff --git a/code_ruby/Maasha/lib/doc/bitarray_rb.html b/code_ruby/Maasha/lib/doc/bitarray_rb.html new file mode 100644 index 0000000..bb50590 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/bitarray_rb.html @@ -0,0 +1,55 @@ + + + + + + + + File: bitarray.rb [RDoc Documentation] + + + + + + + + + + +
+
+
Last Modified
+
2011-03-17 15:02:03 +0100
+ + +
Requires
+
+
    + +
+
+ + + +
+
+ +
+ +
+

Description

+

+Copyright (C) 2007-2011 Martin A. Hansen. +

+ +
+ +
+ + + diff --git a/code_ruby/Maasha/lib/doc/bits_rb.html b/code_ruby/Maasha/lib/doc/bits_rb.html new file mode 100644 index 0000000..2380506 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/bits_rb.html @@ -0,0 +1,55 @@ + + + + + + + + File: bits.rb [RDoc Documentation] + + + + + + + + + + +
+
+
Last Modified
+
2011-03-08 11:37:57 +0100
+ + +
Requires
+
+
    + +
+
+ + + +
+
+ +
+ +
+

Description

+

+Copyright (C) 2007-2011 Martin A. Hansen. +

+ +
+ +
+ + + diff --git a/code_ruby/Maasha/lib/doc/boulder_rb.html b/code_ruby/Maasha/lib/doc/boulder_rb.html new file mode 100644 index 0000000..5416de3 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/boulder_rb.html @@ -0,0 +1,57 @@ + + + + + + + + File: boulder.rb [RDoc Documentation] + + + + + + + + + + +
+
+
Last Modified
+
2011-03-19 09:17:13 +0100
+ + +
Requires
+
+
    + +
  • filesys
    • + +
+
+ + + +
+
+ +
+ +
+

Description

+

+Copyright (C) 2007-2011 Martin A. Hansen. +

+ +
+ +
+ + + diff --git a/code_ruby/Maasha/lib/doc/digest_rb.html b/code_ruby/Maasha/lib/doc/digest_rb.html new file mode 100644 index 0000000..22b22e5 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/digest_rb.html @@ -0,0 +1,57 @@ + + + + + + + + File: digest.rb [RDoc Documentation] + + + + + + + + + + +
+
+
Last Modified
+
2011-03-19 15:41:06 +0100
+ + +
Requires
+
+
    + +
  • seq
    • + +
+
+ + + +
+
+ +
+ +
+

Description

+

+Copyright (C) 2007-2011 Martin A. Hansen. +

+ +
+ +
+ + + diff --git a/code_ruby/Maasha/lib/doc/fasta_rb.html b/code_ruby/Maasha/lib/doc/fasta_rb.html new file mode 100644 index 0000000..1782158 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/fasta_rb.html @@ -0,0 +1,59 @@ + + + + + + + + File: fasta.rb [RDoc Documentation] + + + + + + + + + + +
+
+
Last Modified
+
2011-03-19 09:11:06 +0100
+ + +
Requires
+
+
    + +
  • seq
    • + +
  • filesys
    • + +
+
+ + + +
+
+ +
+ +
+

Description

+

+Copyright (C) 2007-2011 Martin A. Hansen. +

+ +
+ +
+ + + diff --git a/code_ruby/Maasha/lib/doc/fastq_rb.html b/code_ruby/Maasha/lib/doc/fastq_rb.html new file mode 100644 index 0000000..0d97142 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/fastq_rb.html @@ -0,0 +1,59 @@ + + + + + + + + File: fastq.rb [RDoc Documentation] + + + + + + + + + + +
+
+
Last Modified
+
2011-03-19 09:09:52 +0100
+ + +
Requires
+
+
    + +
  • seq
    • + +
  • filesys
    • + +
+
+ + + +
+
+ +
+ +
+

Description

+

+Copyright (C) 2007-2011 Martin A. Hansen. +

+ +
+ +
+ + + diff --git a/code_ruby/Maasha/lib/doc/filesys_rb.html b/code_ruby/Maasha/lib/doc/filesys_rb.html new file mode 100644 index 0000000..7d9ac37 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/filesys_rb.html @@ -0,0 +1,57 @@ + + + + + + + + File: filesys.rb [RDoc Documentation] + + + + + + + + + + +
+
+
Last Modified
+
2011-03-18 22:13:22 +0100
+ + +
Requires
+
+
    + +
  • zlib
    • + +
+
+ + + +
+
+ +
+ +
+

Description

+

+Copyright (C) 2007-2011 Martin A. Hansen. +

+ +
+ +
+ + + diff --git a/code_ruby/Maasha/lib/doc/genbank_rb.html b/code_ruby/Maasha/lib/doc/genbank_rb.html new file mode 100644 index 0000000..7434343 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/genbank_rb.html @@ -0,0 +1,59 @@ + + + + + + + + File: genbank.rb [RDoc Documentation] + + + + + + + + + + +
+
+
Last Modified
+
2011-03-19 09:19:25 +0100
+ + +
Requires
+
+
    + +
  • seq
    • + +
  • filesys
    • + +
+
+ + + +
+
+ +
+ +
+

Description

+

+Copyright (C) 2007-2010 Martin A. Hansen. +

+ +
+ +
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/dev/null +++ b/code_ruby/Maasha/lib/doc/js/quicksearch.js @@ -0,0 +1,114 @@ +/** + * + * JQuery QuickSearch - Hook up a form field to hide non-matching elements. + * $Id: quicksearch.js 53 2009-01-07 02:52:03Z deveiant $ + * + * Author: Michael Granger + * + */ +jQuery.fn.quicksearch = function( target, searchElems, options ) { + // console.debug( "Quicksearch fn" ); + + var settings = { + delay: 250, + clearButton: false, + highlightMatches: false, + focusOnLoad: false, + noSearchResultsIndicator: null + }; + if ( options ) $.extend( settings, options ); + + return jQuery(this).each( function() { + // console.debug( "Creating a new quicksearch on %o for %o", this, searchElems ); + new jQuery.quicksearch( this, searchElems, settings ); + }); +}; + + +jQuery.quicksearch = function( searchBox, searchElems, settings ) { + var timeout; + var boxdiv = $(searchBox).parents('div').eq(0); + + function init() { + setupKeyEventHandlers(); + focusOnLoad(); + }; + + function setupKeyEventHandlers() { + // console.debug( "Hooking up the 'keypress' event to %o", searchBox ); + $(searchBox). + unbind( 'keyup' ). + keyup( function(e) { return onSearchKey( e.keyCode ); }); + $(searchBox). + unbind( 'keypress' ). + keypress( function(e) { + switch( e.which ) { + // Execute the search on Enter, Tab, or Newline + case 9: + case 13: + case 10: + clearTimeout( timeout ); + e.preventDefault(); + doQuickSearch(); + break; + + // Allow backspace + case 8: + return true; + break; + + // Only allow valid search characters + default: + return validQSChar( e.charCode ); + } + }); + }; + + function focusOnLoad() { + if ( !settings.focusOnLoad ) return false; + $(searchBox).focus(); + }; + + function onSearchKey ( code ) { + clearTimeout( timeout ); + // console.debug( "...scheduling search." ); + timeout = setTimeout( doQuickSearch, settings.delay ); + }; + + function validQSChar( code ) { + var c = String.fromCharCode( code ); + return ( + (c == ':') || + (c >= 'a' && c <= 'z') || + (c >= 'A' && c <= 'Z') + ); + }; + + function doQuickSearch() { + var searchText = searchBox.value; + var pat = new RegExp( searchText, "im" ); + var shownCount = 0; + + if ( settings.noSearchResultsIndicator ) { + $('#' + settings.noSearchResultsIndicator).hide(); + } + + // All elements start out hidden + $(searchElems).each( function(index) { + var str = $(this).text(); + + if ( pat.test(str) ) { + shownCount += 1; + $(this).fadeIn(); + } else { + $(this).hide(); + } + }); + + if ( shownCount == 0 && settings.noSearchResultsIndicator ) { + $('#' + settings.noSearchResultsIndicator).slideDown(); + } + }; + + init(); +}; diff --git a/code_ruby/Maasha/lib/doc/js/thickbox-compressed.js b/code_ruby/Maasha/lib/doc/js/thickbox-compressed.js new file mode 100644 index 0000000..3a3fdae --- /dev/null +++ b/code_ruby/Maasha/lib/doc/js/thickbox-compressed.js @@ -0,0 +1,10 @@ +/* + * Thickbox 3 - One Box To Rule Them All. + * By Cody Lindley (http://www.codylindley.com) + * Copyright 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none; +} +:link:hover, +:visited:hover { + border-bottom: 1px dotted #6C8C22; +} + +pre { + background: #ddd; + padding: 0.5em 0; +} + + +/* @group Generic Classes */ + +.initially-hidden { + display: none; +} + +.quicksearch-field { + width: 98%; + background: #ddd; + border: 1px solid #aaa; + height: 1.5em; + -webkit-border-radius: 4px; +} +.quicksearch-field:focus { + background: #f1edba; +} + +.missing-docs { + font-size: 120%; + background: white url(images/wrench_orange.png) no-repeat 4px center; + color: #ccc; + line-height: 2em; + border: 1px solid #d00; + opacity: 1; + padding-left: 20px; + text-indent: 24px; + letter-spacing: 3px; + font-weight: bold; + -webkit-border-radius: 5px; + -moz-border-radius: 5px; +} + +.target-section { + border: 2px solid #dcce90; + border-left-width: 8px; + padding: 0 1em; + background: #fff3c2; +} + +/* @end */ + + +/* @group Index Page, Standalone file pages */ +body.indexpage { + margin: 1em 3em; +} +body.indexpage p, +body.indexpage div, +body.file p { + margin: 1em 0; +} + +.indexpage ul, +.file #documentation ul { + line-height: 160%; + list-style: none; +} +.indexpage ul :link, +.indexpage ul :visited { + font-size: 16px; +} + +.indexpage li, +.file #documentation li { + padding-left: 20px; + background: url(images/bullet_black.png) no-repeat left 4px; +} +.indexpage li.module { + background: url(images/package.png) no-repeat left 4px; +} +.indexpage li.class { + background: url(images/ruby.png) no-repeat left 4px; +} +.indexpage li.file { + background: url(images/page_white_text.png) no-repeat left 4px; +} +.file li p, +.indexpage li p { + margin: 0 0; +} + +/* @end */ + +/* @group Top-Level Structure */ + +.class #metadata, +.file #metadata, +.module #metadata { + float: left; + width: 260px; +} + +.class #documentation, +.file #documentation, +.module #documentation { + margin: 2em 1em 5em 300px; + min-width: 340px; +} + +.file #metadata { + margin: 0.8em; +} + +#validator-badges { + clear: both; + margin: 1em 1em 2em; +} + +/* @end */ + +/* @group Metadata Section */ +#metadata .section { + background-color: #dedede; + -moz-border-radius: 5px; + -webkit-border-radius: 5px; + border: 1px solid #aaa; + margin: 0 8px 16px; + font-size: 90%; + overflow: hidden; +} +#metadata h3.section-header { + margin: 0; + padding: 2px 8px; + background: #ccc; + color: #666; + -moz-border-radius-topleft: 4px; + -moz-border-radius-topright: 4px; + -webkit-border-top-left-radius: 4px; + -webkit-border-top-right-radius: 4px; + border-bottom: 1px solid #aaa; +} +#metadata #home-section h3.section-header { + border-bottom: 0; +} + +#metadata ul, +#metadata dl, +#metadata p { + padding: 8px; + list-style: none; +} + +#file-metadata ul { + padding-left: 28px; + list-style-image: url(images/page_green.png); +} + +dl.svninfo { + color: #666; + margin: 0; +} +dl.svninfo dt { + font-weight: bold; +} + +ul.link-list li { + white-space: nowrap; +} +ul.link-list .type { + font-size: 8px; + text-transform: uppercase; + color: white; + background: #969696; + padding: 2px 4px; + -webkit-border-radius: 5px; +} + +/* @end */ + + +/* @group Project Metadata Section */ +#project-metadata { + margin-top: 3em; +} + +.file #project-metadata { + margin-top: 0em; +} + +#project-metadata .section { + border: 1px solid #aaa; +} +#project-metadata h3.section-header { + border-bottom: 1px solid #aaa; + position: relative; +} +#project-metadata h3.section-header .search-toggle { + position: absolute; + right: 5px; +} + + +#project-metadata form { + color: #777; + background: #ccc; + padding: 8px 8px 16px; + border-bottom: 1px solid #bbb; +} +#project-metadata fieldset { + border: 0; +} + +#no-class-search-results { + margin: 0 auto 1em; + text-align: center; + font-size: 14px; + font-weight: bold; + color: #aaa; +} + +/* @end */ + + +/* @group Documentation Section */ +#description { + font-size: 100%; + color: #333; +} + +#description p { + margin: 1em 0.4em; +} + +#description li p { + margin: 0; +} + +#description ul { + margin-left: 1.5em; +} +#description ul li { + line-height: 1.4em; +} + +#description dl, +#documentation dl { + margin: 8px 1.5em; + border: 1px solid #ccc; +} +#description dl { + font-size: 14px; +} + +#description dt, +#documentation dt { + padding: 2px 4px; + font-weight: bold; + background: #ddd; +} +#description dd, +#documentation dd { + padding: 2px 12px; +} +#description dd + dt, +#documentation dd + dt { + margin-top: 0.7em; +} + +#documentation .section { + font-size: 90%; +} +#documentation h3.section-header { + margin-top: 2em; + padding: 0.75em 0.5em; + background-color: #dedede; + color: #333; + font-size: 150%; + border: 1px solid #bbb; + -moz-border-radius: 3px; + -webkit-border-radius: 3px; +} + +#constants-list > dl, +#attributes-list > dl { + margin: 1em 0 2em; + border: 0; +} +#constants-list > dl dt, +#attributes-list > dl dt { + padding-left: 0; + font-weight: bold; + font-family: Monaco, "Andale Mono"; + background: inherit; +} +#constants-list > dl dt a, +#attributes-list > dl dt a { + color: inherit; +} +#constants-list > dl dd, +#attributes-list > dl dd { + margin: 0 0 1em 0; + padding: 0; + color: #666; +} + +/* @group Method Details */ + +#documentation .method-source-code { + display: none; +} + +#documentation .method-detail { + margin: 0.5em 0; + padding: 0.5em 0; + cursor: pointer; +} +#documentation .method-detail:hover { + background-color: #f1edba; +} +#documentation .method-heading { + position: relative; + padding: 2px 4px 0 20px; + font-size: 125%; + font-weight: bold; + color: #333; + background: url(images/brick.png) no-repeat left bottom; +} +#documentation .method-heading :link, +#documentation .method-heading :visited { + color: inherit; +} +#documentation .method-click-advice { + position: absolute; + top: 2px; + right: 5px; + font-size: 10px; + color: #9b9877; + visibility: hidden; + padding-right: 20px; + line-height: 20px; + background: url(images/zoom.png) no-repeat right top; +} +#documentation .method-detail:hover .method-click-advice { + visibility: visible; +} + +#documentation .method-alias .method-heading { + color: #666; + background: url(images/brick_link.png) no-repeat left bottom; +} + +#documentation .method-description, +#documentation .aliases { + margin: 0 20px; + line-height: 1.2em; + color: #666; +} +#documentation .aliases { + padding-top: 4px; + font-style: italic; + cursor: default; +} +#documentation .method-description p { + padding: 0; +} +#documentation .method-description p + p { + margin-bottom: 0.5em; +} +#documentation .method-description ul { + margin-left: 1.5em; +} + +#documentation .attribute-method-heading { + background: url(images/tag_green.png) no-repeat left bottom; +} +#documentation #attribute-method-details .method-detail:hover { + background-color: transparent; + cursor: default; +} +#documentation .attribute-access-type { + font-size: 60%; + text-transform: uppercase; + vertical-align: super; + padding: 0 2px; +} +/* @end */ + +/* @end */ + + + +/* @group Source Code */ + +div.method-source-code { + background: #262626; + color: #efefef; + margin: 1em; + padding: 0.5em; + border: 1px dashed #999; + overflow: hidden; +} + +div.method-source-code pre { + background: inherit; + padding: 0; + color: white; + overflow: auto; +} + +/* @group Ruby keyword styles */ + +.ruby-constant { color: #7fffd4; background: transparent; } +.ruby-keyword { color: #00ffff; background: transparent; } +.ruby-ivar { color: #eedd82; background: transparent; } +.ruby-operator { color: #00ffee; background: transparent; } +.ruby-identifier { color: #ffdead; background: transparent; } +.ruby-node { color: #ffa07a; background: transparent; } +.ruby-comment { color: #b22222; font-weight: bold; background: transparent; } +.ruby-regexp { color: #ffa07a; background: transparent; } +.ruby-value { color: #7fffd4; background: transparent; } + +/* @end */ +/* @end */ + + +/* @group File Popup Contents */ + +.file #metadata, +.file-popup #metadata { +} + +.file-popup dl { + font-size: 80%; + padding: 0.75em; + background-color: #dedede; + color: #333; + border: 1px solid #bbb; + -moz-border-radius: 3px; + -webkit-border-radius: 3px; +} +.file dt { + font-weight: bold; + padding-left: 22px; + line-height: 20px; + background: url(images/page_white_width.png) no-repeat left top; +} +.file dt.modified-date { + background: url(images/date.png) no-repeat left top; +} +.file dt.requires { + background: url(images/plugin.png) no-repeat left top; +} +.file dt.scs-url { + background: url(images/wrench.png) no-repeat left top; +} + +.file dl dd { + margin: 0 0 1em 0; +} +.file #metadata dl dd ul { + list-style: circle; + margin-left: 20px; + padding-top: 0; +} +.file #metadata dl dd ul li { +} + + +.file h2 { + margin-top: 2em; + padding: 0.75em 0.5em; + background-color: #dedede; + color: #333; + font-size: 120%; + border: 1px solid #bbb; + -moz-border-radius: 3px; + -webkit-border-radius: 3px; +} + +/* @end */ + + + + +/* @group ThickBox Styles */ +#TB_window { + font: 12px Arial, Helvetica, sans-serif; + color: #333333; +} + +#TB_secondLine { + font: 10px Arial, Helvetica, sans-serif; + color:#666666; +} + +#TB_window :link, +#TB_window :visited { color: #666666; } +#TB_window :link:hover, +#TB_window :visited:hover { color: #000; } +#TB_window :link:active, +#TB_window :visited:active { color: #666666; } +#TB_window :link:focus, +#TB_window :visited:focus { color: #666666; } + +#TB_overlay { + position: fixed; + z-index:100; + top: 0px; + left: 0px; + height:100%; + width:100%; +} + +.TB_overlayMacFFBGHack {background: url(images/macFFBgHack.png) repeat;} +.TB_overlayBG { + background-color:#000; + filter:alpha(opacity=75); + -moz-opacity: 0.75; + opacity: 0.75; +} + +* html #TB_overlay { /* ie6 hack */ + position: absolute; + height: expression(document.body.scrollHeight > document.body.offsetHeight ? document.body.scrollHeight : document.body.offsetHeight + 'px'); +} + +#TB_window { + position: fixed; + background: #ffffff; + z-index: 102; + color:#000000; + display:none; + border: 4px solid #525252; + text-align:left; + top:50%; + left:50%; +} + +* html #TB_window { /* ie6 hack */ +position: absolute; +margin-top: expression(0 - parseInt(this.offsetHeight / 2) + (TBWindowMargin = document.documentElement && document.documentElement.scrollTop || document.body.scrollTop) + 'px'); +} + +#TB_window img#TB_Image { + display:block; + margin: 15px 0 0 15px; + border-right: 1px solid #ccc; + border-bottom: 1px solid #ccc; + border-top: 1px solid #666; + border-left: 1px solid #666; +} + +#TB_caption{ + height:25px; + padding:7px 30px 10px 25px; + float:left; +} + +#TB_closeWindow{ + height:25px; + padding:11px 25px 10px 0; + float:right; +} + +#TB_closeAjaxWindow{ + padding:7px 10px 5px 0; + margin-bottom:1px; + text-align:right; + float:right; +} + +#TB_ajaxWindowTitle{ + float:left; + padding:7px 0 5px 10px; + margin-bottom:1px; + font-size: 22px; +} + +#TB_title{ + background-color: #6C8C22; + color: #dedede; + height:40px; +} +#TB_title :link, +#TB_title :visited { + color: white !important; + border-bottom: 1px dotted #dedede; +} + +#TB_ajaxContent{ + clear:both; + padding:2px 15px 15px 15px; + overflow:auto; + text-align:left; + line-height:1.4em; +} + +#TB_ajaxContent.TB_modal{ + padding:15px; +} + +#TB_ajaxContent p{ + padding:5px 0px 5px 0px; +} + +#TB_load{ + position: fixed; + display:none; + height:13px; + width:208px; + z-index:103; + top: 50%; + left: 50%; + margin: -6px 0 0 -104px; /* -height/2 0 0 -width/2 */ +} + +* html #TB_load { /* ie6 hack */ +position: absolute; +margin-top: expression(0 - parseInt(this.offsetHeight / 2) + (TBWindowMargin = document.documentElement && document.documentElement.scrollTop || document.body.scrollTop) + 'px'); +} + +#TB_HideSelect{ + z-index:99; + position:fixed; + top: 0; + left: 0; + background-color:#fff; + border:none; + filter:alpha(opacity=0); + -moz-opacity: 0; + opacity: 0; + height:100%; + width:100%; +} + +* html #TB_HideSelect { /* ie6 hack */ + position: absolute; + height: expression(document.body.scrollHeight > document.body.offsetHeight ? document.body.scrollHeight : document.body.offsetHeight + 'px'); +} + +#TB_iframeContent{ + clear:both; + border:none; + margin-bottom:-1px; + margin-top:1px; + _margin-bottom:1px; +} + +/* @end */ + +/* @group Debugging Section */ + +#debugging-toggle { + text-align: center; +} +#debugging-toggle img { + cursor: pointer; +} + +#rdoc-debugging-section-dump { + display: none; + margin: 0 2em 2em; + background: #ccc; + border: 1px solid #999; +} + + + +/* @end */ diff --git a/code_ruby/Maasha/lib/doc/seq_rb.html b/code_ruby/Maasha/lib/doc/seq_rb.html new file mode 100644 index 0000000..3c50f10 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/seq_rb.html @@ -0,0 +1,59 @@ + + + + + + + + File: seq.rb [RDoc Documentation] + + + + + + + + + + +
+
+
Last Modified
+
2011-03-19 16:29:08 +0100
+ + +
Requires
+
+
    + +
  • amatch
    • + +
  • digest
    • + +
+
+ + + +
+
+ +
+ +
+

Description

+

+Copyright (C) 2007-2011 Martin A. Hansen. +

+ +
+ +
+ + + diff --git a/code_ruby/Maasha/lib/doc/sff_rb.html b/code_ruby/Maasha/lib/doc/sff_rb.html new file mode 100644 index 0000000..294f9a0 --- /dev/null +++ b/code_ruby/Maasha/lib/doc/sff_rb.html @@ -0,0 +1,57 @@ + + + + + + + + File: sff.rb [RDoc Documentation] + + + + + + + + + + +
+
+
Last Modified
+
2011-02-11 19:55:38 +0100
+ + +
Requires
+
+
    + +
  • base36
    • + +
+
+ + + +
+
+ +
+ +
+

Description

+

+Copyright (C) 2011 Martin A. Hansen. +

+ +
+ +
+ + + -- 2.39.5