ms-core 0.0.14 → 0.0.16

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Files changed (4) hide show
  1. data/VERSION +1 -1
  2. data/lib/io/bookmark.rb +13 -0
  3. data/lib/ms/mass/aa.rb +78 -85
  4. metadata +4 -3
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.0.14
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+ 0.0.16
data/lib/io/bookmark.rb ADDED
@@ -0,0 +1,13 @@
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+
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+ class IO
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+ # saves the position and returns to it after the block
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+ # is executed. Returns the block's reply. if rewind, io.rewind is called
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+ # before handing the io object to the block.
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+ def bookmark(rewind=false, &block)
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+ start = self.pos
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+ self.rewind if rewind
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+ reply = block.call(self)
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+ self.pos = start
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+ reply
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+ end
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+ end
data/lib/ms/mass/aa.rb CHANGED
@@ -1,5 +1,3 @@
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- require 'yaml'
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-
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  require 'ms/mass'
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  module Ms
@@ -26,87 +24,82 @@ module Ms
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  # library for more serious work with masses.
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  module AA
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- yaml = <<-END
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- ---
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- avg:
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- "*": 118.88603
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- A: 71.0779
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- B: 172.1405
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- C: 103.1429
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- D: 115.0874
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- E: 129.11398
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- F: 147.17386
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- G: 57.05132
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- H: 137.13928
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- I: 113.15764
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- K: 128.17228
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- L: 113.15764
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- M: 131.19606
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- N: 114.10264
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- O: 211.28076
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- P: 97.11518
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- Q: 128.12922
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- R: 156.18568
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- S: 87.0773
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- T: 101.10388
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- U: 150.0379
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- V: 99.13106
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- W: 186.2099
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- X: 118.88603
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- Y: 163.17326
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- Z: 128.6231
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- mono:
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- "*": 118.805716
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- A: 71.0371137878
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- B: 172.048405
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- C: 103.0091844778
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- D: 115.026943032
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- E: 129.0425930962
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- F: 147.0684139162
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- G: 57.0214637236
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- H: 137.0589118624
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- I: 113.0840639804
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- K: 128.0949630177
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- L: 113.0840639804
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- M: 131.0404846062
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- N: 114.0429274472
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- O: 211.1446528645
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- P: 97.052763852
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- Q: 128.0585775114
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- R: 156.1011110281
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- S: 87.0320284099
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- T: 101.0476784741
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- U: 150.9536355878
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- V: 99.0684139162
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- W: 186.0793129535
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- X: 118.805716
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- Y: 163.0633285383
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- Z: 128.550585
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- END
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-
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-
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- embedded_mass_hashes = YAML.load(yaml)
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- # amino_acids keys as strings, monoisotopic masses
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- MONO_STRING = embedded_mass_hashes['mono']
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- # amino_acids keys as symbols, monoisotopic masses
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- MONO_SYM = Hash[MONO_STRING.map {|aa,mass| [aa.to_sym, mass] } ]
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-
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  # amino_acids keys as strings, average masses
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- AVG_STRING = embedded_mass_hashes['avg']
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- # amino_acids keys as symbols, average masses
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- AVG_SYM = Hash[AVG_STRING.map {|aa,mass| [aa.to_sym, mass] } ]
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-
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- # Monoisotopic amino acid masses keyed as symbols and also strings (all
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- # upper case). Also includes Ms::Mass::MONO for things like protons ('h+')
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- MONO = MONO_SYM.merge(MONO_STRING).merge(Ms::Mass::MONO)
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- # Average amino acid masses keyed as symbols and also strings (all
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- # uppder case). Also includes Ms::Mass::AVG for things like protons ('h+')
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- AVG = AVG_SYM.merge(AVG_STRING).merge(Ms::Mass::AVG)
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-
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- ###########################################################################
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- # This section is broken in 1.9 (ruby-units fault), so we generate the
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- # data and include it.
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- ###########################################################################
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+ AVG_STRING = {
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+ "*"=>118.88603,
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+ "A"=>71.0779,
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+ "B"=>172.1405,
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+ "C"=>103.1429,
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+ "D"=>115.0874,
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+ "E"=>129.11398,
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+ "F"=>147.17386,
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+ "G"=>57.05132,
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+ "H"=>137.13928,
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+ "I"=>113.15764,
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+ "K"=>128.17228,
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+ "L"=>113.15764,
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+ "M"=>131.19606,
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+ "N"=>114.10264,
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+ "O"=>211.28076,
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+ "P"=>97.11518,
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+ "Q"=>128.12922,
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+ "R"=>156.18568,
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+ "S"=>87.0773,
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+ "T"=>101.10388,
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+ "U"=>150.0379,
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+ "V"=>99.13106,
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+ "W"=>186.2099,
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+ "X"=>118.88603,
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+ "Y"=>163.17326,
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+ "Z"=>128.6231
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+ }
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+ # amino_acids keys as strings, monoisotopic masses
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+ MONO_STRING = {
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+ "*"=>118.805716,
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+ "A"=>71.0371137878,
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+ "B"=>172.048405,
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+ "C"=>103.0091844778,
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+ "D"=>115.026943032,
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+ "E"=>129.0425930962,
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+ "F"=>147.0684139162,
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+ "G"=>57.0214637236,
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+ "H"=>137.0589118624,
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+ "I"=>113.0840639804,
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+ "K"=>128.0949630177,
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+ "L"=>113.0840639804,
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+ "M"=>131.0404846062,
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+ "N"=>114.0429274472,
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+ "O"=>211.1446528645,
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+ "P"=>97.052763852,
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+ "Q"=>128.0585775114,
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+ "R"=>156.1011110281,
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+ "S"=>87.0320284099,
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+ "T"=>101.0476784741,
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+ "U"=>150.9536355878,
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+ "V"=>99.0684139162,
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+ "W"=>186.0793129535,
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+ "X"=>118.805716,
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+ "Y"=>163.0633285383,
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+ "Z"=>128.550585}
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+ }
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+
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+ # amino_acids keys as symbols, monoisotopic masses
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+ MONO_SYM = Hash[MONO_STRING.map {|aa,mass| [aa.to_sym, mass] } ]
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+
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+ # amino_acids keys as symbols, average masses
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+ AVG_SYM = Hash[AVG_STRING.map {|aa,mass| [aa.to_sym, mass] } ]
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+
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+ # Monoisotopic amino acid masses keyed as symbols and also strings (all
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+ # upper case). Also includes Ms::Mass::MONO for things like protons ('h+')
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+ MONO = MONO_SYM.merge(MONO_STRING).merge(Ms::Mass::MONO)
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+ # Average amino acid masses keyed as symbols and also strings (all
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+ # uppder case). Also includes Ms::Mass::AVG for things like protons ('h+')
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+ AVG = AVG_SYM.merge(AVG_STRING).merge(Ms::Mass::AVG)
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+
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+ ###########################################################################
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+ # This section is broken in 1.9 (ruby-units fault), so we generate the
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+ # data and include it.
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+ ###########################################################################
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  =begin
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  # These are included here to offer maximum functionality
@@ -172,9 +165,9 @@ module Ms
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  =end
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- ###########################################################################
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- # End fudge
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- ###########################################################################
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+ ###########################################################################
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+ # End fudge
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+ ###########################################################################
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  end
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  end
metadata CHANGED
@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
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  segments:
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  - 0
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  - 0
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- - 14
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- version: 0.0.14
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+ - 16
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+ version: 0.0.16
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  platform: ruby
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  authors:
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  - John T. Prince
@@ -108,6 +108,7 @@ files:
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  - lib/cv.rb
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  - lib/cv/description.rb
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  - lib/cv/param.rb
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+ - lib/io/bookmark.rb
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  - lib/ms.rb
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  - lib/ms/calc.rb
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  - lib/ms/data.rb
@@ -143,7 +144,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  requirements:
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  - - ">="
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  - !ruby/object:Gem::Version
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- hash: 1895205922860773162
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+ hash: 4415238762267398352
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  segments:
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  - 0
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  version: "0"