ms-in_silico 0.2.3 → 0.3.0

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data/History CHANGED
@@ -1,3 +1,7 @@
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+ == 0.3.0 / 2009-05-25
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+
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+ * updates to use tap-0.17.0
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+
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  == 0.2.3 / 2009-03-31
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  * Digest now allows fasta entry inputs
@@ -1,12 +1,12 @@
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+ require 'tap/task'
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  require 'ms/in_silico/digester'
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  module Ms
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  module InSilico
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- # Ms::InSilico::Digest::manifest digest a protein sequence into peptides
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+ # :startdoc::task digest a protein sequence into peptides
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  # Digest a protein sequence into an array of peptides.
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  #
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  # % rap digest MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG --:i dump
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- # I[14:37:55] digest MIVIGRSIVHP... to 3 peptides
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  # MIVIGR
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  # SIVHPYITNEYEPFAAEK
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  # QQILSIMAG
@@ -1,9 +1,10 @@
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+ require 'tap/task'
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  require 'ms/in_silico/spectrum'
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  module Ms
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  module InSilico
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- # :startdoc::manifest calculates a theoretical ms/ms spectrum
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+ # :startdoc::task calculates a theoretical ms/ms spectrum
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  #
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  # Calculates the theoretical ms/ms spectrum for a peptide sequence.
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  # Configurations allow the specification of one or more fragmentation series
@@ -13,18 +14,20 @@ module Ms
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  # a hash of header data, including the parent ion mass.
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  class Fragment < Tap::Task
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- # A block to validate a config input
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- # is an EmpericalFormula.
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- MOLECULE = lambda do |value|
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+ empirical_formula_block = lambda do |value|
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  case value
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  when Molecules::EmpiricalFormula then value
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  else Molecules::EmpiricalFormula.parse(value)
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  end
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  end
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+ # A block to validate a config input
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+ # is an EmpericalFormula.
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+ MOLECULE = empirical_formula_block
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+
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  config :series, ['y', 'b'], &c.list # a list of the series to include
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  config :charge, 1, &c.integer # the charge for the parent ion
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- config :intensity, nil, &c.num_or_nil # a uniform intensity value
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+ config :intensity, nil, &c.numeric_or_nil # a uniform intensity value
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  config :nterm, 'H', &MOLECULE # the n-terminal modification
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  config :cterm, 'OH', &MOLECULE # the c-terminal modification
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  config :sort, true, &c.switch # sorts the data by mass
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: ms-in_silico
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  version: !ruby/object:Gem::Version
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- version: 0.2.3
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+ version: 0.3.0
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  platform: ruby
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  authors:
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  - Simon Chiang
@@ -9,7 +9,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2009-03-31 00:00:00 -06:00
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+ date: 2009-05-25 00:00:00 -06:00
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  default_executable:
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  dependencies:
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  - !ruby/object:Gem::Dependency
@@ -20,7 +20,17 @@ dependencies:
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  requirements:
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 0.12.4
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+ version: 0.17.0
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: tap-test
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+ type: :development
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+ version_requirement:
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+ version_requirements: !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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+ version: 0.1.0
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  version:
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  - !ruby/object:Gem::Dependency
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  name: molecules
@@ -30,7 +40,7 @@ dependencies:
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  requirements:
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 0.1.0
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+ version: 0.2.0
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  version:
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  description:
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  email: simon.a.chiang@gmail.com