ms-in_silico 0.2.3 → 0.3.0

data/History

@@ -1,3 +1,7 @@
+== 0.3.0 / 2009-05-25
+
+* updates to use tap-0.17.0
+
 == 0.2.3 / 2009-03-31
 
 * Digest now allows fasta entry inputs

data/lib/ms/in_silico/digest.rb

@@ -1,12 +1,12 @@
+require 'tap/task'
 require 'ms/in_silico/digester'
 
 module Ms
   module InSilico
-    # Ms::InSilico::Digest::manifest digest a protein sequence into peptides
+    # :startdoc::task digest a protein sequence into peptides
     # Digest a protein sequence into an array of peptides.
     #
     #   % rap digest MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG --:i dump
-    #     I[14:37:55]             digest MIVIGRSIVHP... to 3 peptides
     #   MIVIGR
     #   SIVHPYITNEYEPFAAEK
     #   QQILSIMAG

data/lib/ms/in_silico/fragment.rb

@@ -1,9 +1,10 @@
+require 'tap/task'
 require 'ms/in_silico/spectrum'
 
 module Ms
   module InSilico
     
-    # :startdoc::manifest calculates a theoretical ms/ms spectrum
+    # :startdoc::task calculates a theoretical ms/ms spectrum
     #
     # Calculates the theoretical ms/ms spectrum for a peptide sequence.
     # Configurations allow the specification of one or more fragmentation series
@@ -13,18 +14,20 @@ module Ms
     # a hash of header data, including the parent ion mass.
     class Fragment < Tap::Task
       
-      # A block to validate a config input
-      # is an EmpericalFormula.
-      MOLECULE = lambda do |value|
+      empirical_formula_block = lambda do |value|
         case value
         when Molecules::EmpiricalFormula then value
         else Molecules::EmpiricalFormula.parse(value)
         end
       end
       
+      # A block to validate a config input
+      # is an EmpericalFormula.
+      MOLECULE = empirical_formula_block
+      
       config :series, ['y', 'b'], &c.list    # a list of the series to include
       config :charge, 1, &c.integer          # the charge for the parent ion
-      config :intensity, nil, &c.num_or_nil  # a uniform intensity value
+      config :intensity, nil, &c.numeric_or_nil  # a uniform intensity value
       config :nterm, 'H', &MOLECULE          # the n-terminal modification
       config :cterm, 'OH', &MOLECULE         # the c-terminal modification
       config :sort, true, &c.switch          # sorts the data by mass

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: ms-in_silico
 version: !ruby/object:Gem::Version 
-  version: 0.2.3
+  version: 0.3.0
 platform: ruby
 authors: 
 - Simon Chiang
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-03-31 00:00:00 -06:00
+date: 2009-05-25 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -20,7 +20,17 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.12.4
+        version: 0.17.0
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: tap-test
+  type: :development
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.1.0
     version: 
 - !ruby/object:Gem::Dependency 
   name: molecules
@@ -30,7 +40,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.1.0
+        version: 0.2.0
     version: 
 description: 
 email: simon.a.chiang@gmail.com