ms-in_silico 0.2.1 → 0.2.2

data/History

@@ -1,3 +1,7 @@
+== 0.2.2 / 2009-02-24
+
+* updated return value of Fragment
+
 == 0.2.1 / 2009-02-17
 
 Maintenance release with minor updates to use

data/lib/ms/in_silico/digest.rb

@@ -5,7 +5,7 @@ module Ms
     # Ms::InSilico::Digest::manifest digest a protein sequence into peptides
     # Digest a protein sequence into an array of peptides.
     #
-    #   % rap digest MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG --+ dump --no-audit
+    #   % rap digest MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG --: dump --no-audit
     #     I[14:37:55]             digest MIVIGRSIVHP... to 3 peptides
     #   # date: 2008-09-15 14:37:55
     #   ---

data/lib/ms/in_silico/fragment.rb

@@ -3,32 +3,14 @@ require 'ms/in_silico/spectrum'
 module Ms
   module InSilico
     
-    # Ms::InSilico::Fragment::manifest calculates a theoretical ms/ms spectrum
+    # :startdoc::manifest calculates a theoretical ms/ms spectrum
     #
-    # Calculates the parent ion mass and theoretical ms/ms spectrum for a 
-    # peptide sequence.  Configurations allow the specification of one or 
-    # more fragmentation series to include, as well as charge, and intensity.
+    # Calculates the theoretical ms/ms spectrum for a peptide sequence.
+    # Configurations allow the specification of one or more fragmentation series
+    # to include, as well as charge, and intensity.
     #
-    #   % rap fragment TVQQEL --+ dump --no-audit
-    #   # date: 2008-09-15 14:37:55
-    #   --- 
-    #   ms/in_silico/fragment (:...:): 
-    #   - - 717.377745628191
-    #     - - 102.054954926291
-    #       - 132.101905118891
-    #       - 201.123368842491
-    #       - 261.144498215091
-    #       - 329.181946353891
-    #       - 389.203075726491
-    #       - 457.240523865291
-    #       - 517.261653237891
-    #       - 586.283116961491
-    #       - 616.330067154091
-    #       - 699.367180941891
-    #       - 717.377745628191
-    #
-    # In the output, the parent ion mass is given first, followed by an
-    # array of the sorted fragmentation data.
+    # In the output the sorted fragmentation data is given first, followed by
+    # a hash of header data, including the parent ion mass.
     class Fragment < Tap::Task
       
       # A block to validate a config input
@@ -48,6 +30,17 @@ module Ms
       config :sort, true, &c.switch          # sorts the data by mass
       config :unmask, true, &c.switch        # remove masked (negative) masses
       
+      # Constructs a hash of header data pertinent to the spectrum.
+      def headers(spec)
+        {
+          :charge => charge,
+          :parent_ion_mass => spec.parent_ion_mass(charge),
+          :series => series,
+          :nterm => spec.nterm.to_s,
+          :cterm => spec.cterm.to_s
+        }
+      end
+      
       def process(peptide)
         log :fragment, peptide
         spec = spectrum(peptide)
@@ -58,7 +51,7 @@ module Ms
         masses.sort! if sort
         masses.collect! {|m| [m, intensity] } if intensity
         
-        [spec.parent_ion_mass(charge), masses]
+        [masses, headers(spec)]
       end
       
       protected

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: ms-in_silico
 version: !ruby/object:Gem::Version 
-  version: 0.2.1
+  version: 0.2.2
 platform: ruby
 authors: 
 - Simon Chiang
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-02-17 00:00:00 -07:00
+date: 2009-02-24 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency