ms-sequest 0.0.20 → 0.0.21

data/Gemfile

@@ -5,7 +5,7 @@ source "http://rubygems.org"
 gem "ms-ident", ">= 0.0.17"
 gem "ms-core", ">= 0.0.14"
 gem "arrayclass", ">= 0.1.0"
-gem "ms-msrun", ">= 0.3.3"
+#gem "ms-msrun", ">= 0.3.3"
 gem "trollop", "~> 1.16"
 
 # Add dependencies to develop your gem here.

data/Gemfile.lock

@@ -16,12 +16,7 @@ GEM
       andand
       ms-core (>= 0.0.12)
       nokogiri
-    ms-msrun (0.3.3)
-      ms-core (>= 0.0.3)
-      narray
-      nokogiri
     ms-testdata (0.1.1)
-    narray (0.5.9.9)
     nokogiri (1.4.4)
     rake (0.8.7)
     rcov (0.9.9)
@@ -38,7 +33,6 @@ DEPENDENCIES
   jeweler (~> 1.5.2)
   ms-core (>= 0.0.14)
   ms-ident (>= 0.0.17)
-  ms-msrun (>= 0.3.3)
   ms-testdata (>= 0.1.1)
   rcov
   spec-more

data/VERSION

@@ -1 +1 @@
-0.0.20
+0.0.21

data/lib/ms/sequest/srf/pepxml.rb

@@ -2,7 +2,7 @@ require 'ms/ident/pepxml'
 require 'ms/ident/pepxml/spectrum_query'
 require 'ms/ident/pepxml/search_result'
 require 'ms/ident/pepxml/search_hit'
-require 'ms/msrun'
+#require 'ms/msrun'
 require 'ms/sequest/srf'
 require 'ms/sequest/pepxml'
 
@@ -138,14 +138,15 @@ class Ms::Sequest::Srf
 
       scan_to_ret_time = 
         if opt[:retention_times]
-          mz_file = Dir[File.join(opt[:mz_dir], srf.base_name_noext + opt[:raw_data].first)].first
-          if mz_file
-            Ms::Msrun.scans_to_times(mz_file) 
-          else
-            warn "turning retention_times off since no valid mz[X]ML file was found!!!"
-            opt[:retention_times] = false
-            nil
-          end
+          raise NotImplementedError, "will implement shortly"
+          #mz_file = Dir[File.join(opt[:mz_dir], srf.base_name_noext + opt[:raw_data].first)].first
+          #if mz_file
+          #  Ms::Msrun.scans_to_times(mz_file) 
+          #else
+          #  warn "turning retention_times off since no valid mz[X]ML file was found!!!"
+          #  opt[:retention_times] = false
+          #  nil
+          #end
         end
 
       summary_xml_filename = srf.base_name_noext + '.xml'

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 20
-  version: 0.0.20
+  - 21
+  version: 0.0.21
 platform: ruby
 authors: 
 - John T. Prince
@@ -62,24 +62,9 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: ms-msrun
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        - 3
-        - 3
-        version: 0.3.3
-  type: :runtime
-  prerelease: false
-  version_requirements: *id004
 - !ruby/object:Gem::Dependency 
   name: trollop
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -90,10 +75,10 @@ dependencies:
         version: "1.16"
   type: :runtime
   prerelease: false
-  version_requirements: *id005
+  version_requirements: *id004
 - !ruby/object:Gem::Dependency 
   name: ms-testdata
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -105,10 +90,10 @@ dependencies:
         version: 0.1.1
   type: :development
   prerelease: false
-  version_requirements: *id006
+  version_requirements: *id005
 - !ruby/object:Gem::Dependency 
   name: spec-more
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  requirement: &id006 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -118,10 +103,10 @@ dependencies:
         version: "0"
   type: :development
   prerelease: false
-  version_requirements: *id007
+  version_requirements: *id006
 - !ruby/object:Gem::Dependency 
   name: bundler
-  requirement: &id008 !ruby/object:Gem::Requirement 
+  requirement: &id007 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -133,10 +118,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *id008
+  version_requirements: *id007
 - !ruby/object:Gem::Dependency 
   name: jeweler
-  requirement: &id009 !ruby/object:Gem::Requirement 
+  requirement: &id008 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -148,10 +133,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *id009
+  version_requirements: *id008
 - !ruby/object:Gem::Dependency 
   name: rcov
-  requirement: &id010 !ruby/object:Gem::Requirement 
+  requirement: &id009 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -161,7 +146,7 @@ dependencies:
         version: "0"
   type: :development
   prerelease: false
-  version_requirements: *id010
+  version_requirements: *id009
 description: reads .SRF, .SQT and supports conversions
 email: jtprince@gmail.com
 executables: 
@@ -232,7 +217,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 2449106576710684635
+      hash: -4159888076227295252
       segments: 
       - 0
       version: "0"