ms-core 0.0.2 → 0.0.4

data/.gitignore

@@ -0,0 +1,9 @@
+.DS_Store
+pkg/
+rdoc/
+backup/
+config/
+data/
+doc/
+*.swp
+*.gemspec

data/History

@@ -1,3 +1,11 @@
+== version 0.0.3
+
+* switched specs to spec/more
+* added ability to decompress mzxml data
+
+== version 0.0.2
+
+* round function in Ms::Calc
 
 == version 0.0.1
 

data/MIT-LICENSE

@@ -1,13 +1,23 @@
-Copyright (c) 2006, The University of Texas at Austin("U.T. Austin"). All rights reserved.  
+The MIT License
 
-Software by John T. Prince under the direction of Edward M. Marcotte.
+Copyright (c) 2006-2010 University of Texas at Austin, Howard Hughes Medical Institute, Reagents of the University of Colorado, and Brigham Young University
 
-By using this software the USER indicates that he or she has read, understood and will comply with the following:
+Authored by John T. Prince and Simon Chiang.
 
-U. T. Austin hereby grants USER permission to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of this software and its documentation for any purpose and without fee, provided that a full copy of this notice is included with the software and its documentation.
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-Title to copyright this software and its associated documentation shall at all times remain with U. T. Austin. No right is granted to use in advertising, publicity or otherwise any trademark, service mark, or the name of U. T. Austin.
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
 
-This software and any associated documentation are provided "as is," and U. T. AUSTIN MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESSED OR IMPLIED, INCLUDING THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT USE OF THE SOFTWARE, MODIFICATIONS, OR ASSOCIATED DOCUMENTATION WILL NOT INFRINGE ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER INTELLECTUAL PROPERTY RIGHTS OF A THIRD PARTY. U. T. Austin, The University of Texas System, its Regents, officers, and employees shall not be liable under any circumstances for any direct, indirect, special, incidental, or consequential damages with respect to any claim by USER or any third party on account of or arising from the use, or inability to use, this software or its associated documentation, even if U. T. Austin has been advised of the possibility of those damages.
-
-Submit software operation questions to: Edward M. Marcotte, Department of Chemistry and Biochemistry, U. T. Austin, Austin, Texas 78712.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.rdoc

@@ -1,27 +1,21 @@
-= {ms-core}[http://mspire.rubyforge.org/projects/ms-core]
+= ms-core
 
-The core mspire[http://mspire.rubyforge.org] library for working with mass spectrometry proteomics data.
-Generally, This will be used as a dependency and won't be all that useful on
-its own.
+The core mspire[http://jtprince.github.com/mspire] library for working with
+mass spectrometry proteomics data.  Generally, This will be used as a
+dependency and won't be all that useful on its own.
 
 == Description
 
 * Github[http://github.com/jtprince/ms-core/tree/master]
-* Lighthouse[http://bahuvrihi.lighthouseapp.com/projects/16692-mspire/tickets]
 * {Google Group}[http://groups.google.com/group/mspire-forum]
 
 == Installation
 
-Available as a gem on RubyForge[http://rubyforge.org/projects/mspire].  Use:
-
-  % gem install ms-mascot
+  % gem install ms-core
 
 Typically, it will be included as a dependency so it will be installed with
 another gem 
 
-== Info 
+== Copyright
 
-Copyright (c) 2006-2008, Regents of the University of Colorado and HHMI
-Developers:: {Simon Chiang}[http://bahuvrihi.wordpress.com], {Biomolecular Structure Program}[http://biomol.uchsc.edu/], {Hansen Lab}[http://hsc-proteomics.uchsc.edu/hansenlab/], John Prince, {Edward Marcotte Lab}[http://polaris.icmb.utexas.edu/home.html], {Natalie Ahn Lab}[http://www.colorado.edu/chem/people/ahnn.html], {Howard Hughes Medical Institute}[http://www.hhmi.org/], {BYU Dept. of Chemistry and Biochemistry}[http://www.chem.byu.edu/]
-Support:: CU Denver School of Medicine Deans Academic Enrichment Fund, HHMI
-License:: {MIT-Style}[link:files/MIT-LICENSE.html]
+MIT-LICENSE

data/Rakefile

@@ -0,0 +1,43 @@
+require 'rubygems'
+require 'rake'
+require 'jeweler'
+require 'rcov/rcovtask'
+require 'rake/rdoctask'
+require 'rake/testtask'
+
+Jeweler::Tasks.new do |gem|
+  gem.name = "ms-core"
+  gem.summary = "basic, shared functionality for mspire libraries"
+  gem.description = "basic, shared functionality for mspire libraries"
+ gem.email = "jtprince@gmail.com"
+  gem.homepage = "http://github.com/jtprince/ms-core/rdoc"
+  gem.authors = ["Simon Chiang", "John Prince"]
+  # dependencies:
+  gem.add_dependency("molecules", ">= 0.2.0")
+
+  # dev dependencies:
+  gem.add_development_dependency "spec-more", ">= 0"
+end
+
+Rake::TestTask.new(:spec) do |spec|
+  spec.libs << 'lib' << 'spec'
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.verbose = true
+end
+
+Rcov::RcovTask.new do |spec|
+  spec.libs << 'spec'
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.verbose = true
+end
+
+task :default => :spec
+
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "ms-core #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

@@ -0,0 +1 @@
+0.0.4

data/lib/ms/data/interleaved.rb

@@ -9,51 +9,51 @@ module Ms
       Interleaved.new(unresolved_data, n=2)
     end
     
-    # An Interleaved data array lazily evaluates it's unresolved data as 
-    # an interleaved array of n members.  The unresolved data is evaluated 
+    # An Interleaved data array lazily evaluates it's unresolved data as 
+    # an interleaved array of n members.  The unresolved data is evaluated 
     # into an array using to_a.
     #
     #   i = Ms::Data::Interleaved.new([1,4,2,5,3,6])
-    #   i.unresolved_data    # => [1,4,2,5,3,6]
+    #   i.unresolved_data    # => [1,4,2,5,3,6]
     #   i.data               # => []
     #   i[0]                 # => [1,2,3]
-    #   i[1]                 # => [4,5,6]
+    #   i[1]                 # => [4,5,6]
     #   i.data               # => [[1,2,3], [4,5,6]]
     #
-    class Interleaved < Simple
-      attr_reader :n
-      
-      def initialize(unresolved_data, n=2)
-        @n = 2
-        super(unresolved_data)
-      end
-      
-      def [](index)
-        resolve.data[index]
-      end
-      
-      def resolved?
-        !@data.empty?
-      end
+    class Interleaved < Simple
+      attr_reader :n
+      
+      def initialize(unresolved_data, n=2)
+        @n = 2
+        super(unresolved_data)
+      end
+      
+      def [](index)
+        resolve.data[index]
+      end
+      
+      def resolved?
+        !@data.empty?
+      end
     
-      def resolve
-        return(self) if resolved?
+      def resolve
+        return(self) if resolved?
         
         unresolved_data = @unresolved_data.to_a
         
         unless unresolved_data.length % n == 0
           raise ArgumentError, "interleaved data must have a number of elements evenly divisible by n (#{n})"
         end
-        
+        
         n.times { @data << [] }
         map = @data * (unresolved_data.length/n)
         
         unresolved_data.each_with_index do |item, i|
           map[i] << item
         end
-
+
         self
-      end
+      end
       
     end
   end

data/lib/ms/data/lazy_io.rb

@@ -1,3 +1,5 @@
+require 'zlib'
+
 module Ms
   module Data
     
@@ -40,12 +42,16 @@ module Ms
       # Indicates a decoding format, may be false to unpack string
       # without decoding.
       attr_reader :decode_format
+
+      # boolean: whether the peaks string is zlib compressed
+      attr_reader :compressed
       
-      def initialize(io, start_index=io.pos, num_bytes=nil, unpack_format=NETWORK_FLOAT, decode_format=BASE_64)
+      def initialize(io, start_index=io.pos, num_bytes=nil, unpack_format=NETWORK_FLOAT, compressed=false, decode_format=BASE_64)
         @io = io
         @start_index = start_index
         @num_bytes = num_bytes
         @unpack_format = unpack_format
+        @compressed = compressed
         @decode_format = decode_format
       end
       
@@ -61,13 +67,15 @@ module Ms
       def reset
         @array = nil
       end
-      
+
       # Reads string and unpacks using decode_format and unpack_code.  The
       # array is cached internally; to re-read the array, use reset.
       def to_a
-        @array ||= (decode_format ? string.unpack(decode_format)[0] : string).unpack(unpack_format)
+        return @array if @array
+        decoded = decode_format ?  string.unpack(decode_format)[0] : string
+        uncompressed = @compressed ? Zlib::Inflate.inflate(decoded) : decoded
+        uncompressed.unpack(unpack_format)
       end
-
     end
   end
 end

data/lib/ms/data/lazy_string.rb

@@ -7,9 +7,9 @@ module Ms
     # LazyString is a LazyIO initialized from a string, which is converted into
     # a StringIO.
     class LazyString < LazyIO
-      def initialize(string, unpack_format=NETWORK_FLOAT, decode_format=BASE_64)
-        super(StringIO.new(string), 0, string.length, unpack_format, decode_format)
+      def initialize(string, unpack_format=NETWORK_FLOAT, compression=false, decode_format=BASE_64)
+        super(StringIO.new(string), 0, string.length, unpack_format, compression, decode_format)
       end
     end
   end
-end
+end

data/lib/ms/spectrum.rb

@@ -5,12 +5,11 @@ module Ms
     # The underlying data store.
     attr_reader :data
     
-    # Associated headers
-    attr_reader :headers
-    
-    def initialize(data, headers={})
+    # data takes an array: [mzs, intensities]
+    # @return [Ms::Spectrum]
+    # @param [Array] data two element array of mzs and intensities
+    def initialize(data)
       @data = data
-      @headers = headers
     end
 
     def self.from_peaks(ar_of_doublets)

data/spec/ms/calc_spec.rb

@@ -0,0 +1,30 @@
+require File.dirname(__FILE__) + "/../spec_helper.rb"
+require 'ms/calc'
+
+describe 'Ms::Calc - calculating ppm tolerances' do
+  extend Ms::Calc
+  
+  it "returns the ppm tolerance at the specified mass, ppm" do
+    ppm_tol_at(100, 100).is 0.01
+    ppm_tol_at(1000, 100).is 0.1
+    ppm_tol_at(1000, 10).is 0.01
+  end
+  
+  it "works for any numeric inputs" do
+    ppm_tol_at(100, 100).is 0.01
+    ppm_tol_at(100.0, 100.0).is 0.01
+    ppm_tol_at(1e2, 1e2).is 0.01
+  end
+
+  it "should return a span of ppm_tol_at centered on the specified mass" do
+    ppm_span_at(100, 100).is [99.99, 100.01]
+    ppm_span_at(1000, 100).is [999.9, 1000.1]
+    ppm_span_at(1000, 10).is [999.99, 1000.01]
+  end
+  
+  it "should work for any numeric inputs" do
+    ppm_span_at(100, 100).is [99.99, 100.01]
+    ppm_span_at(100.0, 100.0).is [99.99, 100.01]
+    ppm_span_at(1e2, 1e2).is [99.99, 100.01]
+  end
+end

data/spec/ms/data_spec.rb

@@ -0,0 +1,35 @@
+require File.dirname(__FILE__) + "/../spec_helper.rb"
+require 'ms/data'
+
+describe "Data.new" do
+  it "satisfies documentation" do
+    s = Ms::Data.new([[1,2,3], [4,5,6]], :simple)
+    s.resolve.data.is [[1,2,3], [4,5,6]]
+  
+    t = Ms::Data.new([[1,4],[2,5],[3,6]], :transposed)
+    t.resolve.data.is [[1,2,3], [4,5,6]]
+  
+    i = Ms::Data.new([1,4,2,5,3,6], :interleaved)
+    i.resolve.data.is [[1,2,3], [4,5,6]]
+  
+    str = [[1,4,2,5,3,6].pack("g*")].pack("m")
+    unresolved_data = Ms::Data::LazyString.new(str)
+  
+    i = Ms::Data.new(unresolved_data, :interleaved)
+    i.resolve.data.is [[1,2,3], [4,5,6]]
+  end
+  
+  it "should return a new data of the specified type" do
+    data = Ms::Data.new([[1,2,3], [4,5,6]])
+    data.class.is Ms::Data::Simple
+    
+    data = Ms::Data.new([[1,2,3], [4,5,6]], :simple)
+    data.class.is Ms::Data::Simple
+    
+    data = Ms::Data.new([1,4,2,5,3,6], :interleaved)
+    data.class.is Ms::Data::Interleaved
+    
+    data = Ms::Data.new([[1,4],[2,5],[3,6]], :transposed)
+    data.class.is Ms::Data::Transposed
+  end
+end

data/spec/ms/support/binary_search_spec.rb

@@ -0,0 +1,35 @@
+require File.dirname(__FILE__) + "/../../spec_helper.rb"
+require 'ms/support/binary_search'
+
+describe 'binary searching' do
+  extend Ms::Support::BinarySearch
+  
+  it "satisfies documentation" do
+    search_first(%w(a b c c c d e f)) {|x| x <=> "c"}.is 2
+    search_last(%w(a b c c c d e f)) {|x| x <=> "c"}.is 4
+    search_first(%w(a b c e f)) {|x| x <=> "c"}.is 2
+    search_first(%w(a b e f)) {|x| x <=> "c"}.is nil
+    search_last(%w(a b e f)) {|x| x <=> "c"}.is nil
+    search_lower_boundary(%w(a b e f)) {|x| x <=> "c"}.is 2
+    search_upper_boundary(%w(a b e f)) {|x| x <=> "c"}.is 2
+    search_range(%w(a b c c c d e f)) {|x| x <=> "c"}.is(2...5)
+    search_range(%w(a b c d e f)) {|x| x <=> "c"}.is(2...3)
+    search_range(%w(a b d e f)) {|x| x <=> "c"}.is(2...2)
+  end
+  
+  it "is fast" do
+    start = Time.now
+    if ENV['BENCHMARK']
+      Benchmark.bm(25) do |x|
+        array = (0..100000).to_a
+
+        x.report("100k/1kx search_range") do 
+          1000.times do 
+            search_range(array) {|x| x <=> 88 }
+          end
+        end
+      end
+    end
+    true.is true
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,5 @@
+require 'rubygems'
+require 'spec/more'
+require 'benchmark'
+
+Bacon.summary_on_exit

metadata

@@ -1,7 +1,12 @@
 --- !ruby/object:Gem::Specification 
 name: ms-core
 version: !ruby/object:Gem::Version 
-  version: 0.0.2
+  prerelease: false
+  segments: 
+  - 0
+  - 0
+  - 4
+  version: 0.0.4
 platform: ruby
 authors: 
 - Simon Chiang
@@ -10,54 +15,50 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-09-08 00:00:00 -06:00
+date: 2010-07-08 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: molecules
-  type: :runtime
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        - 2
+        - 0
         version: 0.2.0
-    version: 
+  type: :runtime
+  version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  name: tap
-  type: :development
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
+  name: spec-more
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.11.2
-    version: 
-- !ruby/object:Gem::Dependency 
-  name: minitest
+        segments: 
+        - 0
+        version: "0"
   type: :development
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: 1.3.0
-    version: 
-description: 
-email: 
-- jtprince@gmail.com
+  version_requirements: *id002
+description: basic, shared functionality for mspire libraries
+email: jtprince@gmail.com
 executables: []
 
 extensions: []
 
 extra_rdoc_files: 
 - README.rdoc
-- MIT-LICENSE
-- History
 files: 
+- .gitignore
+- History
 - MIT-LICENSE
 - README.rdoc
-- History
+- Rakefile
+- VERSION
 - lib/ms.rb
 - lib/ms/calc.rb
 - lib/ms/data.rb
@@ -74,33 +75,42 @@ files:
 - lib/ms/mass/aa.rb
 - lib/ms/spectrum.rb
 - lib/ms/support/binary_search.rb
+- spec/ms/calc_spec.rb
+- spec/ms/data_spec.rb
+- spec/ms/support/binary_search_spec.rb
+- spec/spec_helper.rb
 has_rdoc: true
-homepage: http://mspire.rubyforge.org/ms-core/
+homepage: http://github.com/jtprince/ms-core/rdoc
 licenses: []
 
 post_install_message: 
-rdoc_options: []
-
+rdoc_options: 
+- --charset=UTF-8
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      segments: 
+      - 0
       version: "0"
-  version: 
 required_rubygems_version: !ruby/object:Gem::Requirement 
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      segments: 
+      - 0
       version: "0"
-  version: 
 requirements: []
 
-rubyforge_project: mspire
-rubygems_version: 1.3.2
+rubyforge_project: 
+rubygems_version: 1.3.6
 signing_key: 
 specification_version: 3
 summary: basic, shared functionality for mspire libraries
-test_files: []
-
+test_files: 
+- spec/ms/support/binary_search_spec.rb
+- spec/ms/calc_spec.rb
+- spec/ms/data_spec.rb
+- spec/spec_helper.rb