ms-core 0.0.2 → 0.0.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.gitignore +9 -0
- data/History +8 -0
- data/MIT-LICENSE +18 -8
- data/README.rdoc +7 -13
- data/Rakefile +43 -0
- data/VERSION +1 -0
- data/lib/ms/data/interleaved.rb +24 -24
- data/lib/ms/data/lazy_io.rb +12 -4
- data/lib/ms/data/lazy_string.rb +3 -3
- data/lib/ms/spectrum.rb +4 -5
- data/spec/ms/calc_spec.rb +30 -0
- data/spec/ms/data_spec.rb +35 -0
- data/spec/ms/support/binary_search_spec.rb +35 -0
- data/spec/spec_helper.rb +5 -0
- metadata +46 -36
data/.gitignore
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data/History
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data/MIT-LICENSE
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@@ -1,13 +1,23 @@
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The MIT License
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Copyright (c) 2006-2010 University of Texas at Austin, Howard Hughes Medical Institute, Reagents of the University of Colorado, and Brigham Young University
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Authored by John T. Prince and Simon Chiang.
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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data/README.rdoc
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=
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= ms-core
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The core mspire[http://
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Generally, This will be used as a
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its own.
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The core mspire[http://jtprince.github.com/mspire] library for working with
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mass spectrometry proteomics data. Generally, This will be used as a
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dependency and won't be all that useful on its own.
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== Description
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* Github[http://github.com/jtprince/ms-core/tree/master]
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* Lighthouse[http://bahuvrihi.lighthouseapp.com/projects/16692-mspire/tickets]
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* {Google Group}[http://groups.google.com/group/mspire-forum]
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== Installation
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-
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% gem install ms-mascot
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% gem install ms-core
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Typically, it will be included as a dependency so it will be installed with
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another gem
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==
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== Copyright
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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/]
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Support:: CU Denver School of Medicine Deans Academic Enrichment Fund, HHMI
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License:: {MIT-Style}[link:files/MIT-LICENSE.html]
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MIT-LICENSE
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data/Rakefile
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require 'rubygems'
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require 'rake'
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require 'jeweler'
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require 'rcov/rcovtask'
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require 'rake/rdoctask'
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require 'rake/testtask'
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Jeweler::Tasks.new do |gem|
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gem.name = "ms-core"
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gem.summary = "basic, shared functionality for mspire libraries"
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gem.description = "basic, shared functionality for mspire libraries"
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gem.email = "jtprince@gmail.com"
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gem.homepage = "http://github.com/jtprince/ms-core/rdoc"
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gem.authors = ["Simon Chiang", "John Prince"]
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# dependencies:
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gem.add_dependency("molecules", ">= 0.2.0")
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# dev dependencies:
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gem.add_development_dependency "spec-more", ">= 0"
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end
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Rake::TestTask.new(:spec) do |spec|
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spec.libs << 'lib' << 'spec'
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spec.pattern = 'spec/**/*_spec.rb'
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spec.verbose = true
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end
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Rcov::RcovTask.new do |spec|
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spec.libs << 'spec'
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spec.pattern = 'spec/**/*_spec.rb'
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spec.verbose = true
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end
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task :default => :spec
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Rake::RDocTask.new do |rdoc|
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version = File.exist?('VERSION') ? File.read('VERSION') : ""
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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = "ms-core #{version}"
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rdoc.rdoc_files.include('README*')
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rdoc.rdoc_files.include('lib/**/*.rb')
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end
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data/VERSION
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1
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0.0.4
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data/lib/ms/data/interleaved.rb
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Interleaved.new(unresolved_data, n=2)
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end
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# An Interleaved data array lazily evaluates it's unresolved data as
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# an interleaved array of n members. The unresolved data is evaluated
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# An Interleaved data array lazily evaluates it's unresolved data as
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# an interleaved array of n members. The unresolved data is evaluated
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# into an array using to_a.
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#
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# i = Ms::Data::Interleaved.new([1,4,2,5,3,6])
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# i.unresolved_data # => [1,4,2,5,3,6]
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# i.unresolved_data # => [1,4,2,5,3,6]
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# i.data # => []
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# i[0] # => [1,2,3]
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# i[1] # => [4,5,6]
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# i[1] # => [4,5,6]
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# i.data # => [[1,2,3], [4,5,6]]
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#
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class Interleaved < Simple
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attr_reader :n
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def initialize(unresolved_data, n=2)
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@n = 2
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super(unresolved_data)
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end
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def [](index)
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resolve.data[index]
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end
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def resolved?
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!@data.empty?
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end
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class Interleaved < Simple
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attr_reader :n
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def initialize(unresolved_data, n=2)
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@n = 2
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super(unresolved_data)
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end
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def [](index)
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resolve.data[index]
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end
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def resolved?
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!@data.empty?
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end
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def resolve
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return(self) if resolved?
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def resolve
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return(self) if resolved?
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unresolved_data = @unresolved_data.to_a
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unless unresolved_data.length % n == 0
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raise ArgumentError, "interleaved data must have a number of elements evenly divisible by n (#{n})"
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end
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n.times { @data << [] }
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map = @data * (unresolved_data.length/n)
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unresolved_data.each_with_index do |item, i|
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map[i] << item
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end
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self
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end
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end
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end
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end
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data/lib/ms/data/lazy_io.rb
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require 'zlib'
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module Ms
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module Data
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# Indicates a decoding format, may be false to unpack string
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# without decoding.
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attr_reader :decode_format
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# boolean: whether the peaks string is zlib compressed
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attr_reader :compressed
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def initialize(io, start_index=io.pos, num_bytes=nil, unpack_format=NETWORK_FLOAT, decode_format=BASE_64)
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def initialize(io, start_index=io.pos, num_bytes=nil, unpack_format=NETWORK_FLOAT, compressed=false, decode_format=BASE_64)
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@io = io
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@start_index = start_index
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@num_bytes = num_bytes
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@unpack_format = unpack_format
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@compressed = compressed
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@decode_format = decode_format
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end
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def reset
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@array = nil
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end
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# Reads string and unpacks using decode_format and unpack_code. The
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# array is cached internally; to re-read the array, use reset.
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def to_a
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@array
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return @array if @array
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decoded = decode_format ? string.unpack(decode_format)[0] : string
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uncompressed = @compressed ? Zlib::Inflate.inflate(decoded) : decoded
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uncompressed.unpack(unpack_format)
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end
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end
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end
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end
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data/lib/ms/data/lazy_string.rb
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# LazyString is a LazyIO initialized from a string, which is converted into
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# a StringIO.
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class LazyString < LazyIO
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def initialize(string, unpack_format=NETWORK_FLOAT, decode_format=BASE_64)
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super(StringIO.new(string), 0, string.length, unpack_format, decode_format)
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def initialize(string, unpack_format=NETWORK_FLOAT, compression=false, decode_format=BASE_64)
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super(StringIO.new(string), 0, string.length, unpack_format, compression, decode_format)
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end
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end
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end
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end
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end
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data/lib/ms/spectrum.rb
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# The underlying data store.
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attr_reader :data
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#
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def initialize(data
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# data takes an array: [mzs, intensities]
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# @return [Ms::Spectrum]
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# @param [Array] data two element array of mzs and intensities
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def initialize(data)
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@data = data
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@headers = headers
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end
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def self.from_peaks(ar_of_doublets)
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require File.dirname(__FILE__) + "/../spec_helper.rb"
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require 'ms/calc'
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describe 'Ms::Calc - calculating ppm tolerances' do
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extend Ms::Calc
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it "returns the ppm tolerance at the specified mass, ppm" do
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ppm_tol_at(100, 100).is 0.01
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ppm_tol_at(1000, 100).is 0.1
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ppm_tol_at(1000, 10).is 0.01
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end
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it "works for any numeric inputs" do
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ppm_tol_at(100, 100).is 0.01
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ppm_tol_at(100.0, 100.0).is 0.01
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ppm_tol_at(1e2, 1e2).is 0.01
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end
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it "should return a span of ppm_tol_at centered on the specified mass" do
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ppm_span_at(100, 100).is [99.99, 100.01]
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ppm_span_at(1000, 100).is [999.9, 1000.1]
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ppm_span_at(1000, 10).is [999.99, 1000.01]
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end
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it "should work for any numeric inputs" do
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ppm_span_at(100, 100).is [99.99, 100.01]
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ppm_span_at(100.0, 100.0).is [99.99, 100.01]
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ppm_span_at(1e2, 1e2).is [99.99, 100.01]
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end
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end
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require File.dirname(__FILE__) + "/../spec_helper.rb"
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require 'ms/data'
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describe "Data.new" do
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it "satisfies documentation" do
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s = Ms::Data.new([[1,2,3], [4,5,6]], :simple)
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s.resolve.data.is [[1,2,3], [4,5,6]]
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t = Ms::Data.new([[1,4],[2,5],[3,6]], :transposed)
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t.resolve.data.is [[1,2,3], [4,5,6]]
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i = Ms::Data.new([1,4,2,5,3,6], :interleaved)
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i.resolve.data.is [[1,2,3], [4,5,6]]
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str = [[1,4,2,5,3,6].pack("g*")].pack("m")
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unresolved_data = Ms::Data::LazyString.new(str)
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i = Ms::Data.new(unresolved_data, :interleaved)
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i.resolve.data.is [[1,2,3], [4,5,6]]
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end
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it "should return a new data of the specified type" do
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data = Ms::Data.new([[1,2,3], [4,5,6]])
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data.class.is Ms::Data::Simple
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data = Ms::Data.new([[1,2,3], [4,5,6]], :simple)
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data.class.is Ms::Data::Simple
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data = Ms::Data.new([1,4,2,5,3,6], :interleaved)
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data.class.is Ms::Data::Interleaved
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data = Ms::Data.new([[1,4],[2,5],[3,6]], :transposed)
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data.class.is Ms::Data::Transposed
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end
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end
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require File.dirname(__FILE__) + "/../../spec_helper.rb"
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require 'ms/support/binary_search'
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describe 'binary searching' do
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extend Ms::Support::BinarySearch
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it "satisfies documentation" do
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search_first(%w(a b c c c d e f)) {|x| x <=> "c"}.is 2
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search_last(%w(a b c c c d e f)) {|x| x <=> "c"}.is 4
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search_first(%w(a b c e f)) {|x| x <=> "c"}.is 2
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search_first(%w(a b e f)) {|x| x <=> "c"}.is nil
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search_last(%w(a b e f)) {|x| x <=> "c"}.is nil
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search_lower_boundary(%w(a b e f)) {|x| x <=> "c"}.is 2
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search_upper_boundary(%w(a b e f)) {|x| x <=> "c"}.is 2
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search_range(%w(a b c c c d e f)) {|x| x <=> "c"}.is(2...5)
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search_range(%w(a b c d e f)) {|x| x <=> "c"}.is(2...3)
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search_range(%w(a b d e f)) {|x| x <=> "c"}.is(2...2)
|
18
|
+
end
|
19
|
+
|
20
|
+
it "is fast" do
|
21
|
+
start = Time.now
|
22
|
+
if ENV['BENCHMARK']
|
23
|
+
Benchmark.bm(25) do |x|
|
24
|
+
array = (0..100000).to_a
|
25
|
+
|
26
|
+
x.report("100k/1kx search_range") do
|
27
|
+
1000.times do
|
28
|
+
search_range(array) {|x| x <=> 88 }
|
29
|
+
end
|
30
|
+
end
|
31
|
+
end
|
32
|
+
end
|
33
|
+
true.is true
|
34
|
+
end
|
35
|
+
end
|
data/spec/spec_helper.rb
ADDED
metadata
CHANGED
@@ -1,7 +1,12 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: ms-core
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
|
4
|
+
prerelease: false
|
5
|
+
segments:
|
6
|
+
- 0
|
7
|
+
- 0
|
8
|
+
- 4
|
9
|
+
version: 0.0.4
|
5
10
|
platform: ruby
|
6
11
|
authors:
|
7
12
|
- Simon Chiang
|
@@ -10,54 +15,50 @@ autorequire:
|
|
10
15
|
bindir: bin
|
11
16
|
cert_chain: []
|
12
17
|
|
13
|
-
date:
|
18
|
+
date: 2010-07-08 00:00:00 -06:00
|
14
19
|
default_executable:
|
15
20
|
dependencies:
|
16
21
|
- !ruby/object:Gem::Dependency
|
17
22
|
name: molecules
|
18
|
-
|
19
|
-
|
20
|
-
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
prerelease: false
|
24
|
+
requirement: &id001 !ruby/object:Gem::Requirement
|
21
25
|
requirements:
|
22
26
|
- - ">="
|
23
27
|
- !ruby/object:Gem::Version
|
28
|
+
segments:
|
29
|
+
- 0
|
30
|
+
- 2
|
31
|
+
- 0
|
24
32
|
version: 0.2.0
|
25
|
-
|
33
|
+
type: :runtime
|
34
|
+
version_requirements: *id001
|
26
35
|
- !ruby/object:Gem::Dependency
|
27
|
-
name:
|
28
|
-
|
29
|
-
|
30
|
-
version_requirements: !ruby/object:Gem::Requirement
|
36
|
+
name: spec-more
|
37
|
+
prerelease: false
|
38
|
+
requirement: &id002 !ruby/object:Gem::Requirement
|
31
39
|
requirements:
|
32
40
|
- - ">="
|
33
41
|
- !ruby/object:Gem::Version
|
34
|
-
|
35
|
-
|
36
|
-
|
37
|
-
name: minitest
|
42
|
+
segments:
|
43
|
+
- 0
|
44
|
+
version: "0"
|
38
45
|
type: :development
|
39
|
-
|
40
|
-
|
41
|
-
|
42
|
-
- - ">="
|
43
|
-
- !ruby/object:Gem::Version
|
44
|
-
version: 1.3.0
|
45
|
-
version:
|
46
|
-
description:
|
47
|
-
email:
|
48
|
-
- jtprince@gmail.com
|
46
|
+
version_requirements: *id002
|
47
|
+
description: basic, shared functionality for mspire libraries
|
48
|
+
email: jtprince@gmail.com
|
49
49
|
executables: []
|
50
50
|
|
51
51
|
extensions: []
|
52
52
|
|
53
53
|
extra_rdoc_files:
|
54
54
|
- README.rdoc
|
55
|
-
- MIT-LICENSE
|
56
|
-
- History
|
57
55
|
files:
|
56
|
+
- .gitignore
|
57
|
+
- History
|
58
58
|
- MIT-LICENSE
|
59
59
|
- README.rdoc
|
60
|
-
-
|
60
|
+
- Rakefile
|
61
|
+
- VERSION
|
61
62
|
- lib/ms.rb
|
62
63
|
- lib/ms/calc.rb
|
63
64
|
- lib/ms/data.rb
|
@@ -74,33 +75,42 @@ files:
|
|
74
75
|
- lib/ms/mass/aa.rb
|
75
76
|
- lib/ms/spectrum.rb
|
76
77
|
- lib/ms/support/binary_search.rb
|
78
|
+
- spec/ms/calc_spec.rb
|
79
|
+
- spec/ms/data_spec.rb
|
80
|
+
- spec/ms/support/binary_search_spec.rb
|
81
|
+
- spec/spec_helper.rb
|
77
82
|
has_rdoc: true
|
78
|
-
homepage: http://
|
83
|
+
homepage: http://github.com/jtprince/ms-core/rdoc
|
79
84
|
licenses: []
|
80
85
|
|
81
86
|
post_install_message:
|
82
|
-
rdoc_options:
|
83
|
-
|
87
|
+
rdoc_options:
|
88
|
+
- --charset=UTF-8
|
84
89
|
require_paths:
|
85
90
|
- lib
|
86
91
|
required_ruby_version: !ruby/object:Gem::Requirement
|
87
92
|
requirements:
|
88
93
|
- - ">="
|
89
94
|
- !ruby/object:Gem::Version
|
95
|
+
segments:
|
96
|
+
- 0
|
90
97
|
version: "0"
|
91
|
-
version:
|
92
98
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
93
99
|
requirements:
|
94
100
|
- - ">="
|
95
101
|
- !ruby/object:Gem::Version
|
102
|
+
segments:
|
103
|
+
- 0
|
96
104
|
version: "0"
|
97
|
-
version:
|
98
105
|
requirements: []
|
99
106
|
|
100
|
-
rubyforge_project:
|
101
|
-
rubygems_version: 1.3.
|
107
|
+
rubyforge_project:
|
108
|
+
rubygems_version: 1.3.6
|
102
109
|
signing_key:
|
103
110
|
specification_version: 3
|
104
111
|
summary: basic, shared functionality for mspire libraries
|
105
|
-
test_files:
|
106
|
-
|
112
|
+
test_files:
|
113
|
+
- spec/ms/support/binary_search_spec.rb
|
114
|
+
- spec/ms/calc_spec.rb
|
115
|
+
- spec/ms/data_spec.rb
|
116
|
+
- spec/spec_helper.rb
|