mzml 0.2.2 → 0.3.0

data/test/test_mzml-helper.rb

@@ -0,0 +1,15 @@
+require 'test/unit'
+require 'mzml'
+
+class TestMzMLHelper < Test::Unit::TestCase
+  def setup
+    # set the input file name
+    @file = File.join(File.dirname(__FILE__),  "sample.mzML")
+    @compressed = File.join(File.dirname(__FILE__),  "sample.compressed.mzML")
+    @mgf = File.join(File.dirname(__FILE__),  "sample.mgf")
+  end
+
+  def test_canary
+    pass
+  end
+end

data/test/test_mzml.rb

@@ -0,0 +1,94 @@
+require 'test/unit'
+require 'mzml'
+
+class TestMzML < Test::Unit::TestCase
+
+  def setup
+    # set the input file name
+    @file = File.join(File.dirname(__FILE__), "fixtures", "sample.mzML")
+    @compressed = File.join(File.dirname(__FILE__), "fixtures", "sample.compressed.mzML")
+    @mgf = File.join(File.dirname(__FILE__), "fixtures", "sample.mgf")
+    @mzml = MzML::Doc.open(@file)
+  end
+
+  def test_canary
+    pass
+  end
+
+  def test_mzml_file_open
+    assert_instance_of(MzML::Doc, @mzml)
+  end
+
+  def test_index_created
+    assert_not_nil(@mzml.index)
+    assert(@mzml.index.keys.length > 0, "Index not parsed correctly, zero index keys")
+  end
+
+  def test_spectrum_fetch
+    spectrum = @mzml.spectrum(@mzml.spectrum_list.first)
+    assert_instance_of(MzML::Spectrum, spectrum)
+    assert(spectrum.id == "controllerType=0 controllerNumber=1 scan=1")
+  end
+
+  def test_chromatogram_fetch
+    # STDERR.puts @mzml.chromatogram_list.first
+    chromatogram = @mzml.chromatogram(@mzml.chromatogram_list.first)
+    assert_instance_of(MzML::Chromatogram, chromatogram)
+    assert(chromatogram.id == "TIC")
+  end
+
+  # test the spectrum object.
+  # attr_reader :id, :default_array_length, :type,
+  #   :charge, :precursor, :base_peak_mz, :base_peak_intensity, :ms_level,
+  #   :high_mz, :low_mz, :title, :tic, :polarity, :representation, :mz_node, :intensity_node,
+  #   :mz, :intensity, :precursor_list, :scan_list, :retention_time, :precursor_mass,
+  #   :precursor_intensity, :node, :params
+
+  def test_spectrum_object
+    spectrum = @mzml.spectrum(@mzml.spectrum_list[2])
+    assert_instance_of(MzML::Spectrum, spectrum)
+    assert_equal("controllerType=0 controllerNumber=1 scan=3",spectrum.id)
+    assert_equal(2, spectrum.ms_level)
+    assert_equal(231.38883972167969, spectrum.low_mz)
+    assert_equal(1560.7198486328125, spectrum.high_mz)
+    assert_equal(586279, spectrum.tic)
+    assert_equal(161140.859375, spectrum.base_peak_intensity)
+    assert_equal(736.6370849609375, spectrum.base_peak_mz)
+  end
+
+  def test_spectrum_decode
+    spectrum = @mzml.spectrum(@mzml.spectrum_list[2])
+    assert_instance_of(MzML::Spectrum, spectrum)
+    assert_equal(spectrum.mz[3], 240.3084716796875)
+  end
+
+  def test_compressed_spectrum_decode
+    mzml = MzML::Doc.open(@compressed)
+    spectrum = mzml.spectrum(@mzml.spectrum_list[2])
+    assert_instance_of(MzML::Spectrum, spectrum)
+    assert_equal(spectrum.mz[3], 240.3084716796875)
+  end
+
+  # test the chromatogram object.
+
+  def test_chromatogram_object
+    chromatogram = @mzml.chromatogram(@mzml.chromatogram_list[0])
+    assert_instance_of(MzML::Chromatogram,chromatogram)
+    assert_equal("TIC", chromatogram.id)
+    assert_equal(0, chromatogram.index)
+    assert_equal(0, chromatogram.index_position)
+    assert_equal("minute", chromatogram.time_unit)
+  end
+
+  def test_chromatogram_decode
+    chromatogram = @mzml.chromatogram(@mzml.chromatogram_list[0])
+    assert_equal(0.022838333333333332,chromatogram.timepoint[3])
+    assert_equal(441570.15625,chromatogram.intensity[3])
+  end
+  def test_compressed_chromatogram_decode
+    mzml = MzML::Doc.open(@compressed)
+    chromatogram = mzml.chromatogram(mzml.chromatogram_list[0])
+    assert_equal(0.022838333333333332,chromatogram.timepoint[3])
+    assert_equal(441570.15625,chromatogram.intensity[3])
+  end
+end

metadata

@@ -1,115 +1,122 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: mzml
-version: !ruby/object:Gem::Version 
-  hash: 19
-  prerelease: false
-  segments: 
-  - 0
-  - 2
-  - 2
-  version: 0.2.2
+version: !ruby/object:Gem::Version
+  version: 0.3.0
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - Angel Pizarro
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2010-10-01 00:00:00 +00:00
-default_executable: mzML2mgf.rb
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  name: rspec
+date: 2012-06-27 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: &70120743498360 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.5'
+  type: :runtime
   prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  version_requirements: *70120743498360
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: &70120743497840 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - "="
-      - !ruby/object:Gem::Version 
-        hash: 27
-        segments: 
-        - 1
-        - 3
-        - 0
-        version: 1.3.0
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: nokogiri
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: *70120743497840
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: &70120743497360 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - "="
-      - !ruby/object:Gem::Version 
-        hash: 5
-        segments: 
-        - 1
-        - 4
-        - 1
-        version: 1.4.1
-  type: :runtime
-  version_requirements: *id002
-description: A non-validating mzML parser. MzML is a standard data format for representing mass spectrometry data.
-email: angel@delagoya.com
-executables: 
-- mzML2mgf.rb
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *70120743497360
+description: A non-validating mzML parser. MzML is a standard data format for representing
+  mass spectrometry data.
+email:
+- angel@upenn.edu
+executables: []
 extensions: []
-
-extra_rdoc_files: 
-- LICENSE
-- README.rdoc
-files: 
-- .document
+extra_rdoc_files: []
+files:
 - .gitignore
-- .yardoc
+- Gemfile
 - LICENSE
 - README.rdoc
 - Rakefile
-- VERSION
-- bin/mzML2mgf.rb
+- bin/mzml2mgf
 - lib/mzml.rb
+- lib/mzml/chromatogram.rb
+- lib/mzml/doc.rb
+- lib/mzml/spectrum.rb
+- lib/mzml/version.rb
 - mzml.gemspec
 - spec/mzml_spec.rb
 - spec/sample.compressed.mzML
 - spec/sample.mgf
 - spec/sample.mzML
+- spec/sample.unindexed.mzML
 - spec/spec.opts
 - spec/spec_helper.rb
-has_rdoc: true
+- test/fixtures/sample.compressed.mzML
+- test/fixtures/sample.mgf
+- test/fixtures/sample.mzML
+- test/test_mzml-helper.rb
+- test/test_mzml.rb
 homepage: http://github.com/delagoya/mzml
 licenses: []
-
 post_install_message: 
-rdoc_options: 
-- --charset=UTF-8
-require_paths: 
+rdoc_options: []
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: 483551756782191696
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
+      hash: 483551756782191696
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 1.8.11
 signing_key: 
 specification_version: 3
 summary: A non-validating mzML parser
-test_files: 
+test_files:
 - spec/mzml_spec.rb
+- spec/sample.compressed.mzML
+- spec/sample.mgf
+- spec/sample.mzML
+- spec/sample.unindexed.mzML
+- spec/spec.opts
 - spec/spec_helper.rb
+- test/fixtures/sample.compressed.mzML
+- test/fixtures/sample.mgf
+- test/fixtures/sample.mzML
+- test/test_mzml-helper.rb
+- test/test_mzml.rb
+has_rdoc: 

data/.document

@@ -1,5 +0,0 @@
-README.rdoc
-lib/**/*.rb
-bin/*
-features/**/*.feature
-LICENSE

data/VERSION

@@ -1 +0,0 @@
-0.2.2