mzml 0.3.0 → 0.3.1

data/LICENSE

@@ -1,20 +1,21 @@
+The MIT License
+
 Copyright (c) 2009 Angel Pizarro
 
-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:
+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:
 
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
 
-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.
+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

@@ -1,12 +1,31 @@
-= mzml
+= mzML
 
 MzML is a standard data format for encoding mass spectrometry data. For more information see mzML the specification at http://psidev.info/index.php?q=node/257
 
-This library is a non-validating mzML version 1.1 parser/reader.
+This library is a non-validating, read-only mzML parser for mzML version 1.1.x
 
+It is built on top of the nokogiri gem for XML parsing, which itself relies on
+the libxml2 C library. The library It is relatively fast
+
+==USAGE:
+
+    require 'mzml'
+    mzml =  MzML::Doc.open("test.mzXML")
+    # to iterate through spectra
+    mzml.each do |spectrum|
+      # ... do something interesting
+    end
+    # to get an Array of spectrum IDs
+    mzml.spectrum_list
+    # to fetch a specific spectrum, whose ID you already know
+    mzml.spectrum("controllerType=0 controllerNumber=1 scan=1")
+
+You can also get chromatograms
+  mzml.each_chromatogram
+  mzml.chromatogram("TIC")
 
 == Note on Patches/Pull Requests
- 
+
 * Fork the project. It is hosted @ http://github.com/delagoya/mzml
 * Make your feature addition or bug fix.
 * Add tests for it. This is important so I don't break it in a

data/lib/mzml/doc.rb

@@ -18,7 +18,15 @@
 # ===USAGE:
 #
 #     require 'mzml'
-#     mzml =  MzML::Doc.new("test.mzXML")
+#     mzml =  MzML::Doc.open("test.mzXML")
+#     # to iterate through spectra
+#     mzml.each do |spectrum|
+#       # ... do something interesting
+#     end
+#     # to get an Array of spectrum IDs
+#     mzml.spectrum_list
+#     # to fetch a specific spectrum, whose ID you already know
+#     mzml.spectrum("controllerType=0 controllerNumber=1 scan=1")
 module MzML
 
   # An internal module containing useful regular expressions
@@ -61,6 +69,7 @@ module MzML
       @spectrum_count = @spectrum_list.length
       @chromatogram_count = @chromatogram_list.length
       @current_spectrum_index = 0
+      @current_chromatogram_index = 0
     end
     attr_reader :index, :fname, :spectrum_list, :spectrum_count, :chromatogram_list, :chromatogram_count
 
@@ -93,7 +102,14 @@ module MzML
     end
     alias_method :each_spectrum, :each
 
-    def next &block
+    def each_chromatogram &block
+      @chromatogram_list.each do |chromatogram_id|
+        block.call(self.chromatogram(chromatogram_id))
+        @current_chromatogram_index += 1
+      end
+    end
+
+    def next
       if @current_spectrum_index < @spectrum_list.length
         @current_spectrum_index += 1
         self.spectrum(@spectrum_list[@current_spectrum_index - 1])
@@ -103,9 +119,20 @@ module MzML
     end
     alias_method :next_spectrum, :next
 
+    def next_chromatogram
+      if @current_chromatogram_index < @chromatogram_list.length
+        @current_chromatogram_index += 1
+        self.chromatogram(@chromatogram_list[@current_chromatogram_index - 1])
+      else
+        nil
+      end
+    end
+
     def rewind
       super
       @current_spectrum_index = 0
+      @current_chromatogram_index = 0
+      self.pos
     end
 
     private

data/lib/mzml/version.rb

@@ -1,4 +1,4 @@
 module MzML
-  VERSION = "0.3.0"
+  VERSION = "0.3.1"
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mzml
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.3.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-06-27 00:00:00.000000000 Z
+date: 2012-06-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &70120743498360 !ruby/object:Gem::Requirement
+  requirement: &70118841419920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: '1.5'
   type: :runtime
   prerelease: false
-  version_requirements: *70120743498360
+  version_requirements: *70118841419920
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &70120743497840 !ruby/object:Gem::Requirement
+  requirement: &70118841419360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70120743497840
+  version_requirements: *70118841419360
 - !ruby/object:Gem::Dependency
   name: yard
-  requirement: &70120743497360 !ruby/object:Gem::Requirement
+  requirement: &70118841418840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,7 +43,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70120743497360
+  version_requirements: *70118841418840
 description: A non-validating mzML parser. MzML is a standard data format for representing
   mass spectrometry data.
 email:
@@ -90,7 +90,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 483551756782191696
+      hash: 1368085886114290395
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -99,7 +99,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 483551756782191696
+      hash: 1368085886114290395
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.11