mspire 0.6.12 → 0.6.18

data/VERSION

@@ -1 +1 @@
-0.6.12
+0.6.18

data/lib/ms/mzml.rb

@@ -9,6 +9,8 @@ require 'ms/mzml/file_description'
 require 'ms/mzml/software'
 require 'ms/mzml/scan_list'
 require 'ms/mzml/scan'
+require 'ms/mzml/scan_settings'
+require 'ms/mzml/processing_method'
 require 'ms/mzml/run'
 require 'ms/mzml/spectrum_list'
 require 'ms/mzml/chromatogram_list'

data/lib/ms/mzml/data_array.rb

@@ -1,9 +1,11 @@
 require 'base64'
 require 'zlib'
+require 'ms/cv/paramable'
 
 module MS
   class Mzml
     class DataArray < Array
+      include MS::CV::Paramable
 
       DEFAULT_DTYPE = :float64
       DEFAULT_COMPRESSION = true
@@ -18,13 +20,14 @@ module MS
       # the type of data array (:mz or :intensity)
       attr_accessor :type
 
-      # requires a type, :mz or :intensity
-      def initialize(_type, ar=[])
+      # requires a type, :mz, :intensity, :mz_external, or :intensity_external
+      # (external types used in imzml)
+      def initialize(_type, opts={params: []})
         @type = _type
-        super(ar)
+        @external = !!(@type.to_s =~ /external$/)
       end
 
-      def self.to_mzml_string(array_ish, dtype=DEFAULT_DTYPE, compression=DEFAULT_COMPRESSION)
+      def self.to_binary(array_ish, dtype=DEFAULT_DTYPE, compression=DEFAULT_COMPRESSION)
         pack_code = 
           case dtype
           when :float64 ; 'E*'
@@ -40,12 +43,22 @@ module MS
       end
 
       def to_xml(builder, dtype=DEFAULT_DTYPE, compression=DEFAULT_COMPRESSION)
-        base64 = self.class.to_mzml_string(self, dtype, compression)
-        builder.binaryDataArray(encodedLength: base64.bytesize) do |bda_n|
-          MS::CV::Param[ DTYPE_TO_ACC[dtype] ].to_xml(bda_n)
-          MS::CV::Param[ compression ? 'MS:1000574' : 'MS:1000576' ].to_xml(bda_n)
-          MS::CV::Param[ (@type == :mz) ? 'MS:1000514' : 'MS:1000515' ].to_xml(bda_n) # must be m/z or intensity 
-          bda_n.binary(base64)
+        encoded_length = 
+          if @external
+            0
+          else
+            base64 = self.class.to_binary(self, dtype, compression)
+            base64.bytesize
+          end
+
+        builder.binaryDataArray(encodedLength: encoded_length) do |bda_n|
+          @params.each {|param| param.to_xml(bda_n) } if @params
+          unless @external
+            MS::CV::Param[ DTYPE_TO_ACC[dtype] ].to_xml(bda_n)
+            MS::CV::Param[ compression ? 'MS:1000574' : 'MS:1000576' ].to_xml(bda_n)
+            MS::CV::Param[ (@type == :mz) ? 'MS:1000514' : 'MS:1000515' ].to_xml(bda_n) # must be m/z or intensity 
+            bda_n.binary(base64)
+          end
         end
       end
 
@@ -53,7 +66,14 @@ module MS
       def self.list_xml(arrays, builder)
         builder.binaryDataArrayList(count: arrays.size) do |bdal_n|
           arrays.zip([:mz, :intensity]) do |data_ar, typ|
-            ar = data_ar.is_a?(MS::Mzml::DataArray) ? data_ar : MS::Mzml::DataArray.new(typ, data_ar)
+            ar = 
+              if data_ar.is_a?(MS::Mzml::DataArray)
+                data_ar
+              else
+                real_data_array = MS::Mzml::DataArray.new(typ)
+                real_data_array.replace(data_ar)
+                real_data_array
+              end
             ar.type = typ unless ar.type
             ar.to_xml(bdal_n)
           end

data/lib/ms/mzml/data_array_container_like.rb

@@ -32,7 +32,15 @@ module MS
       end
 
       def default_array_length
-        @data_arrays ? @data_arrays.first.size : 0
+        if @data_arrays
+          if @data_arrays.first
+            @data_arrays.first.size
+          else
+            0
+          end
+        else
+          0
+        end
       end
 
       # see SpectrumList for generating the entire list

data/lib/ms/mzml/scan_list.rb

@@ -19,7 +19,7 @@ module MS
 
       def to_xml(builder)
         builder.scanList(count: self.size) do |sl_n|
-          @description.to_xml(sl_n) if @description
+          @params.each {|param| param.to_xml(sl_n) } if @params
           self.each do |scan|
             scan.to_xml(sl_n)
           end

data/obo/ims.obo

@@ -299,7 +299,7 @@ relationship: is_a IMS:1000001 ! Ibd Offest Handle
 relationship: has_units UO:0000189 ! Count
 
 [Term]
-id: IMS:100104
+id: IMS:1000104
 name: external encoded length
 def: "Describes the length of the written data." [COMPUTIS:IMS]
 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.6.12
+  version: 0.6.18
   prerelease: 
 platform: ruby
 authors:
@@ -14,7 +14,7 @@ date: 2012-02-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &7957300 !ruby/object:Gem::Requirement
+  requirement: &19554840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: '1.5'
   type: :runtime
   prerelease: false
-  version_requirements: *7957300
+  version_requirements: *19554840
 - !ruby/object:Gem::Dependency
   name: bsearch
-  requirement: &8341740 !ruby/object:Gem::Requirement
+  requirement: &19553820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *8341740
+  version_requirements: *19553820
 - !ruby/object:Gem::Dependency
   name: andand
-  requirement: &8425040 !ruby/object:Gem::Requirement
+  requirement: &19552180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: 1.3.1
   type: :runtime
   prerelease: false
-  version_requirements: *8425040
+  version_requirements: *19552180
 - !ruby/object:Gem::Dependency
   name: obo
-  requirement: &8500240 !ruby/object:Gem::Requirement
+  requirement: &19550640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.1.0
   type: :runtime
   prerelease: false
-  version_requirements: *8500240
+  version_requirements: *19550640
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &8496940 !ruby/object:Gem::Requirement
+  requirement: &19565640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: '2.6'
   type: :development
   prerelease: false
-  version_requirements: *8496940
+  version_requirements: *19565640
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &8574880 !ruby/object:Gem::Requirement
+  requirement: &19564260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *8574880
+  version_requirements: *19564260
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &8588620 !ruby/object:Gem::Requirement
+  requirement: &19563540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *8588620
+  version_requirements: *19563540
 description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
   merging of ms-* gems
 email: jtprince@gmail.com