spec/ms/msrun_spec.rb in ms-msrun-0.2.4 vs spec/ms/msrun_spec.rb in ms-msrun-0.3.0

@@ -1,14 +1,13 @@
 require File.expand_path(File.dirname(__FILE__) + '/../spec_helper.rb')
-
 require 'ms/msrun'
 
 module MsrunSpec
 
   before_all = lambda do |file|
-    nums = (1..20).to_a  # define scan numbers
     key = YAML.load_file(file + '.key.yml')
+    nums = (1..key['scan_count'][0]).to_a  # define scan numbers
     [key, nums]
   end
 
   shared 'an msrun object' do
 
@@ -18,11 +17,11 @@
           #puts "K: #{k} Vexp: #{v} Vact: #{ms.send(k.to_sym)}"
           ms.send(k.to_sym).is v
         end
       end
     end
-
+    
     it 'can access random scans' do
       Ms::Msrun.open(@file) do |ms|
         scan = ms.scan(20)
         hash_match(@key['scans'][20], scan)
       end
@@ -41,17 +40,23 @@
       num_required_scans.is 0
     end
 
     it 'can read scans of a certain ms_level' do
       nums = [1,5,9,13,17]
+      nums = [4,10,16] if @file.include? "mzML"
+      temp = nums.dup
+      
       Ms::Msrun.open(@file) do |ms|
         ms.each(:ms_level => 1) do |scan|
-          scan.num.is nums.shift 
+          break if scan.num > 20
+          scan.num.is temp.shift 
         end
       end
-      nums = [2,3,4,6,7,8,10,11,12,14,15,16,18,19,20]
+      
+      nums = (1..20).to_a - nums
       Ms::Msrun.foreach(@file, :ms_level => 2) do |scan|
+        break if scan.num > 20
         scan.num.is nums.shift 
       end
     end
 
     it 'can avoid reading spectra' do 
@@ -132,8 +137,13 @@
       Ms::Msrun.open(newname) do |ms|
         ms.start_and_end_mz.is([300.0, 1500.0])
       end
       File.unlink(newname) if File.exist?(newname)
     end
-
+  end
+  
+  describe 'reading an mzML file' do
+    @file = TESTFILES + '/J/test.mzML'
+    (@key, @nums) = before_all.call(@file)
+    behaves_like 'an msrun object'
   end
 end