mspire 0.7.11 → 0.7.12

data/VERSION

@@ -1 +1 @@
-0.7.11
+0.7.12

data/lib/mspire/imzml/writer.rb

@@ -327,6 +327,15 @@ module Mspire::Imzml
       end
 
       data_info_pairs = write_binary(config[:ibd_filename], all_spectra_iter, config)
+      xy_positions_array = x_y_positions(config)
+
+      unless data_info_pairs.size == xy_positions_array.size
+        STDERR.puts "Input Error! The number of calculated scans must equal the number of actual scans!" 
+        STDERR.puts "The number of calculated positions: #{xy_positions_array.size}"
+        STDERR.puts "The number of actual scans: #{data_info_pairs.size}"
+        raise
+      end
+
       config[:ibd_sha1] = Digest::SHA1.hexdigest(IO.read(config[:ibd_filename]))
 
       source_files = mzml_filenames.zip(sourcefile_ids).map do |mzml_filename, source_file_id|
@@ -374,7 +383,7 @@ module Mspire::Imzml
         # low intensity data point removal: "MS:1000594"
         imzml.run = Mspire::Mzml::Run.new("run1", default_instrument_config) do |run|
           spec_list = Mspire::Mzml::SpectrumList.new(data_processing_obj)
-          data_info_pairs.zip(x_y_positions(config), sourcefile_id_parallel_to_spectra).each_with_index do |(pair, xy, sourcefile_id),i|
+          data_info_pairs.zip(xy_positions_array, sourcefile_id_parallel_to_spectra).each_with_index do |(pair, xy, sourcefile_id),i|
             # TODO: we should probably copy the id from the orig mzml (e.g.
             # scan=1)
             spectrum = Mspire::Mzml::Spectrum.new("spectrum#{i}", params: [rparms_by_id[:spectrum1]])

data/lib/mspire/peak_list.rb

@@ -1,4 +1,5 @@
 require 'mspire/bin'
+require 'mspire/peak'
 
 module Mspire
   # a collection of peak objects.  At a minimum, each peak should respond to

data/script/quant_compare_direct_injections.rb

@@ -34,6 +34,7 @@ parser = Trollop::Parser.new do
   opt :mz_prefix, "use this prefix for mz values", :default => DEFAULTS[:mz_prefix]
   opt :round_mz, "round the final m/z values to this place", :default => DEFAULTS[:round_mz]
   opt :round_intensity, "round the final int values to this place", :default => DEFAULTS[:round_intensity]
+  opt :simple_calibrate, "adjust the m/z values by that amount", :default => 0.0
   opt :verbose, "talk about it"
 end
 
@@ -129,7 +130,7 @@ File.open(opts[:outfile],'w') do |out|
       signal_by_sample_index[peak.sample_id] += peak.y
     end
 
-    row = [opts[:mz_prefix] + meta_peak.x.round(opts[:round_mz]).to_s, *sample_ids.each_with_index.map {|id,index| signal_by_sample_index[index].round(opts[:round_intensity]) }]
+    row = [opts[:mz_prefix] + (meta_peak.x + opts[:simple_calibrate]).round(opts[:round_mz]).to_s, *sample_ids.each_with_index.map {|id,index| signal_by_sample_index[index].round(opts[:round_intensity]) }]
     out.puts row.join("\t")
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.7.11
+  version: 0.7.12
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-04-19 00:00:00.000000000 Z
+date: 2012-05-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri