ms-msrun 0.1.0 → 0.2.0

data/.gitignore

@@ -0,0 +1,3 @@
+rdoc
+*.swp
+pkg

data/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "submodules/ms-testdata"]
+	path = submodules/ms-testdata
+	url = git@github.com:bahuvrihi/ms-testdata.git

data/History

@@ -0,0 +1,18 @@
+== 0.1.1 / 2009-11-19
+* using unified mspire template
+* using spec-more (bacon) rather than minitest-spec
+
+== 0.1.0
+* switched to nokogiri as the xml parser
+* using mzxml indices to read scans (lazy reading of scans)
+* semi-lazy reading of spectrum (lazy string)
+*   the string is not converted into a spectrum until an mz value is asked for
+* lots of interface changes
+
+== 0.0.1
+* initial release as gem
+* some differences from mspire:
+*   all spectra are read in lazy
+*   cleaned up code a lot
+*   uses Struct instead of Arrayclass to minimize dependencies
+*   bumps task of providing indices for peak data onto AXML 

data/Rakefile

@@ -1,128 +1,114 @@
-require 'rake'
 require 'rubygems'
-require 'rake/rdoctask'
-require 'rake/gempackagetask'
+require 'rake'
+require 'jeweler'
 require 'rake/testtask'
-require 'rake/clean'
-require 'fileutils'
-
-###############################################
-# GLOBAL
-###############################################
+require 'rcov/rcovtask'
 
-FL = FileList
 NAME = "ms-msrun"
-FU = FileUtils
-
-readme = "README"
-
-rdoc_dir = 'rdoc'
-rdoc_extra_includes = [readme, "LICENSE"]
-rdoc_options = ['--main', readme, '--title', NAME, '--line-numbers', '--inline-source']
-
-lib_files = FL["lib/**/*.rb"]
-dist_files = lib_files + FL[readme, "LICENSE", "Rakefile", "{specs}/**/*"]
-changelog = 'CHANGELOG'
-
-###############################################
-# DOC
-###############################################
-Rake::RDocTask.new do |rd|
-  rd.rdoc_dir = rdoc_dir
-  rd.main = readme
-  rd.rdoc_files.include( rdoc_extra_includes )
-  rd.rdoc_files.include( lib_files.uniq )
-  rd.options.push( *rdoc_options )
+WEBSITE_BASE = "website"
+WEBSITE_OUTPUT = WEBSITE_BASE + "/output"
+
+gemspec = Gem::Specification.new do |s|
+  s.name = NAME
+  s.authors = ["John T. Prince"]
+  s.email = "jtprince@gmail.com"
+  s.homepage = "http://jtprince.github.com/" + NAME + "/"
+  s.summary = "an mspire library for working with LC/MS runs (mzxml, mzData, mzML)"
+  s.description = 'A library for working with LC/MS runs. Part of mspire.  Has parsers for mzXML v1, 2, and 3, mzData (currently broken) and mzML (planned).  Can convert to commonly desired search output (such as mgf).  Fast random access of scans, and fast reading of the entire file.'
+  s.rubyforge_project = 'mspire'
+  s.add_dependency 'ms-core'
+  s.add_dependency 'nokogiri'
+  s.add_dependency 'narray'
+  s.add_development_dependency("spec-more")
 end
 
+Jeweler::Tasks.new(gemspec)
 
-desc "Publish RDoc to RubyForge"
-task :publish_rdoc => [:rdoc] do
-  require 'yaml'
-  
-  config = YAML.load(File.read(File.expand_path("~/.rubyforge/user-config.yml")))
-  host = "#{config["username"]}@rubyforge.org"
-  
-  rsync_args = "-v -c -r"
-  remote_dir = "/var/www/gforge-projects/mspire/projects/#{NAME}"
-  local_dir = "rdoc"
- 
-  sh %{rsync #{rsync_args} #{local_dir}/ #{host}:#{remote_dir}}
+Rake::TestTask.new(:spec) do |spec|
+  ENV['TEST'] = ENV['SPEC'] if ENV['SPEC']  
+  spec.libs << 'lib' << 'spec'
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.verbose = true
 end
 
-#desc "create and upload docs to server"
-#task :upload_docs => [:rdoc] do
-#  sh "scp -r #{rdoc_dir}/* jtprince@rubyforge.org:/var/www/gforge-projects/mspire/projects/ms-msrun/"
-#end
-
-###############################################
-# TESTS
-###############################################
-
-desc 'Default: Run specs.'
-task :default => :spec
-
-desc 'Run specs.'
-Rake::TestTask.new(:spec) do |t|
-  #t.verbose = true
-  #t.warning = true
-  ENV['TEST'] = ENV['SPEC'] if ENV['SPEC']
-  t.libs = ['lib']
-  t.test_files = Dir.glob( File.join('spec', ENV['pattern'] || '**/*_spec.rb') )
-  #t.options = "-v"
+Rcov::RcovTask.new do |spec|
+  spec.libs << 'spec'
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.verbose = true
 end
 
-###############################################
-# PACKAGE / INSTALL / UNINSTALL
-###############################################
-
-tm = Time.now
-gemspec = Gem::Specification.new do |t|
-  description = 'A library for working with LC/MS runs. Part of mspire.  Has parsers for mzXML v1, 2, and 3, mzData and mzML.  Can convert to commonly desired search output (such as mgf)'
-  summary = "A library for working with LC/MS runs"
-  t.platform = Gem::Platform::RUBY
-  t.name = NAME
-  t.version =  IO.readlines(changelog).grep(/##.*version/).pop.split(/\s+/).last.chomp
-  t.homepage = 'http://mspire.rubyforge.org/projects/ms-msrun'
-  t.rubyforge_project = 'mspire'
-  t.summary = summary
-  t.date = "#{tm.year}-#{tm.month}-#{tm.day}"
-  t.email = "jtprince@gmail.com"
-  t.description = description
-  t.has_rdoc = true
-  t.authors = ["John Prince"]
-  t.files = dist_files
-  t.add_dependency 'ms-core'
-  t.add_dependency 'nokogiri'
-  t.add_dependency 'runarray'
-  t.rdoc_options = rdoc_options
-  t.extra_rdoc_files = rdoc_extra_includes
-  t.executables = FL["bin/*"].map {|file| File.basename(file) }
-  t.test_files = FL["spec/**/*_spec.rb"]
+def rdoc_redirect(base_rdoc_output_dir, package_website_page, version)
+  content = %Q{
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<html><head><title>mspire: } + NAME + %Q{rdoc</title>
+<meta http-equiv="REFRESH" content="0;url=#{package_website_page}/rdoc/#{version}/">
+</head> </html> 
+  }
+  FileUtils.mkpath(base_rdoc_output_dir)
+  File.open(base_rdoc_output_dir + "/index.html", 'w') {|out| out.print content }
 end
 
-desc "Create packages."
-Rake::GemPackageTask.new(gemspec) do |pkg|
-  #pkg.need_zip = true
-  #pkg.need_tar = true
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  base_rdoc_output_dir = WEBSITE_OUTPUT + '/rdoc'
+  version = File.read('VERSION')
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = NAME + ' ' + version
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
 end
 
-task :remove_pkg do 
-  FileUtils.rm_rf "pkg"
+task :create_redirect do
+  base_rdoc_output_dir = WEBSITE_OUTPUT + '/rdoc'
+  rdoc_redirect(base_rdoc_output_dir, gemspec.homepage,version)
 end
 
-task :install => [:reinstall]
-
-desc "uninstalls the package, packages a fresh one, and installs"
-task :reinstall => [:remove_pkg, :clean, :package] do
-  reply = `#{$gemcmd} list -l #{NAME}`
-  if reply.include?(NAME + " (")
-    %x( #{$gemcmd} uninstall -a -x #{NAME} )
+namespace :website do
+  desc "checkout and configure the gh-pages submodule (assumes you have it)"
+  task :submodule_update do
+    if File.exist?(WEBSITE_OUTPUT + "/.git")
+      puts "!! not doing anything, #{WEBSITE_OUTPUT + "/.git"} already exists !!"
+    else
+
+      puts "(not sure why this won't work programmatically)"
+      puts "################################################"
+      puts "[Execute these commands]"
+      puts "################################################"
+      puts "git submodule init"
+      puts "git submodule update"
+      puts "pushd #{WEBSITE_OUTPUT}"
+      puts "git co --track -b gh-pages origin/gh-pages ;"
+      puts "popd"
+      puts "################################################"
+
+      # not sure why this won't work!
+      #%x{git submodule init}
+      #%x{git submodule update}
+      #Dir.chdir(WEBSITE_OUTPUT) do
+      #  %x{git co --track -b gh-pages origin/gh-pages ;}
+      #end
+    end
   end
-  FileUtils.cd("pkg") do
-    cmd = "#{$gemcmd} install #{NAME}*.gem"
-    puts "EXECUTING: #{cmd}" 
-    system cmd
+
+  desc "setup your initial gh-pages"
+  task :init_ghpages do
+    puts "################################################"
+    puts "[Execute these commands]"
+    puts "################################################"
+    puts "git symbolic-ref HEAD refs/heads/gh-pages"
+    puts "rm .git/index"
+    puts "git clean -fdx"
+    puts 'echo "Hello" > index.html'
+    puts "git add ."
+    puts 'git commit -a -m "my first gh-page"'
+    puts "git push origin gh-pages"
   end
+
 end
 
+task :default => :spec
+
+task :build => :gemspec
+
+# credit: Rakefile modeled after Jeweler's
+

data/VERSION

@@ -0,0 +1 @@
+0.2.0

data/lib/lmat.rb

@@ -1,13 +1,22 @@
 
-require 'runarray'
-include Runarray
+require 'gsl'
+require 'narray'
+#include Runarray
+
+include Math
+include GSL
 
 ## Labeled matrix
 
 class Lmat
+
+  NUM_BYTE_SIZE = 4
+
+  # an narray object numerically labelling the m-axis
   attr_accessor :mvec
+  # an narray object numerically labelling the n-axis
   attr_accessor :nvec
-  # an array of narray objects
+  # an mvec.size X nvec.size narray
   attr_accessor :mat
 
   ## Takes an array of narray objects
@@ -17,28 +26,66 @@ class Lmat
     @nvec = nvec
   end
 
-  def max
-    max = mat[0][0]
-    mat.each do |row|
-      row.each do |v|
-        max = v if v > max
-      end
+  class << self
+    def [](*args)
+      mat = NArray[*args]
+      (nlen, mlen) = mat.shape
+      obj = new(mat)
+      obj.mvec = NArray[0...mlen]
+      obj.nvec = NArray[0...nlen]
+      obj
     end
-    max
+  end
+
+  def [](*args)
+    @mat[*args]
+  end
+
+  def []=(*args)
+    @mat.send('[]=', *args)
+  end
+
+  def slice=(*args)
+    @mat.send(:slice, *args)
+  end
+
+  def slice(*args)
+    @mat.slice(*args)
+  end
+
+  def inspect
+    # TODO: needs work (see ruport pivotted table output)
+    ["nvec=#{@nvec.inspect}", "mvec=#{@mvec.inspect}", "mat=#{@mat.inspect}"].join("\n")
+
+    start = '   ' << nvec.to_a.join(", ") << "\n"
+    start << ("    " + ("-" * (start.size - 4))) << "\n"
+    mvec[].indgen!.each do |i|
+      start << "#{mvec[i]} | " << @mat[true, i].to_a.join(" ") << "\n"
+    end
+    start
+  end
+
+  def max
+    @mat.max
+  end
+
+  def dup
+    a = Lmat.new
+    a.mvec = self.mvec[]
+    a.nvec = self.nvec[]
+    a.mat = self.mat[]
+    a
   end
 
   # returns self
   def from_lmat(file)
-    string = IO.read(file)
-    mdim = string.unpack("i")
-    @mvec = NArray.new(string.unpack("f#{mdim}"))
-    ndim = string.unpack("i")
-    @nvec = NArray.new(string.unpack("f#{ndim}"))
-    rows = []
-    mdim.times do
-      rows << string.unpack("f#{ndim}")
+    File.open(file) do |io|
+      (@mvec, @nvec) = [true, true].map do |iv|
+        _len = io.read(4).unpack('I').first
+        NArray.to_na( io.read(_len*NUM_BYTE_SIZE), 'sfloat' )
+      end
+      @mat = NArray.to_na(io.read, 'sfloat', @nvec.size, @mvec.size)
     end
-    @mat = rows
     self
   end
 
@@ -48,17 +95,16 @@ class Lmat
     File.open(file) do |io|
       num_m = io.readline.to_i
       mline = io.readline.chomp
-      @mvec = NArray.new( mline.split(' ').map {|v| v.to_f } )
+      @mvec = NArray.to_na( mline.split(' ').map {|v| v.to_f } )
       raise RuntimeError, "bad m vec size" if mvec.size != num_m
       num_n = io.readline.to_i
       nline = io.readline.chomp
-      @nvec = NArray.new( nline.split(' ').map {|v| v.to_f } )
+      @nvec = NArray.to_na( nline.split(' ').map {|v| v.to_f } )
       raise RuntimeError, "bad n vec size" if nvec.size != num_n
-      @mat = NArray.new(num_m)
+      @mat = NArray.float(num_n, num_m)
       num_m.times do |m|
-        line = io.readline
-        line.chomp!
-        @mat[m] = NArray.new(line.split(' ').map {|v| v.to_f })
+        line = io.readline.chomp!
+        @mat[true, m] = line.split(' ').map {|v| v.to_f }
       end
     end
     self
@@ -103,7 +149,7 @@ class Lmat
       num_scans = msrun.scan_count
       printf "Reading #{num_scans} spectra [.=100]" if $VERBOSE
       spectrum_cnt = 0
-      msrun.each do |scan|
+      msrun.each(:ms_level => 1) do |scan|
         spectrum = scan.spectrum
         times << scan.time
         #(mz,inten) = spectrum_to_mz_and_inten(spectrum, VecD)
@@ -130,36 +176,92 @@ class Lmat
   # outputs vec lengths if set to true
   def to_s(with_vec_lengths=false)
     arr = []
-    if with_vec_lengths; arr.push(@mvec.size) end
-    arr.push(@mvec.join(" "))
-    if with_vec_lengths; arr.push(@nvec.size) end
-    arr.push(@nvec.join(" "), @mat.map {|v| v.join(" " ) }.join("\n")).join("\n")
+    arr.push(@mvec.size) if with_vec_lengths
+    arr.push(@mvec.to_a.join(" "))
+    arr.push(@nvec.size) if with_vec_lengths
+    arr.push(@nvec.to_a.join(" "))
+    (0...@mvec.size).each do |m_index|
+      arr.push(@mat[true, m_index].to_a.join(" "))
+    end
+    arr.join("\n")
   end
 
   def ==(other)
      other != nil && self.class == other.class && @nvec == other.nvec && @mvec == other.mvec && @mat == other.mat
   end
 
-  def write(file=nil)
+  # returns a fresh lmat object
+  def warp_cols(new_m_values, deep_copy=false)
+    new_guy = self.dup
+    new_guy.warp_cols!(new_m_values, deep_copy)
+    new_guy
+  end
+
+  # warps the data in self based on interpolation of the cols.  Evaluates the
+  # new_m_values for each column and returns a new lmat object with the m
+  # values set to new_m_values.  nvec will be the same is in self.
+  def warp_cols!(new_m_values, deep_copy=false)
+    nvec[].indgen.each do |n|
+      self[n,true] = Spline.alloc(Interp::AKIMA, mvec, self[n, true]).eval(new_m_values)
+    end
+    self.nvec = deep_copy ? self.nvec[] : self.nvec
+    self.mvec = deep_copy ? new_m_values[] : new_m_values
+    self
+  end
+
+  def write(file=nil, int_format_string='i')
     handle = $>
     if file; handle = File.open(file, "wb") end
     bin_string = ""
-    bin_string << [@mvec.size].pack("i")
-    bin_string << @mvec.pack("f*")
-    bin_string << [@nvec.size].pack("i")
-    bin_string << @nvec.pack("f*")
-    bin_string << @mat.flatten.pack("f*")
+    bin_string << [@mvec.size].pack(int_format_string)
+    bin_string << @mvec.to_s
+    bin_string << [@nvec.size].pack(int_format_string)
+    bin_string << @nvec.to_s
+    bin_string << @mat.to_s
     handle.print bin_string
     if file; handle.close end
   end
 
   def print(file=nil)
     handle = $>
-    if file; handle = File.new(file, "w") end
+    handle = File.new(file, "w") if file
     handle.print( self.to_s(true) )
-    #$stdout.print( self.to_s(true) )
-    if file; handle.close end
+    handle.close if file
   end
+end
+
+class Lmat
+  module Gnuplot
+
+    # png output only right now, given no outfile, plot to X11
+    def plot(outfile=nil)
+      # modified from Hornet's eye
+      require 'gnuplot'
+      ::Gnuplot.open do |gp| 
+        ::Gnuplot::SPlot.new(gp) do |plot|
+          if outfile
+            plot.terminal 'png'
+            plot.output outfile
+          end
+          plot.pm3d
+          plot.hidden3d
+          plot.palette 'defined ( 0 "black", 51 "blue", 102 "green", ' +
+            '153 "yellow", 204 "red", 255 "white" )'
+          plot.xlabel 'n'
+          plot.ylabel 'm'
+          plot.data << ::Gnuplot::DataSet.new( self ) do |ds|
+            ds.with = 'pm3d'
+            ds.matrix = true
+          end
+        end
+      end
+    end
 
+    def to_gsplot
+      require 'gnuplot'
+      [@mvec.to_a, @nvec.to_a, @mat.to_a].to_gsplot
+    end
+  end
+  include Gnuplot
 end