mspire-simulator 0.1.2 → 0.2.0

data/lib/progress.rb

@@ -1,24 +1,25 @@
 
-module Progress
-  module_function
-  def progress(message, num, time = '')
-    # move cursor to beginning of line
-    cr = "\r"           
-
-    # ANSI escape code to clear line from cursor to end of line
-    # "\e" is an alternative to "\033"
-    # cf. http://en.wikipedia.org/wiki/ANSI_escape_code
-    clear = "\e[0K"     
-
+class Progress
+  # ANSI escape code to clear line from cursor to end of line
+  # "\e" is an alternative to "\033"
+  # cf. http://en.wikipedia.org/wiki/ANSI_escape_code
+  def initialize(message, time = nil)
+    @message = message
+    @time = time ? time : Time.now
+    @reset = "\r\e[0K"
+  end
+  def progress(num, message_addition = "")
+    message = @message+message_addition
     # reset lines
-    reset = cr + clear
-    if time == ''
-      print "#{reset} #{message}" + "#{num}%".rjust(60-message.length)
-      $stdout.flush
-    else
-      str = "#{reset} #{message}" + "#{num}%".rjust(60-message.length)
-      print  str + "Took: #{"%.2f" % time} sec.".rjust(100-str.length)
-      $stdout.flush
-    end
+    print "#{@reset} #{message}" + "#{num}%".rjust(60-message.length)
+    $stdout.flush
+  end
+  def finish!(message_addition = "")
+    time = Time.now - @time
+    message = @message + message_addition
+    str = "#{@reset} #{message}" + "100%".rjust(60-message.length)
+    print  str + "Took: #{"%.2f" % time} sec.\n".rjust(100-str.length)
+    $stdout.flush
   end
+  alias :update :progress
 end

data/mspire-simulator.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "mspire-simulator"
-  s.version = "0.1.2"
+  s.version = "0.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["anoyce"]
-  s.date = "2012-08-10"
+  s.date = "2012-12-13"
   s.description = "Simulates MS1 runs given amino acid FASTA files. Outputs an MZML file.\n\t\t\tCan simulate specific data if given an MZML file containing a single isolated peptide peak."
   s.email = "andrewbnoyce@gmail.com"
   s.executables = ["mspire-simulator", "sim_mail"]
@@ -24,6 +24,7 @@ Gem::Specification.new do |s|
     "VERSION",
     "bin/mspire-simulator",
     "bin/sim_mail",
+    "lib/cv_parser.rb",
     "lib/ms/curvefit.rb",
     "lib/ms/curvefit/curve_fit_helper.rb",
     "lib/ms/curvefit/fit_graph.rb",
@@ -49,14 +50,13 @@ Gem::Specification.new do |s|
     "spec/merger_spec.rb",
     "spec/ms-simulate_spec.rb",
     "spec/peptide_spec.rb",
-    "spec/progress_spec.rb",
     "spec/spec_helper.rb",
     "spec/spectra_spec.rb"
   ]
-  s.homepage = "http://dl.dropbox.com/u/42836826/Ms_Sim_Homepage.html"
+  s.homepage = "https://github.com/princelab/mspire-simulator"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.21"
+  s.rubygems_version = "1.8.24"
   s.summary = "Simulates MS1 runs given amino acid FASTA files. Outputs an MZML file."
 
   if s.respond_to? :specification_version then

data/spec/file_writer_spec.rb

@@ -1,4 +1,5 @@
-
+$LOAD_PATH << './lib'
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 require 'time'
 require 'mspire'
 require 'ms/sim_spectra'

data/spec/merger_spec.rb

@@ -1,4 +1,5 @@
-
+$LOAD_PATH << './lib'
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 require 'ms/merger'
 
 describe Merger do 

data/spec/ms-simulate_spec.rb

@@ -3,7 +3,7 @@ require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 
 describe "MSsimulate" do
   it "Gathers parameters from the cmd line and runs the simulator; If no params are given or --help a help message is displayed" do
-    output = `ruby bin/ms-simulate.rb --help`
+    output = `ruby bin/mspire-simulator --help`
     output.should =~ /where/
   end
 end

data/spec/peptide_spec.rb

@@ -1,5 +1,6 @@
 #peptide_spec.rb
-
+$LOAD_PATH << './lib'
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 require 'mspire'
 require 'ms/sim_peptide'
 

data/spec/spec_helper.rb

@@ -2,10 +2,15 @@ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'rspec'
 
-# Requires supporting files with custom matchers and macros, etc,
-# in ./support/ and its subdirectories.
-Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+Dir["#{File.dirname(__FILE__)}/lib/**/*.rb"].each {|f| require f}
 
 RSpec.configure do |config|
+
+  config.before(:all) do 
+    system("mkdir .m .i")
+    system("mkdir .m/A .m/R .m/N .m/D .m/C .m/E .m/Q .m/G .m/H .m/I .m/L .m/K .m/M .m/F .m/P .m/S .m/T .m/W .m/Y .m/V .m/U .m/O")
+    system("mkdir .i/A .i/R .i/N .i/D .i/C .i/E .i/Q .i/G .i/H .i/I .i/L .i/K .i/M .i/F .i/P .i/S .i/T .i/W .i/Y .i/V .i/U .i/O")
+  end
   
+  config.after(:all) {system("rm -r -f .m .i")}
 end

data/spec/spectra_spec.rb

@@ -1,5 +1,6 @@
 #spectra_spec.rb
-
+$LOAD_PATH << './lib'
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 require 'mspire'
 require 'ms/sim_spectra'
 require 'ms/sim_peptide'
@@ -91,8 +92,8 @@ describe MS::Sim_Spectra do
   end
   
   it "Each feature should have a predicted retention time and intensity" do 
-      p_rts = [(2079..2082),(1774..1777),(1400..1402)]
-      p_ints = [2.325,2.927,3.559]
+      p_rts = [(823..826),(769..772),(1485..1490)]
+      p_ints = [2.058,2.095,2.219]
     @spectra.features.each_with_index do |fe,i|
       p_rts[i].should cover(fe.p_rt)
       fe.p_int.should == p_ints[i]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire-simulator
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.2.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-10 00:00:00.000000000 Z
+date: 2012-12-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: mspire
@@ -189,6 +189,7 @@ files:
 - VERSION
 - bin/mspire-simulator
 - bin/sim_mail
+- lib/cv_parser.rb
 - lib/ms/curvefit.rb
 - lib/ms/curvefit/curve_fit_helper.rb
 - lib/ms/curvefit/fit_graph.rb
@@ -214,10 +215,9 @@ files:
 - spec/merger_spec.rb
 - spec/ms-simulate_spec.rb
 - spec/peptide_spec.rb
-- spec/progress_spec.rb
 - spec/spec_helper.rb
 - spec/spectra_spec.rb
-homepage: http://dl.dropbox.com/u/42836826/Ms_Sim_Homepage.html
+homepage: https://github.com/princelab/mspire-simulator
 licenses:
 - MIT
 post_install_message: 
@@ -238,7 +238,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.21
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: Simulates MS1 runs given amino acid FASTA files. Outputs an MZML file.

data/spec/progress_spec.rb

@@ -1,22 +0,0 @@
-#progress_spec.rb
-
-require 'progress'
-require 'time'
-
-describe Progress, "#progress" do
-  it "Prints out a given message and percentage, refreshing the current line with each call." do
-    101.times do |i|
-      Progress.progress("Message:",i)
-      sleep 0.01
-    end
-  end
-  
-  it "Also can take a final time to show how long a process took." do 
-    start = Time.now
-    101.times do |i|
-      Progress.progress("Message:",i)
-      sleep 0.01
-    end
-    Progress.progress("Message:",100,Time.now - start)
-  end
-end