sequence_logo 1.0.3 → 1.0.4

data/lib/sequence_logo/pmflogo_lib.rb

@@ -1,114 +1,114 @@
-require_relative 'ytilib'
-require 'RMagick'
-
-module SequenceLogo
-  def self.draw_threshold_lines(i_logo, ppm)
-    x_size = i_logo.columns
-    y_size = i_logo.rows
-
-    line2of4 = y_size - ppm.get_line(ppm.icd2of4) * y_size
-    lineThc = y_size - ppm.get_line(ppm.icdThc) * y_size
-    lineTlc = y_size - ppm.get_line(ppm.icdTlc) * y_size
-
-    dr = Magick::Draw.new
-    dr.fill('transparent')
-
-    dr.stroke_width(y_size / 200.0)
-    dr.stroke_dasharray(7,7)
-
-    dr.stroke('silver')
-    dr.line(0, line2of4, x_size, line2of4)
-    dr.line(0, lineThc, x_size, lineThc)
-    dr.line(0, lineTlc, x_size, lineTlc)
-
-    dr.draw(i_logo)
-  end
-
-  def self.create_canvas(ppm, options)
-    x_size = options[:x_unit] * ppm.length
-    y_size = options[:y_unit]
-
-    i_logo = Magick::ImageList.new
-    if options[:icd_mode] == :discrete
-      i_logo.new_image(x_size, y_size, Magick::HatchFill.new('white', 'white'))
-      draw_threshold_lines(i_logo, ppm)  if options[:threshold_lines]
-    else
-      i_logo.new_image(x_size, y_size, Magick::HatchFill.new('white', 'bisque'))
-    end
-
-    i_logo
-  end
-
-  def self.letter_images(scheme_dir)
-    if File.exist?(File.join(scheme_dir,'a.png'))
-      extension = 'png'
-    elsif File.exist?(File.join(scheme_dir,'a.gif'))
-      extension = 'gif'
-    else
-      raise "Scheme not exists in folder #{scheme_dir}"
-    end
-
-    letter_files = %w[a c g t].collect{|letter| File.join(scheme_dir, "#{letter}.#{extension}") }
-    Magick::ImageList.new(*letter_files)
-  end
-
-  def self.draw_letters_on_canvas(i_logo, i_letters, ppm, options)
-    y_unit = options[:y_unit]
-    x_unit = options[:x_unit]
-    matrix = ppm.get_logo(options[:icd_mode])
-    matrix['A'].each_index { |i|
-      y_pos = 0
-      sorted_letters = ['A', 'C', 'G', 'T'].collect { |letter| {:score => matrix[letter][i], :letter => letter} }.sort_by { |pair| pair[:score] }.collect { |pair| pair[:letter] }.reverse
-      sorted_letters.each { |letter|
-        next if y_unit * matrix[letter][i] <= 1
-        letter_index = {'A' => 0, 'C' => 1, 'G' => 2, 'T' => 3}[letter]
-        y_block = (y_unit * matrix[letter][i]).round
-        i_logo << i_letters[letter_index].dup.resize(x_unit, y_block)
-        y_pos += y_block
-        i_logo.cur_image.page = Magick::Rectangle.new(0, 0, i * x_unit, y_unit - y_pos )
-      }
-    }
-  end
-
-  def self.draw_logo(ppm, options = {})
-    ppm.words_count = options[:words_count]  if options[:words_count]
-    unless ppm.words_count
-      report "words count for PPM is undefined, assuming weblogo mode"
-      options[:icd_mode] = :weblogo
-    end
-    i_logo = create_canvas(ppm, options)
-    scheme_dir = File.join(AssetsPath, options[:scheme])
-    draw_letters_on_canvas(i_logo, letter_images(scheme_dir), ppm, options)
-    i_logo = i_logo.flatten_images
-  end
-
-  # logos = { filename => {shift: ..., length: ..., name: ...} }
-  def self.glue_files(logos, output_file, options)
-    logo_shift = options[:logo_shift] || 300
-    x_unit = options[:x_unit] || 30
-    y_unit = options[:y_unit] || 60
-    text_size = options[:text_size] || 24
-
-    leftmost_shift = logos.map{|file,infos| infos[:shift] }.min
-    logos.each{|file, infos| infos[:shift] -= leftmost_shift}
-    full_alignment_size = logos.map{|file,infos| infos[:length] + infos[:shift] }.max
-
-    x_size = logo_shift + full_alignment_size * x_unit
-    y_size = logos.size * y_unit
-    command_string = "convert -size #{ x_size }x#{ y_size } -pointsize #{text_size} xc:white "
-    logos.each_with_index do |(logo_filename,infos), idx|
-      logo_x_start = logo_shift + infos[:shift] * x_unit
-      logo_y_start = y_unit * idx
-      command_string << "\"#{ logo_filename }\" -geometry +#{ logo_x_start }+#{ logo_y_start } -composite "
-    end
-
-    command_draw_names = ""
-    logos.each_with_index do |(logo_filename,infos), idx|
-      text_x_start = 10
-      text_y_start = y_unit * (idx + 0.5)
-      command_draw_names << "-draw \"text #{ text_x_start },#{ text_y_start } '#{infos[:name]}'\" "
-    end
-
-    system(command_string + command_draw_names + "\"#{output_file}\"")
-  end
+require_relative 'ytilib'
+require 'RMagick'
+
+module SequenceLogo
+  def self.draw_threshold_lines(i_logo, ppm)
+    x_size = i_logo.columns
+    y_size = i_logo.rows
+
+    line2of4 = y_size - ppm.get_line(ppm.icd2of4) * y_size
+    lineThc = y_size - ppm.get_line(ppm.icdThc) * y_size
+    lineTlc = y_size - ppm.get_line(ppm.icdTlc) * y_size
+
+    dr = Magick::Draw.new
+    dr.fill('transparent')
+
+    dr.stroke_width(y_size / 200.0)
+    dr.stroke_dasharray(7,7)
+
+    dr.stroke('silver')
+    dr.line(0, line2of4, x_size, line2of4)
+    dr.line(0, lineThc, x_size, lineThc)
+    dr.line(0, lineTlc, x_size, lineTlc)
+
+    dr.draw(i_logo)
+  end
+
+  def self.create_canvas(ppm, options)
+    x_size = options[:x_unit] * ppm.length
+    y_size = options[:y_unit]
+
+    i_logo = Magick::ImageList.new
+    if options[:icd_mode] == :discrete
+      i_logo.new_image(x_size, y_size, Magick::HatchFill.new('white', 'white'))
+      draw_threshold_lines(i_logo, ppm)  if options[:threshold_lines]
+    else
+      i_logo.new_image(x_size, y_size, Magick::HatchFill.new('white', 'bisque'))
+    end
+
+    i_logo
+  end
+
+  def self.letter_images(scheme_dir)
+    if File.exist?(File.join(scheme_dir,'a.png'))
+      extension = 'png'
+    elsif File.exist?(File.join(scheme_dir,'a.gif'))
+      extension = 'gif'
+    else
+      raise "Scheme not exists in folder #{scheme_dir}"
+    end
+
+    letter_files = %w[a c g t].collect{|letter| File.join(scheme_dir, "#{letter}.#{extension}") }
+    Magick::ImageList.new(*letter_files)
+  end
+
+  def self.draw_letters_on_canvas(i_logo, i_letters, ppm, options)
+    y_unit = options[:y_unit]
+    x_unit = options[:x_unit]
+    matrix = ppm.get_logo(options[:icd_mode])
+    matrix['A'].each_index { |i|
+      y_pos = 0
+      sorted_letters = ['A', 'C', 'G', 'T'].collect { |letter| {:score => matrix[letter][i], :letter => letter} }.sort_by { |pair| pair[:score] }.collect { |pair| pair[:letter] }.reverse
+      sorted_letters.each { |letter|
+        next if y_unit * matrix[letter][i] <= 1
+        letter_index = {'A' => 0, 'C' => 1, 'G' => 2, 'T' => 3}[letter]
+        y_block = (y_unit * matrix[letter][i]).round
+        i_logo << i_letters[letter_index].dup.resize(x_unit, y_block)
+        y_pos += y_block
+        i_logo.cur_image.page = Magick::Rectangle.new(0, 0, i * x_unit, y_unit - y_pos )
+      }
+    }
+  end
+
+  def self.draw_logo(ppm, options = {})
+    ppm.words_count = options[:words_count]  if options[:words_count]
+    unless ppm.words_count
+      report "words count for PPM is undefined, assuming weblogo mode"
+      options[:icd_mode] = :weblogo
+    end
+    i_logo = create_canvas(ppm, options)
+    scheme_dir = File.join(AssetsPath, options[:scheme])
+    draw_letters_on_canvas(i_logo, letter_images(scheme_dir), ppm, options)
+    i_logo = i_logo.flatten_images
+  end
+
+  # logos = { filename => {shift: ..., length: ..., name: ...} }
+  def self.glue_files(logos, output_file, options)
+    logo_shift = options[:logo_shift] || 300
+    x_unit = options[:x_unit] || 30
+    y_unit = options[:y_unit] || 60
+    text_size = options[:text_size] || 24
+
+    leftmost_shift = logos.map{|file,infos| infos[:shift] }.min
+    logos.each{|file, infos| infos[:shift] -= leftmost_shift}
+    full_alignment_size = logos.map{|file,infos| infos[:length] + infos[:shift] }.max
+
+    x_size = logo_shift + full_alignment_size * x_unit
+    y_size = logos.size * y_unit
+    command_string = "convert -size #{ x_size }x#{ y_size } -pointsize #{text_size} xc:white "
+    logos.each_with_index do |(logo_filename,infos), idx|
+      logo_x_start = logo_shift + infos[:shift] * x_unit
+      logo_y_start = y_unit * idx
+      command_string << "\"#{ logo_filename }\" -geometry +#{ logo_x_start }+#{ logo_y_start } -composite "
+    end
+
+    command_draw_names = ""
+    logos.each_with_index do |(logo_filename,infos), idx|
+      text_x_start = 10
+      text_y_start = y_unit * (idx + 0.5)
+      command_draw_names << "-draw \"text #{ text_x_start },#{ text_y_start } '#{infos[:name]}'\" "
+    end
+
+    system(command_string + command_draw_names + "\"#{output_file}\"")
+  end
 end

data/lib/sequence_logo/version.rb

@@ -1,3 +1,3 @@
-module SequenceLogo
-  VERSION = "1.0.3"
-end
+module SequenceLogo
+  VERSION = "1.0.4"
+end