bioroebe 0.10.80

data/lib/bioroebe/svg/primitive.rb

@@ -0,0 +1,70 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::SVG::Primitive
+#
+# The very small Bioroebe::SVG::Primitive class is used to describe simple
+# shapes. It is basically a simple data container that has lots of
+# dynamically set instance variables, including a name.
+#
+# The Bioroebe::SVG::Primitive object is later translated to an SVG
+# string by the Bioroebe::SVG::SVGEE class.
+# =========================================================================== #
+# require 'bioroebe/svg/primitive.rb'
+# =========================================================================== #
+module Bioroebe
+
+class SVG
+
+class Primitive # === Bioroebe::SVG::Primitive
+
+  # ========================================================================= #
+  # === initialize
+  #  
+  # Creates a new Primitive and initializes the instance variables
+  # dynamically from the arguments Hash called args. 
+  #
+  # Arguments (2):
+  #
+  #   :primitive = the Primitive type
+  #   args = a hash of parameters needed to describe the attributes
+  #   of the primitive type.
+  #
+  # ========================================================================= #
+  def initialize(
+      primitive, args
+    )
+    @primitive = primitive
+    # ======================================================================= #
+    # Iterate over our Hash next.
+    # ======================================================================= #
+    args.each_key { |key|
+      self.instance_variable_set("@#{key}", args[key])
+    }
+  end
+
+  # ========================================================================= #
+  # === update
+  #
+  # Updates a Primitive and sets the provided values as instance variables.
+  #
+  # Arguments:
+  #
+  #   args = a hash of new parameters for the given primitive type.
+  #
+  # ========================================================================= #
+  def update(args)
+    args.each_key { |key|
+      self.instance_variable_set("@#{key}", args[key])
+    }
+  end
+
+  # ========================================================================= #
+  # === primitive?
+  # ========================================================================= #
+  def primitive?
+    @primitive
+  end; alias primitive primitive? # === primitive
+
+end; end; end

data/lib/bioroebe/svg/svgee.rb

@@ -0,0 +1,326 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::SVG::SVGEE
+#
+# The Bioroebe::SVG::SVGEE class takes argument information in
+# a hash and creates SVG Markup tags, which it will draw.
+# =========================================================================== #
+require 'bioroebe/svg/primitive.rb'
+
+module Bioroebe
+
+class SVG
+
+class SVGEE # === Bioroebe::SVG::SVGEE
+
+  # ========================================================================= #
+  # === initialize
+  #
+  # Creates a new Bioroebe::SVG::SVGEE object which will contain all the
+  # necessary objects to display all the features on a page.
+  #
+  # Arguments to this method:
+  #
+  #   :width = the width of the SVG page (100%)
+  #   :height = the amount of the page height the svg should take up (100%)
+  #   :style = the svg style information
+  #
+  # ========================================================================= #
+  def initialize(args = {})
+    reset
+    opts = {
+      :width  => '100%',
+      :height => '100%'
+    }
+    if args
+      opts.merge!(args) unless args.empty?
+    end
+    reset
+    # ======================================================================= #
+    # === @width
+    # ======================================================================= #
+    @width      = opts[:width]
+    # ======================================================================= #
+    # === @height
+    # ======================================================================= #
+    @height     = opts[:height]
+    # ======================================================================= #
+    # === @style
+    # ======================================================================= #
+    @style      = opts[:style] if opts.has_key? :style
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    # ======================================================================= #
+    # === @style
+    # ======================================================================= #
+    @style = nil
+    # ======================================================================= #
+    # === @primitives
+    # ======================================================================= #
+    @primitives = []
+    # ======================================================================= #
+    # === @defs
+    # ======================================================================= #
+    @defs       = []
+    # ======================================================================= #
+    # === @supported_primitives
+    # ======================================================================= #
+    @supported_primitives = [
+      :circle,
+      :rectangle,
+      :ellipse,
+      :line,
+      :polyline,
+      :text
+    ]
+  end
+
+  # ========================================================================= #
+  # === supported_primitives?
+  # ========================================================================= #
+  def supported_primitives?
+    @supported_primitives
+  end; alias supported_primitives supported_primitives? # === supported_primitives
+
+  # ========================================================================= #
+  # === primitives?
+  # ========================================================================= #
+  def primitives?
+    @primitives
+  end; alias primitives primitives? # === primitives
+
+  # ========================================================================= #
+  # === update_height
+  # ========================================================================= #
+  def update_height(new_height)
+    @height = new_height
+  end
+
+  # ========================================================================= #
+  # === update_width
+  # ========================================================================= #
+  def update_width(new_width)
+    @width = new_width
+  end
+
+  # ========================================================================= #
+  # === defs?
+  # ========================================================================= #
+  def defs?
+    @defs
+  end; alias defs defs? # === defs
+
+  # ========================================================================= #
+  # === open_tag
+  #
+  # Produces the opening text for an svg file.
+  # ========================================================================= #
+  def open_tag
+    %Q{
+      <svg xmlns="https://www.w3.org/2000/svg" version="1.1" width="#{@width}" height="#{@height}" style="#{@style}" xmlns:xlink="http://www.w3.org/1999/xlink">
+    }
+  end
+  
+  # ========================================================================= #
+  # === close_tag
+  #
+  # Produces the closing text for an svg file.
+  # ========================================================================= #
+  def close_tag
+    '</svg>'
+  end
+
+  private
+
+  # ========================================================================= #
+  # === add
+  # ========================================================================= #
+  def add(primitive_string)
+    @primitives << primitive_string
+  end
+
+  # ========================================================================= #
+  # === add_def
+  # ========================================================================= #
+  def add_def(definition_string)
+    @defs << definition_string
+  end
+
+  # ========================================================================= #
+  # === make_tag
+  # ========================================================================= #
+  def make_tag(primitive, args)
+    if args.has_key?(:link)
+      add link_and_tag(primitive, args)
+    else
+      add self.send("#{primitive}_tag", args)
+    end
+    return ::Bioroebe::SVG::Primitive.new(primitive, args)
+  end
+
+  # ========================================================================= #
+  # === link_and_tag
+  # ========================================================================= #
+  def link_and_tag(primitive, args)
+    %Q{<a xlink:href="#{args[:link][:href]}" target="#{args[:link][:target]}">}+
+    send("#{primitive}_tag", args) + '</a>'
+  end
+
+  # ========================================================================= #
+  # === circle_tag
+  # ========================================================================= #
+  def circle_tag(a = {})
+    %Q{<circle cx="#{a[:x_center]}" cy="#{a[:y_center]}" r="#{a[:radius]}" fill="#{a[:fill_color]}" }+
+    common_attributes(a) + %q{/>}
+  end
+
+  # ========================================================================= #
+  # === rectangle_tag
+  # ========================================================================= #
+  def rectangle_tag(a = {})
+    %Q{<rect x="#{a[:x]}" y="#{a[:y]}" width="#{a[:width]}" height="#{a[:height]}" fill="#{a[:fill_color]}" rx="#{a[:x_round]}" ry="#{a[:y_round]}" } + common_attributes(a) + %q{/>}
+  end
+
+  # ========================================================================= #
+  # === ellipse_tag
+  # ========================================================================= #
+  def ellipse_tag(a = {})
+    %Q{<ellipse cx="#{a[:x_center]}" cy="#{a[:y_center]}" rx="#{a[:x_radius]}" ry="#{a[:y_radius]}" stroke="#{a[:stroke]}" stroke-width="#{a[:stroke_width]}" fill="#{a[:fill_color]}" style="#{a[:style]}" />}
+  end
+
+  # ========================================================================= #
+  # === line_tag
+  # ========================================================================= #
+  def line_tag(a = {})
+    %Q{<line x1="#{a[:x1]}" y1="#{a[:y1]}" x2="#{a[:x2]}" y2="#{a[:y2]}" }+
+    common_attributes(a) + %q{/>}
+  end
+
+  # ========================================================================= #
+  # === polyline_tag
+  # ========================================================================= #
+  def polyline_tag(a={})
+    %Q{<polyline points="#{a[:points]}" fill="#{a[:fill]}" }+
+    common_attributes(a) + %{ />}
+  end
+
+  # ========================================================================= #
+  # === polygon_tag
+  # ========================================================================= #
+  def polygon_tag(a={})
+    %Q{<polygon points="#{a[:points]}" fill="#{a[:fill_color]}" }+
+    common_attributes(a) + %{ />}
+  end
+
+  # ========================================================================= #
+  # === text_tag
+  # ========================================================================= #
+  def text_tag(a = {})
+    %Q{<text x="#{a[:x]}" y="#{a[:y]}" fill="#{a[:fill]}" transform="#{a[:transform]}" style="#{a[:style]}">#{a[:text]}</text>}
+  end
+
+  # ========================================================================= #
+  # === common_attributes
+  # ========================================================================= #
+  def common_attributes(a={})
+    param_str = ''.dup
+    a[:params].each{|k,v| param_str << %Q{ #{k}="#{v}"}} if a[:params]
+    %Q{stroke="#{a[:stroke]}" stroke-width="#{a[:stroke_width]}" style="#{a[:style]}"} + param_str
+  end
+
+  # ========================================================================= #
+  # === method_missing
+  #
+  # Only used to dynamically select the primitive type.
+  # ========================================================================= #
+  def method_missing(primitive, args={}) 
+    raise NoMethodError if not self.supported_primitives.include?(primitive) #we're only doing the listed primitive types...
+    self.send('make_tag', primitive, args) 
+  end
+
+  public
+
+  # ========================================================================= #
+  # === add_primitive
+  #
+  # Adds a Primitive object to the SVGEE object and makes the svg text for
+  # that Primitive.
+  # ========================================================================= #
+  def add_primitive(primitive_object)
+    args = {}
+    primitive_object.instance_variables.each {|variable|
+      args[variable.to_s.gsub(/@/,'').to_sym] = primitive_object.instance_variable_get(variable)
+    }
+    primitive_string = args.delete(:primitive)
+    make_tag(primitive_string, args)
+  end
+
+  # ========================================================================= #
+  # === gradient
+  #
+  # Takes the gradient information from a Glyph, which must be of type
+  # 'radial' or 'linear' and creates the svg text for that gradient.
+  #
+  #* +a+ = a gradient (a gradient type, a colour and the parameters for a
+  # given type)
+  # ========================================================================= #
+  def gradient(a)
+    definition_string = case a[:type]
+    when :radial
+      %Q{<radialGradient id="#{a[:id]}" cx="#{a[:cx]}%" cy="#{a[:cy]}%" r="#{a[:r]}%" fx="#{a[:fx]}%" fy="#{a[:fy]}%">}
+    else
+      %Q{<linearGradient id="#{a[:id]}" x1="#{a[:x1]}%" x2="#{a[:x2]}%" y1="#{a[:y1]}%" y2="#{a[:y2]}%">}
+    end
+    a[:stops].each { |s|
+      definition_string = definition_string+"\n"+
+      %Q{<stop offset="#{s[:offset]}%" style="stop-color:#{s[:color]};stop-opacity:#{s[:opacity]}" />}
+    }
+    add_def definition_string + (a[:type] == :linear ? '</linearGradient>' : '</radialGradient>')
+  end
+
+  # ========================================================================= #
+  # === draw (draw tag)
+  #
+  # Produces the svg text to display all the features on a Page.
+  # ========================================================================= #
+  def draw
+    head = self.open_tag
+    defstring = ''.dup
+    defstring << "<defs>\n" + self.defs.join("\n") + "\n </defs>\n" if not defs.empty?
+    shapes = self.primitives.join("\n")
+    close = self.close_tag
+    head+defstring+shapes+close
+  end
+
+end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  # ========================================================================= #
+  # === How to use SVGEE
+  # ========================================================================= #
+  puts 'How to use SVGEE:'
+  s = Bioroebe::SVG::SVGEE.new
+  s.gradient(
+    :radial => 'grad1', :cx => 50, :cy => 50, :r => 50, :fx => 50, :fy => 50, :stops => [ {:offset => 0, :color => 'rgb(255,255,255)', :opacity => 0},  {:offset => 100, :color => 'rgb(0,0,255)', :opacity => 1},]
+  )
+  s.circle(:x_center => 40, :y_center => 40, :radius => 20, :fill_color => "url(#grad1)")
+  s.circle(:x_center => 250, :y_center => 250, :radius => 20, :fill_color => "url(#grad1)", :link => {:href => "http://www.bbc.co.uk"})
+  s.rectangle(:x => 125, :y => 125, :width => 100, :height => 50, :fill_color => 'red', :stroke => 'black', :stroke_width => 2, :style => "fill-opacity:0.1;stroke-opacity:0.9")
+  s.rectangle(:x => 125, :y => 125, :round_x => 5, :round_y => 5, :width => 100, :height => 50, :fill_color => 'red', :stroke => 'black', :stroke_width => 2, :style => "fill-opacity:0.1;stroke-opacity:0.9")
+  prim = s.ellipse(:x_center => 100, :y_center => 190, :x_radius => 40, :y_radius => 20, :fill_color => 'green', :stroke => 'black')
+  s.line(:x1 => 10, :y1 => 10, :x2 => 145, :y2 => 145, :stroke_width => 5, :stroke => 'blue')
+  s.polyline(:points => '2,2 400,440 600,440', :stroke_width => 10, :stroke => "#f00", :fill => "none")
+  s.text(
+    :x => 100, :y => 100, :fill => 'red', :text => 'Look! It is a circle!', :style => 'letter-spacing:2;font-family:Arial'
+  )
+  s.text(:x => 100, :y => 400, :fill => 'green', :text => "This one is a link", :link => {:href => "http://www.bbc.co.uk"})
+  prim.update(x_center: 200)
+  s.add_primitive(prim)  #add one of the returned, updated Primitive objects 
+  puts s.draw
+end

data/lib/bioroebe/svg/track.rb

@@ -0,0 +1,263 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::SVG::Track
+#
+# The Biorieve::SVG::Track object acts as a container for
+# Bio::SVG::MiniFeature objects.
+#
+# The Bio::SVG::Track takes style information on instantiation.
+#
+# Style information is applied to each feature in the track by the track.
+# =========================================================================== #
+module Bioroebe
+
+class SVG
+
+class Track # === Bioroebe::SVG::Track
+
+  attr_reader :args
+  attr_reader :glyph
+  attr_reader :max_y
+
+  attr_accessor :features
+  attr_accessor :feature_rows
+  attr_accessor :name
+  attr_accessor :number_rows
+  attr_accessor :feature_height
+
+  # ========================================================================= #
+  # === initialize
+  #
+  # Creates a new Bioroebe::SVG::Track.
+  #
+  # Arguments:
+  #
+  # :glyph = one of Bioroebe::SVG::Glyphs#glyphs, currently being
+  #   [:generic,   :directed, :transcript, :scale, :label,
+  #    :histogram, :circle, :down_triangle, :up_triangle,
+  #    :span]
+  #
+  # :stroke_color =  the outline colour of the glyphs in the track
+  #  (default = "black"), can be any SVG colour eg rgb(256,0,0)
+  #  or #FF0000.
+  #
+  # :fill_color = the fill colour of the glyphs in the track (default = 'red'),
+  # can be any SVG colour eg rgb(256,0,0) or #FF0000, or one of the built in
+  # gradient types Bioroebe::SVG::Glyph#gradients
+  #
+  # [:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h,
+  # :red_white_radial, :green_white_radial, :blue_white_radial,
+  # :yellow_white_radial ]
+  # or a custom definition of a gradient:
+  # {:type => :radial, 
+  #  :id => :custom, 
+  #  :cx => 5, 
+  #  :cy => 5, 
+  #  :r => 50, 
+  #  :fx => 50, 
+  #  :fy => 50, 
+  #  :stops => [ {
+  #        :offset => 0, 
+  #        :color => 'rgb(255,255,255)', 
+  #        :opacity => 0
+  #        },  {
+  #        :offset => 100, 
+  #        :color => 'rgb(0,127,200)', 
+  #        :opacity => 1
+  #        }, ]
+  # }
+  #
+  # :track_height = minimum height for the track, will be modified
+  # automatically if more space is needed e.g for overlapping features (default = auto),
+  # :name = a displayed name for the track (default = 'feature_track')
+  # :label = display the name given to the track (default = true), 
+  # :stroke_width = width in pixels of the outline of the glyphs (default=1)
+  # :x_round = x radius of the ellipse used to round off the corners of rectangles (default = 1)
+  # :y_round = y radius of the ellipse used to round off the corners of rectangles (default = 1)
+  #:utr_fill_color = the fill colour of the utr part of the glyph (default = 'black'), can be any SVG colour eg rgb(256,0,0) or #FF0000, or one of the built in gradient types Bioroebe::SVG::Glyph#gradients
+  # [:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
+  # or a custom definition of a gradient
+  # {:type => :radial, 
+  # :id => :custom, 
+  # :cx => 5, 
+  # :cy => 5, 
+  # :r => 50, 
+  # :fx => 50, 
+  # :fy => 50, 
+  #   :stops => [ {
+  #        :offset => 0, 
+  #        :color => 'rgb(255,255,255)', 
+  #        :opacity => 0
+  #        },  {
+  #        :offset => 100, 
+  #        :color => 'rgb(0,127,200)', 
+  #        :opacity => 1
+  #        }, ]
+  # }
+  #* :utr_stroke = the outline colour of the utr part of the glyph
+  # (default = "black"), can be any SVG colour eg rgb(256,0,0) or #FF0000
+  #* :utr_stroke_width = The width of the outline stroke for the utr part of the glyph (default = 1)
+  #* :exon_fill_color = the fill colour of the utr part of the glyph (default = 'red'), can be any SVG colour eg rgb(256,0,0) or #FF0000, or one of the built in gradient types Bioroebe::SVG::Glyph#gradients or a custom definition of a gradient 
+  # [:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
+  #or a custom definition of a gradient
+  # {:type => :radial, 
+  # :id => :custom, 
+  # :cx => 5, 
+  # :cy => 5, 
+  # :r => 50, 
+  # :fx => 50, 
+  # :fy => 50, 
+  #   :stops => [ {
+  #        :offset => 0, 
+  #        :color => 'rgb(255,255,255)', 
+  #        :opacity => 0
+  #        },  {
+  #        :offset => 100, 
+  #        :color => 'rgb(0,127,200)', 
+  #        :opacity => 1
+  #        }, ]
+  # 
+  # :exon_stroke = the outline colour of the exon part of the glyph 
+  #  default = "black") can be any SVG colour eg rgb(256,0,0) or #FF0000
+  # :exon_stroke_width = The width of the outline stroke for the exon part of the glyph (default = 1)
+  # :line_color = the colour for the line part that joins the blocks (default = 'black') can be any SVG colour eg rgb(256,0,0) or #FF0000
+  # :line_width = the width ffor the line part that joins the blocks (default = 1)
+  # :exon_style = an arbitrary SVG compliant style string eg "fill-opacity:0.4;" 
+  # :utr_style = an arbitrary SVG compliant style string eg "fill-opacity:0.4;" 
+  # :line_style = an arbitrary SVG compliant style string eg "fill-opacity:0.4;" 
+  # :gap_marker = style of the line between blocks - either angled or straight
+  # ========================================================================= #
+  def initialize(args)
+    @args = {
+      :glyph => :generic, 
+      :name  => 'feature_track', 
+      :label => true, 
+      :feature_height => 10,
+      :track_height => nil
+    }.merge!(args) # Append in the arguments.
+    @glyph = @args[:glyph]
+    @name = @args[:name]
+    @label = @args[:label]
+    @track_height = @args[:track_height]
+    # ======================================================================= #
+    # === @features
+    # ======================================================================= #
+    @features = []
+    # ======================================================================= #
+    # === @feature_rows
+    # ======================================================================= #
+    @feature_rows = []
+    # ======================================================================= #
+    # === @scale
+    # ======================================================================= #
+    @scale = @args[:scale]
+    # ======================================================================= #
+    # === @feature_height
+    # ======================================================================= #
+    @feature_height = @args[:feature_height]
+    @number_of_rows = 1
+    @max_y = args[:max_y]
+    @min_width = args[:min_width]
+  end
+
+  # ========================================================================= #
+  # === scale?
+  # ========================================================================= #
+  def scale?
+    @scale
+  end; alias scale scale? # === scale
+
+  # ========================================================================= #
+  # === label?
+  # ========================================================================= #
+  def label?
+    @label
+  end; alias label label? # === label
+
+  # ========================================================================= #
+  # === add
+  #
+  # Adds a new Bioroebe::SVG::MiniFeature object to the current
+  # Bioroebe::SVG::Track.
+  # ========================================================================= #
+  def add(feature)
+    @features << feature
+  end
+
+  # ========================================================================= #
+  # === track_height?
+  # ========================================================================= #
+  def track_height?
+    @track_height
+  end; alias track_height track_height? # === track_height
+
+  # ========================================================================= #
+  # === get_rows
+  #
+  # Calculates how many rows are needed per track for overlapping
+  # features and which row each feature should be in. Usually only
+  # called by the enclosing Bioroebe::SVG::Page object.
+  # ========================================================================= #
+  def get_rows(
+      page = nil
+    )
+    @feature_rows = Array.new(@features.length, -1)
+    rows = Hash.new { |h, key| h[key] = [] }
+    @features.each_with_index { |f1, i|
+      current_row = 1
+      begin
+        found = true
+        rows[current_row].each_with_index do |f2, j|
+          if overlaps(f1, f2, page)
+            found = false
+            current_row += 1
+            break
+          end
+        end
+      end until found
+      @feature_rows[i] = current_row
+      rows[current_row] << f1
+    }
+    @number_rows = @feature_rows.max
+  end
+
+  # ========================================================================= #
+  # === overlaps
+  #
+  # Calculates whether two Bioroebe::SVG::MiniFeature objects overlap by
+  # examining their start and end positions.
+  #
+  # If the page where they are placed is given, then the function also
+  # considers the features' labels.
+  #
+  # Arguments:
+  #
+  #   f1 - a Bioroebe::SVG::MiniFeature object
+  #   f2 - a Bioroebe::SVG::MiniFeature object
+  #   page - the optional Bioroebe::SVG::Page object where the features
+  #   are placed
+  #
+  # ========================================================================= #
+  def overlaps(
+      f1, f2, page = nil
+    )
+    if !page
+      b1 = [f1.start, f1.end]
+      b2 = [f2.start, f2.end]
+    else
+      b1 = page.compute_boundaries(f1)
+      b2 = page.compute_boundaries(f2)
+    end
+    (b2[0] <= b1[1]) and (b1[0] <= b2[1])
+  end
+
+  # ========================================================================= #
+  # === min_width?
+  # ========================================================================= #
+  def min_width?
+    @min_width
+  end; alias min_width min_width? # === min_width
+
+end; end; end

data/lib/bioroebe/taxonomy/README.md

@@ -0,0 +1 @@
+The old taxonomy project has been integrated into the Bioroebe project.