Class: Bio::KEGG::KGML

Inherits:
Object
  • Object
show all
Defined in:
lib/sylfy/add/bio_kegg_kgml.rb

Overview

Class Bio::KEGG::KGML

Instance Method Summary collapse

Instance Method Details

#to_mjson ⇒ Object

convert KGML to mjson (map json)



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# File 'lib/sylfy/add/bio_kegg_kgml.rb', line 10

def to_mjson()
    mjson = {:identifier => :id}
    
    # <pathway> attributes
    mjson[:name] = @name
    mjson[:org] = @org
    mjson[:number] = @number
    mjson[:title] = @title
    mjson[:link] = @link
    
    
    mjson[:image] = {}
    mjson[:image][:source] = @image
    
    begin
        dim = open(@image).read()[0x10..0x18].unpack('NN')
        mjson[:image][:width] = dim[0]
        mjson[:image][:height] = dim[1]
    rescue
        
    end
    
    
    # <entry> attributes
    @entries.each do |entry|
        entryinfo = {:id => entry.id, :entryname => entry.name, :link => entry.link, :entrytype => entry.type, :keggid => entry.names}
      
        entryinfo[:reaction] = entry.reaction if entry.reaction
        
        # <graphics> attributes
        graphicinfo = {}
        if entry.graphics.length == 1
            graphicinfo[:fill] = entry.graphics[0].bgcolor if entry.graphics[0].bgcolor
            graphicinfo[:stroke] = entry.graphics[0].fgcolor if entry.graphics[0].fgcolor
            graphicinfo[:name] = entry.graphics[0].name if entry.graphics[0].name
    
            case entry.graphics[0].type
            when 'rectangle'
                graphicinfo[:type] = :rect
                graphicinfo[:width] = entry.graphics[0].width
                graphicinfo[:height] = entry.graphics[0].height
                graphicinfo[:x] = entry.graphics[0].x
                graphicinfo[:y] = entry.graphics[0].y
            when 'roundrectangle'
                graphicinfo[:type] = :rect
                graphicinfo[:width] = entry.graphics[0].width
                graphicinfo[:height] = entry.graphics[0].height
                graphicinfo[:x] = entry.graphics[0].x
                graphicinfo[:y] = entry.graphics[0].y
                graphicinfo[:r] = 10
            when 'circle'
                graphicinfo[:type] = :circle
                graphicinfo[:r] = entry.graphics[0].width/2
                graphicinfo[:cx] = entry.graphics[0].x
                graphicinfo[:cy] = entry.graphics[0].y
            when 'line'
                graphicinfo[:type] = :path
                paths = []
                entry.graphics[0].coords.each {|coord| paths.push(coord.join(" "))}
                graphicinfo[:fill] = entry.graphics[0].bgcolor if entry.graphics[0].bgcolor
                graphicinfo[:stroke] = entry.graphics[0].fgcolor if entry.graphics[0].fgcolor
                graphicinfo[:name] = entry.graphics[0].name if entry.graphics[0].name
                graphicinfo[:d] ||= ""
                graphicinfo[:d] += "M #{paths.join("L")}" if !paths.empty?()
                graphicinfo[:"stroke-width"] = 3
                graphicinfo[:"stroke-linecap"] = "square"
            end
            
        else
            entry.graphics.each do |graph|
                if graph.type == 'line'
                    paths = []
                    graph.coords.each {|coord| paths.push(coord.join(" "))}
                    graphicinfo[:type] = :path
                    graphicinfo[:fill] = graph.bgcolor if graph.bgcolor
                    graphicinfo[:stroke] = graph.fgcolor if graph.fgcolor
                    graphicinfo[:name] = graph.name if graph.name
                    graphicinfo[:d] ||= ""
                    graphicinfo[:d] += "M #{paths.join("L")}" if !paths.empty?()
                    graphicinfo[:"stroke-width"] = 3
                    graphicinfo[:"stroke-linecap"] = "square"
                else
                    raise "Graphic parsinf error to #{id}:#{entry.id}"
                end
            end
        end
        
        entryinfo[:graphic] = graphicinfo
        mjson[graphicinfo[:type]] ||= []
        mjson[graphicinfo[:type]].push(entryinfo)
    
        # <component> attributes
        
    end
    return mjson
end