# File lib/bio/shell/irb.rb, line 15
15:     def initialize
16:       require 'irb'
17:       begin
18:         require 'irb/completion'
19:         Bio::Shell.cache[:readline] = true
20:       rescue LoadError
21:         Bio::Shell.cache[:readline] = false
22:       end
23:       IRB.setup(nil)
24:       setup_irb
25:       start_irb
26:     end

    # File lib/bio/shell/irb.rb, line 58
58:     def  setup_irbsetup_irb
59:       # set application name
60:       IRB.conf[:AP_NAME] = 'bioruby'
61: 
62:       # change prompt for bioruby
63:       $_ = Bio::Shell.colors
64:       IRB.conf[:PROMPT][:BIORUBY_COLOR] = {
65:         :PROMPT_I => "bio#{$_[:ruby]}ruby#{$_[:none]}> ",
66:         :PROMPT_S => "bio#{$_[:ruby]}ruby#{$_[:none]}%l ",
67:         :PROMPT_C => "bio#{$_[:ruby]}ruby#{$_[:none]}+ ",
68:         :RETURN   => "  ==> %s\n"
69:       }
70:       IRB.conf[:PROMPT][:BIORUBY] = {
71:         :PROMPT_I => "bioruby> ",
72:         :PROMPT_S => "bioruby%l ",
73:         :PROMPT_C => "bioruby+ ",
74:         :RETURN   => "  ==> %s\n"
75:       }
76:       if Bio::Shell.config[:color]
77:         IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR
78:       else
79:         IRB.conf[:PROMPT_MODE] = :BIORUBY
80:       end
81: 
82:       # echo mode (uncomment to off by default)
83:       #IRB.conf[:ECHO] = Bio::Shell.config[:echo] || false
84: 
85:       # irb/input-method.rb >= v1.5 (not in 1.8.2)
86:       #IRB.conf[:SAVE_HISTORY] = 100000
87: 
88:       # not nicely works
89:       #IRB.conf[:AUTO_INDENT] = true
90:     end

    # File lib/bio/shell/irb.rb, line 28
28:     def start_irb
29:       Bio::Shell.cache[:irb] = IRB::Irb.new
30: 
31:       # needed for method completion
32:       IRB.conf[:MAIN_CONTEXT] = Bio::Shell.cache[:irb].context
33: 
34:       # store binding for evaluation
35:       Bio::Shell.cache[:binding] = IRB.conf[:MAIN_CONTEXT].workspace.binding
36: 
37:       # overwrite gets to store history with time stamp
38:       io = IRB.conf[:MAIN_CONTEXT].io
39:       io.class.class_eval do
40:         alias_method :irb_original_gets, :gets
41:       end
42: 
43:       def io.gets
44:         line = irb_original_gets
45:         if line
46:           Bio::Shell.store_history(line)
47:         end
48:         return line
49:       end
50: 
51:       if File.exists?("./config/boot.rb")
52:         require "./config/boot"
53:         require "./config/environment"
54:         #require 'commands/console'
55:       end
56:     end