1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
|
require "rgfa"
#
# Module defining additional methods for the RGFA class.
#
# RGFATools is an extension to the RGFA library, which allow to perform further
# operations. Thereby additional conventions are required, with respect to the
# GFA specification, which are compatible with it.
#
# The methods defined here allow, e.g., to randomly orient a segment which has
# the same connections on both sides, to compute copy numbers and multiply or
# delete segments according to them, to distribute the links of copies after
# multipling a segment, or to eliminate edges in the graph which are
# incompatible with an hamiltonian path.
#
# Custom optional fields are defined, such as "cn" for the copy number of a
# segment, "or" for the original segment(s) of a duplicated or merged segment,
# "mp" for the starting position of original segments in a merged segment, "rp"
# for the position of possible inversions due to arbitrary orientation of some
# segments by the program.
#
# Furthermore a convention for the naming of the segments is introduced, which
# gives a special meaning to the characters "_^()".
#
# @developer
# In the main file is only the method redefinition infrastructure
# (private methods). The public methods are in the included modules.
#
module RGFATools
end
require_relative "rgfatools/artifacts"
require_relative "rgfatools/copy_number"
require_relative "rgfatools/invertible_segments"
require_relative "rgfatools/multiplication"
require_relative "rgfatools/superfluous_links"
require_relative "rgfatools/linear_paths"
require_relative "rgfatools/p_bubbles"
module RGFATools
include RGFATools::Artifacts
include RGFATools::CopyNumber
include RGFATools::InvertibleSegments
include RGFATools::Multiplication
include RGFATools::SuperfluousLinks
include RGFATools::LinearPaths
include RGFATools::PBubbles
private
def self.included(klass)
included_modules.each do |included_module|
if included_module.const_defined?("Redefined")
self.redefine_methods(included_module::Redefined, klass)
end
if included_module.const_defined?("ClassMethods")
klass.extend(included_module::ClassMethods)
end
end
end
def self.redefine_methods(redefined_methods, klass)
klass.class_eval do
redefined_methods.each do |redefined_method|
was_private = klass.private_instance_methods.include?(redefined_method)
public redefined_method
alias_method :"#{redefined_method}_without_rgfatools", redefined_method
alias_method redefined_method, :"#{redefined_method}_with_rgfatools"
if was_private
private redefined_method,
:"#{redefined_method}_without_rgfatools",
:"#{redefined_method}_with_rgfatools"
end
end
end
end
ProgramName = "RGFATools"
def add_program_name_to_header
set_header_field(:pn, RGFATools::ProgramName)
end
end
class RGFA
include RGFATools
# Enable {RGFATools} extensions of RGFA methods
# @return [void]
def enable_extensions
@extensions_enabled = true
end
# Disable {RGFATools} extensions of RGFA methods
# @return [void]
def disable_extensions
@extensions_enabled = false
end
end
|
