bioinform 0.1.17 → 0.2.0

data/lib/bioinform/parsers/trivial_parser.rb

@@ -1,34 +0,0 @@
-require_relative '../support'
-require_relative '../parsers/parser'
-require_relative '../data_models/collection'
-require 'yaml'
-
-module Bioinform
-  # TrivialParser can be used to parse hashes returned by #parse method of other parsers:
-  # PM.new({matrix:[[1,2,3,4],[5,6,7,8]], name: 'Name'}, TrivialParser)
-  # PM.new(StringParser.new("1 2 3 4\n5 6 7 8").parse)
-  # StringParser.new("First\n1 2 3 4\n5 6 7 8\nSecond\n0 0 0 0").map{|inp| PM.new(inp, TrivialParser)}
-  class TrivialParser < Parser
-    def initialize(input)
-      @input = input
-    end
-    def parse!
-      case input
-      when PM then input
-      when Motif then input.pm
-      when OpenStruct then input
-      when Hash then OpenStruct.new(input)
-      end
-    end
-  end
-
-  class TrivialCollectionParser < Parser
-    include MultipleMotifsParser
-    def initialize(input)
-      @input = input
-    end
-    def parse!
-      input.container.shift.pm
-    end
-  end
-end

data/lib/bioinform/parsers/yaml_parser.rb

@@ -1,35 +0,0 @@
-require_relative '../support'
-require_relative 'parser'
-require_relative '../data_models/collection'
-require 'yaml'
-
-module Bioinform
-  # YAMLParser can be used to parse hashes returned by #parse method of other parsers:
-  # yaml_dump_of_pm = PM.new(...).to_yaml
-  # PM.new(yaml_dump_of_pm, YAMLParser)
-  class YAMLParser < Parser
-    def initialize(input)
-      @input = input
-    end
-    def parse!
-      YAML.load(input)
-    rescue Psych::SyntaxError
-      raise 'parsing error'
-    end
-  end
-
-  class YAMLCollectionParser < Parser
-    include MultipleMotifsParser
-    def initialize(input)
-      @input = input
-    end
-    def collection
-      @collection ||= YAML.load(input)
-    end
-    def parse!
-      collection.container.shift.pm
-    rescue Psych::SyntaxError
-      raise 'parsing error'
-    end
-  end
-end

data/lib/bioinform/support/advanced_scan.rb

@@ -1,8 +0,0 @@
-require 'strscan'
-
-class StringScanner
-  def advanced_scan(pat)
-    result = scan(pat)
-    result && result.match(pat)
-  end
-end

data/lib/bioinform/support/array_product.rb

@@ -1,6 +0,0 @@
-class Array
-  def self.product(*arrays)
-    return []  if arrays.empty?
-    arrays.first.product(*arrays[1..-1])
-  end
-end

data/lib/bioinform/support/array_zip.rb

@@ -1,6 +0,0 @@
-class Array
-  def self.zip(*arrays)
-    return []  if arrays.empty?
-    arrays.first.zip(*arrays[1..-1])
-  end
-end

data/lib/bioinform/support/collect_hash.rb

@@ -1,7 +0,0 @@
-module Enumerable
-  # %w{A C G T}.collect_hash{|k| [k*2, k*3] }
-  # # ==> {"AA" => "AAA", "CC" => "CCC", "GG" => "GGG", "TT" => "TTT"}
-  def collect_hash(&block)
-    block_given?  ?  Hash[ collect(&block) ]  :  Hash[ collect{|k,v| [k,v]} ]
-  end
-end

data/lib/bioinform/support/deep_dup.rb

@@ -1,5 +0,0 @@
-class Object
-  def deep_dup
-    Marshal.load(Marshal.dump(self))
-  end
-end

data/lib/bioinform/support/delete_many.rb

@@ -1,14 +0,0 @@
-class Array
-  def delete_at_many(*indices)
-    indices.uniq.sort.reverse.each{|ind| delete_at ind}
-  end
-  def delete_many(*elements)
-    elements.each{|el| delete el}
-  end
-end
-
-class Hash
-  def delete_many(*keys)
-    keys.each{|el| delete el}
-  end
-end

data/lib/bioinform/support/inverf.rb

@@ -1,13 +0,0 @@
-module Math
-  def self.inverf(x)
-    sign = x < 0 ? -1 : 1
-    x = x.abs
-    a = 8 / (3*Math::PI) * (Math::PI-3) / (4-Math::PI)
-    part0 = ( 2/(Math::PI*a) + (Math.log(1-x*x)) / 2 )**2
-    part = -2 / (Math::PI * a) - Math.log(1-x*x)/2 + Math.sqrt(-1/a * Math.log(1-x*x) + part0)
-    sign * Math.sqrt(part)
-  end
-  def inverf(x)
-    Math.inverf(x)
-  end
-end

data/lib/bioinform/support/multiline_squish.rb

@@ -1,6 +0,0 @@
-require_relative 'third_part/active_support/core_ext/string/filters'
-class String
-  def multiline_squish
-    split("\n").map(&:squish).join("\n").gsub(/\A\n+/,'').gsub(/\n+\z/,'')
-  end
-end

data/lib/bioinform/support/parameters.rb

@@ -1,28 +0,0 @@
-require 'ostruct'
-module Bioinform
-  module Parameters
-    def self.included(base)
-      base.extend(ClassMethods)
-    end
-    module ClassMethods
-      def make_parameters(*params)
-        params.each do |param|
-          define_method(param){ parameters.send(param) }
-          define_method("#{param}="){|new_value| parameters.send("#{param}=", new_value) }
-        end
-      end
-    end
-    def parameters; @parameters ||= OpenStruct.new; end
-    def set_parameters(hsh)
-      hsh.each{|k,v| send("#{k}=", v) }
-      self
-    end
-    # return hash of parameters
-    def get_parameters
-      @parameters.marshal_dump
-    end
-    def parameter_defined?(param_name)
-      get_parameters.has_key?(param_name)
-    end
-  end
-end

data/lib/bioinform/support/partial_sums.rb

@@ -1,16 +0,0 @@
-require_relative 'collect_hash'
-
-class Array
-  def partial_sums(initial = 0.0)
-    sums = initial
-    map{|el| sums += el}
-  end
-end
-
-class Hash
-# {1 => 5, 4 => 3, 3 => 2}.partial_sums == {1=>5, 3=>7, 4=>10}
-  def partial_sums(initial = 0.0)
-    sums = initial
-    sort.collect_hash{|k,v| [k, sums += v]}
-  end
-end

data/lib/bioinform/support/same_by.rb

@@ -1,12 +0,0 @@
-module Enumerable
-  def same_by?(&block)
-    return true if empty?
-    if block_given?
-      first_result = yield(first)
-      all?{|el| first_result == yield(el)}
-    else
-      first_result = first
-      all?{|el| first_result == el}
-    end
-  end
-end

data/lib/bioinform/support/third_part/active_support/core_ext/array/extract_options.rb

@@ -1,29 +0,0 @@
-class Hash
-  # By default, only instances of Hash itself are extractable.
-  # Subclasses of Hash may implement this method and return
-  # true to declare themselves as extractable. If a Hash
-  # is extractable, Array#extract_options! pops it from
-  # the Array when it is the last element of the Array.
-  def extractable_options?
-    instance_of?(Hash)
-  end
-end
-
-class Array
-  # Extracts options from a set of arguments. Removes and returns the last
-  # element in the array if it's a hash, otherwise returns a blank hash.
-  #
-  #   def options(*args)
-  #     args.extract_options!
-  #   end
-  #
-  #   options(1, 2)           # => {}
-  #   options(1, 2, :a => :b) # => {:a=>:b}
-  def extract_options!
-    if last.is_a?(Hash) && last.extractable_options?
-      pop
-    else
-      {}
-    end
-  end
-end

data/lib/bioinform/support/third_part/active_support/core_ext/hash/indifferent_access.rb

@@ -1,23 +0,0 @@
-require_relative '../../hash_with_indifferent_access'
-
-class Hash
-  # Returns an <tt>ActiveSupport::HashWithIndifferentAccess</tt> out of its receiver:
-  #
-  #   {:a => 1}.with_indifferent_access["a"] # => 1
-  #
-  def with_indifferent_access
-    ActiveSupport::HashWithIndifferentAccess.new_from_hash_copying_default(self)
-  end
-
-  # Called when object is nested under an object that receives
-  # #with_indifferent_access. This method will be called on the current object
-  # by the enclosing object and is aliased to #with_indifferent_access by
-  # default. Subclasses of Hash may overwrite this method to return +self+ if
-  # converting to an <tt>ActiveSupport::HashWithIndifferentAccess</tt> would not be
-  # desirable.
-  #
-  #   b = {:b => 1}
-  #   {:a => b}.with_indifferent_access["a"] # calls b.nested_under_indifferent_access
-  #
-  alias nested_under_indifferent_access with_indifferent_access
-end

data/lib/bioinform/support/third_part/active_support/core_ext/hash/keys.rb

@@ -1,54 +0,0 @@
-class Hash
-  # Return a new hash with all keys converted to strings.
-  #
-  #   { :name => 'Rob', :years => '28' }.stringify_keys
-  #   #=> { "name" => "Rob", "years" => "28" }
-  def stringify_keys
-    dup.stringify_keys!
-  end
-
-  # Destructively convert all keys to strings. Same as
-  # +stringify_keys+, but modifies +self+.
-  def stringify_keys!
-    keys.each do |key|
-      self[key.to_s] = delete(key)
-    end
-    self
-  end
-
-  # Return a new hash with all keys converted to symbols, as long as
-  # they respond to +to_sym+.
-  #
-  #   { 'name' => 'Rob', 'years' => '28' }.symbolize_keys
-  #   #=> { :name => "Rob", :years => "28" }
-  def symbolize_keys
-    dup.symbolize_keys!
-  end
-
-  # Destructively convert all keys to symbols, as long as they respond
-  # to +to_sym+. Same as +symbolize_keys+, but modifies +self+.
-  def symbolize_keys!
-    keys.each do |key|
-      self[(key.to_sym rescue key) || key] = delete(key)
-    end
-    self
-  end
-
-  alias_method :to_options,  :symbolize_keys
-  alias_method :to_options!, :symbolize_keys!
-
-  # Validate all keys in a hash match *valid keys, raising ArgumentError on a mismatch.
-  # Note that keys are NOT treated indifferently, meaning if you use strings for keys but assert symbols
-  # as keys, this will fail.
-  #
-  # ==== Examples
-  #   { :name => "Rob", :years => "28" }.assert_valid_keys(:name, :age) # => raises "ArgumentError: Unknown key: years"
-  #   { :name => "Rob", :age => "28" }.assert_valid_keys("name", "age") # => raises "ArgumentError: Unknown key: name"
-  #   { :name => "Rob", :age => "28" }.assert_valid_keys(:name, :age) # => passes, raises nothing
-  def assert_valid_keys(*valid_keys)
-    valid_keys.flatten!
-    each_key do |k|
-      raise(ArgumentError, "Unknown key: #{k}") unless valid_keys.include?(k)
-    end
-  end
-end

data/lib/bioinform/support/third_part/active_support/core_ext/module/attribute_accessors.rb

@@ -1,64 +0,0 @@
-require_relative '../array/extract_options'
-
-class Module
-  def mattr_reader(*syms)
-    options = syms.extract_options!
-    syms.each do |sym|
-      class_eval(<<-EOS, __FILE__, __LINE__ + 1)
-        @@#{sym} = nil unless defined? @@#{sym}
-
-        def self.#{sym}
-          @@#{sym}
-        end
-      EOS
-
-      unless options[:instance_reader] == false || options[:instance_accessor] == false
-        class_eval(<<-EOS, __FILE__, __LINE__ + 1)
-          def #{sym}
-            @@#{sym}
-          end
-        EOS
-      end
-    end
-  end
-
-  def mattr_writer(*syms)
-    options = syms.extract_options!
-    syms.each do |sym|
-      class_eval(<<-EOS, __FILE__, __LINE__ + 1)
-        def self.#{sym}=(obj)
-          @@#{sym} = obj
-        end
-      EOS
-
-      unless options[:instance_writer] == false || options[:instance_accessor] == false
-        class_eval(<<-EOS, __FILE__, __LINE__ + 1)
-          def #{sym}=(obj)
-            @@#{sym} = obj
-          end
-        EOS
-      end
-    end
-  end
-
-  # Extends the module object with module and instance accessors for class attributes,
-  # just like the native attr* accessors for instance attributes.
-  #
-  #  module AppConfiguration
-  #    mattr_accessor :google_api_key
-  #    self.google_api_key = "123456789"
-  #
-  #    mattr_accessor :paypal_url
-  #    self.paypal_url = "www.sandbox.paypal.com"
-  #  end
-  #
-  #  AppConfiguration.google_api_key = "overriding the api key!"
-  #
-  # To opt out of the instance writer method, pass :instance_writer => false.
-  # To opt out of the instance reader method, pass :instance_reader => false.
-  # To opt out of both instance methods, pass :instance_accessor => false.
-  def mattr_accessor(*syms)
-    mattr_reader(*syms)
-    mattr_writer(*syms)
-  end
-end

data/lib/bioinform/support/third_part/active_support/core_ext/object/try.rb

@@ -1,57 +0,0 @@
-class Object
-  # Invokes the method identified by the symbol +method+, passing it any arguments
-  # and/or the block specified, just like the regular Ruby <tt>Object#send</tt> does.
-  #
-  # *Unlike* that method however, a +NoMethodError+ exception will *not* be raised
-  # and +nil+ will be returned instead, if the receiving object is a +nil+ object or NilClass.
-  #
-  # If try is called without a method to call, it will yield any given block with the object.
-  #
-  # Please also note that +try+ is defined on +Object+, therefore it won't work with
-  # subclasses of +BasicObject+. For example, using try with +SimpleDelegator+ will
-  # delegate +try+ to target instead of calling it on delegator itself.
-  #
-  # ==== Examples
-  #
-  # Without +try+
-  #   @person && @person.name
-  # or
-  #   @person ? @person.name : nil
-  #
-  # With +try+
-  #   @person.try(:name)
-  #
-  # +try+ also accepts arguments and/or a block, for the method it is trying
-  #   Person.try(:find, 1)
-  #   @people.try(:collect) {|p| p.name}
-  #
-  # Without a method argument try will yield to the block unless the receiver is nil.
-  #   @person.try { |p| "#{p.first_name} #{p.last_name}" }
-  #--
-  # +try+ behaves like +Object#send+, unless called on +NilClass+.
-  def try(*a, &b)
-    if a.empty? && block_given?
-      yield self
-    else
-      __send__(*a, &b)
-    end
-  end
-end
-
-class NilClass
-  # Calling +try+ on +nil+ always returns +nil+.
-  # It becomes specially helpful when navigating through associations that may return +nil+.
-  #
-  # === Examples
-  #
-  #   nil.try(:name) # => nil
-  #
-  # Without +try+
-  #   @person && !@person.children.blank? && @person.children.first.name
-  #
-  # With +try+
-  #   @person.try(:children).try(:first).try(:name)
-  def try(*args)
-    nil
-  end
-end