Module: Bioroebe::CommandlineArguments

Includes:
ColoursForBase
Included in:
CommandlineApplication, GUI::UniversalWidgets::Alignment, GUI::UniversalWidgets::AminoacidComposition, GUI::UniversalWidgets::AntiSenseStrand, GUI::UniversalWidgets::BlosumMatrixViewer, GUI::UniversalWidgets::CalculateCellNumbersOfBacteria, GUI::UniversalWidgets::Controller, GUI::UniversalWidgets::DnaToAminoacidWidget, GUI::UniversalWidgets::DnaToReverseComplementWidget, GUI::UniversalWidgets::FastaTableWidget, GUI::UniversalWidgets::FormatConverter, GUI::UniversalWidgets::Gene, GUI::UniversalWidgets::HammingDistance, GUI::UniversalWidgets::LevenstheinDistance, GUI::UniversalWidgets::NucleotideAnalyser, GUI::UniversalWidgets::ParsePdbFile, GUI::UniversalWidgets::PrimerDesignWidget, GUI::UniversalWidgets::RandomSequence, GUI::UniversalWidgets::RestrictionEnzymes, GUI::UniversalWidgets::ShowCodonTable, GUI::UniversalWidgets::ShowCodonUsage, GUI::UniversalWidgets::Sizeseq, GUI::UniversalWidgets::ThreeToOne, GUI::UniversalWidgets::WwwFinder, ShowNucleotideSequence
Defined in:
lib/bioroebe/base/commandline_application/commandline_arguments.rb

Overview

Bioroebe::CommandlineArguments

Constant Summary

Constants included from ColoursForBase

Bioroebe::ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Instance Method Summary collapse

Methods included from ColoursForBase

#colourize_this_aminoacid_sequence_for_the_commandline, #colourize_this_nucleotide_sequence, #disable_colours, #ecomment, #efancy, #egold, #enable_colours, #eorange, #eparse, #erev, #red, #remove_trailing_escape_part, #return_colour_for_nucleotides, #rev, #sdir, #set_will_we_use_colours, #sfancy, #sfile, #simp, #swarn, #use_colours?, #use_colours_within_the_bioroebe_namespace?

Instance Method Details

#commandline_arguments? ⇒ Boolean

#

commandline_arguments?

Query method to obtain all commandline arguments given to this class.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/base/commandline_application/commandline_arguments.rb', line 38

def commandline_arguments?
  @commandline_arguments
end

#commandline_arguments_that_are_files? ⇒ Boolean

#

commandline_arguments_that_are_files?

This method will select the entries that are a file (which must exist locally).

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/base/commandline_application/commandline_arguments.rb', line 58

def commandline_arguments_that_are_files?
  @commandline_arguments.select {|entry| File.file?(entry.to_s) }
end

#e(i = '') ⇒ Object

#

e

#


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# File 'lib/bioroebe/base/commandline_application/commandline_arguments.rb', line 18

def e(i = '')
  puts i
end

#first? ⇒ Boolean Also known as: first_argument?, first_argument, input_file?, first_commandline_argument?

#

first?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/base/commandline_application/commandline_arguments.rb', line 45

def first?
  @commandline_arguments.first
end

#first_non_hyphen_argument? ⇒ Boolean Also known as: first_non_hyphened_argument?

#

first_non_hyphen_argument?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/base/commandline_application/commandline_arguments.rb', line 106

def first_non_hyphen_argument?
  return_entries_without_two_leading_hyphens.first
end

#remove_hyphens_from_the_commandline_arguments(i = @commandline_arguments) ⇒ Object Also known as: remove_hyphens_from

#

remove_hyphens_from_the_commandline_arguments

#


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# File 'lib/bioroebe/base/commandline_application/commandline_arguments.rb', line 88

def remove_hyphens_from_the_commandline_arguments(
    i = @commandline_arguments
  )
  i.reject! {|entry| entry.start_with? '--' }
end

#return_commandline_arguments_as_string ⇒ Object

#

return_commandline_arguments_as_string

This method will return the commandline arguments as a String.

#


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# File 'lib/bioroebe/base/commandline_application/commandline_arguments.rb', line 99

def return_commandline_arguments_as_string
  @commandline_arguments.join(' ').strip
end

#return_commandline_arguments_that_are_not_files ⇒ Object

#

return_commandline_arguments_that_are_not_files

This method will grab all entries that are NOT files.

#


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# File 'lib/bioroebe/base/commandline_application/commandline_arguments.rb', line 67

def return_commandline_arguments_that_are_not_files
  @commandline_arguments.reject {|entry| File.file?(entry.to_s) }
end

#return_entries_without_two_leading_hyphens(i = @commandline_arguments) ⇒ Object Also known as: return_commandline_arguments_without_hyphen, reject_hyphens, non_hyphened_commandline_arguments?

#

return_entries_without_two_leading_hyphens

This variant will return all entries WITHOUT leading hyphens.

#


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# File 'lib/bioroebe/base/commandline_application/commandline_arguments.rb', line 142

def return_entries_without_two_leading_hyphens(
    i = @commandline_arguments
  )
  i.reject {|entry| entry.start_with? '--' }
end

#select_commandline_arguments(i = @commandline_arguments) ⇒ Object

#

select_commandline_arguments

This method can be used to select commandline arguments that begin with – hyphens.

#


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# File 'lib/bioroebe/base/commandline_application/commandline_arguments.rb', line 77

def select_commandline_arguments(
    i = @commandline_arguments
  )
  i.select {|entry|
    entry.start_with? '--'
  }
end

#select_entries_starting_with_two_hyphens(i = commandline_arguments? ) ⇒ Object Also known as: return_commandline_arguments_starting_with_hyphens, return_entries_with_two_leading_hyphens_from, return_arguments_with_leading_hyphens, return_commandline_arguments_starting_with_two_hyphens, commandline_arguments_with_leading_hyphens?, commandline_arguments_containing_hyphens?, commandline_arguments_containing_leading_hyphens?, commandline_arguments_with_two_leading_hyphens, commandline_arguments_starting_with_leading_hyphens?, commandline_arguments_starting_with_a_hyphen?, commandline_arguments_starting_with_a_hyphen, select_two_hyphens_from

#

select_entries_starting_with_two_hyphens

This entry can, specifically, be used to filter out proper commandline arguments from an Array (such as ARGV).

#


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# File 'lib/bioroebe/base/commandline_application/commandline_arguments.rb', line 116

def select_entries_starting_with_two_hyphens(
    i = commandline_arguments?
  )
  if i.respond_to? :select
    i.select {|entry| entry.to_s.start_with? '--' } # .to_s to prevent Integers passed.
  else
    []
  end
end

#set_commandline_arguments(i = ARGV) ⇒ Object

#

set_commandline_arguments

This method can be used to set the commandline arguments, which usually refers to ARGV.

#


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# File 'lib/bioroebe/base/commandline_application/commandline_arguments.rb', line 28

def set_commandline_arguments(i = ARGV)
  i = [i].flatten.compact
  @commandline_arguments = i
end