bioroebe 0.10.80 → 0.12.24

data/lib/bioroebe/shell/startup.rb

@@ -1,127 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/startup.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # === ensure_that_the_bioshell_log_directory_exists
-  # ========================================================================= #
-  def ensure_that_the_bioshell_log_directory_exists
-    # ======================================================================= #
-    # We must check whether we really wish to create directories on startup
-    # or not.
-    # ======================================================================= #
-    if @internal_hash and
-       @internal_hash.has_key?(:create_directories_on_startup_of_the_shell) and
-       @internal_hash[:create_directories_on_startup_of_the_shell]
-      _ = bioshell_log_dir?
-      unless File.directory? _
-        unless @internal_hash[:silent_startup]
-          erev "Next creating the directory #{sdir(_)}#{rev}."
-        end
-        mkdir(_)
-      end
-      # ===================================================================== #
-      # Determine the path of the .yml file.
-      # ===================================================================== #
-      yaml_file = ::Bioroebe.project_yaml_directory?+
-                  'create_these_directories_on_startup/'\
-                  'create_these_directories_on_startup.yml'
-      if File.exist? yaml_file
-        YAML.load_file(yaml_file).each {|entry|
-          # ================================================================= #
-          # Create all specified subdirectories next.
-          # ================================================================= #
-          _ = "#{log_dir?}#{entry}/"
-          unless File.directory? _
-            unless @internal_hash[:silent_startup]
-              erev "Next creating the directory #{sdir(rds(_))}#{rev}."
-            end
-            mkdir(_)
-          end
-        }
-      end
-    end
-  end
-
-  # ========================================================================= #
-  # === perform_startup_actions                                 (startup tag)
-  #
-  # Currently, the only startup-action we perform is to add
-  # to the statistics.yml file.
-  #
-  # We must check whether we have proper permissions though.
-  # ========================================================================= #
-  def perform_startup_actions
-    # ======================================================================= #
-    # Initialize the default stop codons, if they are empty.
-    # ======================================================================= #
-    if ::Bioroebe.stop_codons?.empty?
-      ::Bioroebe.initialize_default_stop_codons
-    end
-    _ = Bioroebe.file_statistics? # Assign a shorter handle to it.
-    _ = bioshell_log_dir?+File.basename(_)
-    # ======================================================================= #
-    # We must check here if we can write into the base directory.
-    # ======================================================================= #
-    base_directory = File.dirname(_)
-    if File.writable?(base_directory)
-      if File.exist? _ # If it exists, add one to it.
-        what = YAML.load_file(_)
-        what[:n_times] = what[:n_times]+1
-        write_what_into(YAML.dump(what), _)
-      else # else the file does not yet exist, so we create it.
-        hash = { n_times: 1 }
-        write_what_into(YAML.dump(hash), _)
-        if may_we_show_the_startup_information?
-          show_startup_information
-        end
-      end
-    else
-      e "Can not write into the directory `#{sdir(base_directory)}`."
-    end
-    ensure_that_the_bioshell_log_directory_exists
-    consider_analysing_the_local_dataset_on_startup
-    check_for_local_vectors # Also check for local vectors, such as pBR322 datasets stored in fasta files.
-    considering_changing_the_title_of_the_kde_konsole_tab
-    if is_on_roebe?
-      if dna_sequence?.nil? or
-         dna_sequence?.empty?
-        # =================================================================== #
-        # On my home system, we use a sequence of 150 by default.
-        # =================================================================== #
-        set_dna_sequence(150, :be_quiet)
-      end
-    end
-  end
-
-  # ========================================================================= #
-  # === do_a_silent_startup
-  #
-  # Use this method when you want to perform a silent startup.
-  # ========================================================================= #
-  def do_a_silent_startup
-    @internal_hash[:silent_startup] = true
-  end; alias do_silent_startup do_a_silent_startup # === do_silent_startup
-
-  require 'bioroebe/utility_scripts/analyse_local_dataset.rb'
-  # ========================================================================= #
-  # === consider_analysing_the_local_dataset_on_startup
-  #
-  # This method will analyse the local dataset (should it exist), and
-  # then display some information to the user about it.
-  # ========================================================================= #
-  def consider_analysing_the_local_dataset_on_startup
-    if @internal_hash and
-       @internal_hash.has_key?(:analyse_the_local_dataset_on_startup) and
-       @internal_hash[:analyse_the_local_dataset_on_startup]
-      Bioroebe::AnalyseLocalDataset.new
-    end
-  end
-
-end; end

data/lib/bioroebe/shell/taxonomy.rb

@@ -1,14 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# This file will contain code that is specific to Taxonomy-related aspects,
-# in particular browsing these from the NCBI taxonomy base.
-# =========================================================================== #
-# require 'bioroebe/shell/taxonomy.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-end; end

data/lib/bioroebe/shell/tk.rb

@@ -1,23 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/tk.rb'
-# =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
-
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # === start_three_to_one
-  #
-  # Mostly an ad-hoc way to load up a specific ruby-tk widget.
-  # ========================================================================= #
-  def tk_start_three_to_one
-    require 'bioroebe/gui/tk/three_to_one/three_to_one.rb'
-    Bioroebe::GUI::Tk::ThreeToOne.new(ARGV)
-  end
-
-end; end

data/lib/bioroebe/shell/user_input.rb

@@ -1,88 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/user_input.rb'
-# =========================================================================== #
-require 'bioroebe/shell/readline/readline.rb'
-
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  # ========================================================================= #
-  # === user_input?
-  # ========================================================================= #
-  def user_input?
-    @internal_hash[:user_input]
-  end
-
-  # ========================================================================= #
-  # === read_user_input                                           (input tag)
-  #
-  # This method is used to fetch/read user input. The user input
-  # will be kept in an instance variable (called @internal_hash[:user_input],
-  # which is actually a Hash).
-  # ========================================================================= #
-  def read_user_input
-    if readline_is_available?
-      # ===================================================================== #
-      # This clause is the case for the Readline module.
-      # ===================================================================== #
-      user_input = Readline.readline(
-        # =================================================================== #
-        # The second argument enables or disables history support.
-        # =================================================================== #
-        obtain_current_prompt_while_honouring_colours.to_s, true
-      )
-      # ===================================================================== #
-      # === Disallow empty lines to taint the Readline-History
-      #
-      # Ignore empty lines - or rather, remove them after they were input.
-      # ===================================================================== #
-      if user_input =~ /^\s*$/
-        Readline::HISTORY.pop
-      # ===================================================================== #
-      # If we did input the same command as before, on the previous
-      # run, then we will not record this into the readline-history
-      # session.
-      # ===================================================================== #
-      elsif last_inputted_command? == user_input
-        Readline::HISTORY.pop
-      end
-    else
-      # ===================================================================== #
-      # This entry point reads in user-input without depending on Readline.
-      # ===================================================================== #
-      print obtain_current_prompt_while_honouring_colours
-      user_input = $stdin.gets.chomp
-    end
-    user_input.strip! # We do not need or want trailing or leading whitespace.
-    unless user_input.strip.empty?
-      # ===================================================================== #
-      # First, let's get rid of input including '#' - these are assumed
-      # to be comments and are simply ignored.
-      # ===================================================================== #
-      if user_input.include?('#') and (user_input.size > 1)
-        user_input = user_input[0 .. (user_input.index('#')-1)]
-        user_input.rstrip!
-      end
-      # ===================================================================== #
-      # Next sanitize the situation where the user input consists of only
-      # nucleotides, such as ATCG and so forth.
-      # ===================================================================== #
-      if user_input.include?(' ') and only_nucleotides?(user_input.delete(' '))
-        user_input.delete!(' ') # We chop off ' ' tokens, if we only input a nucleotide sequence.
-      end
-      # ===================================================================== #
-      # === Enable multiline input separated via ; next
-      # ===================================================================== #
-      if user_input.include? ';'
-        user_input = user_input.split(';')
-      end
-      @internal_hash[:user_input] = user_input
-      return user_input # Not strictly necessary, but we return anyway.
-    end
-  end; alias get_user_input read_user_input # === get_user_input
-
-end; end

data/lib/bioroebe/shell/xorg.rb

@@ -1,45 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/shell/xorg.rb'
-# =========================================================================== #
-module Bioroebe
-
-class Shell < ::Bioroebe::CommandlineApplication
-
-  begin
-    require 'xorg_buffer/module'
-  rescue LoadError; end
-
-  # ========================================================================= #
-  # === toggle_xorg_buffer
-  # ========================================================================= #
-  def toggle_xorg_buffer
-    @config.additionally_set_xorg_buffer = !@config.additionally_set_xorg_buffer
-    @config.save
-  end
-
-  # ========================================================================= #
-  # === feedback_whether_we_will_also_set_the_xorg_buffer
-  # ========================================================================= #
-  def feedback_whether_we_will_also_set_the_xorg_buffer
-    erev "Will we also set the Xorg buffer? "\
-         "#{sfancy(vt(@config.additionally_set_xorg_buffer.to_s))}"
-  end
-
-  # ========================================================================= #
-  # === set_xclip                           (xclip tag, xorg tag, buffer tag)
-  #
-  # Use this method to assign to the Linux Xorg Buffer.
-  #
-  # By default we will assign the DNA nucleotide sequence to be
-  # the new buffer.
-  # ========================================================================= #
-  def set_xclip(
-      i = dna_string?
-    )
-    XorgBuffer.set_xorg_buffer(i)
-  end
-
-end; end

data/lib/bioroebe/utility_scripts/compacter.rb

@@ -1,131 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::Compacter
-#
-# This class can be used to compact a file, in particular FASTA files.
-#
-# The first line will be removed if it starts with a ">" token.
-#
-# Usage example:
-#
-#   Bioroebe::Compacter.new(ARGV)
-#
-# =========================================================================== #
-# require 'bioroebe/utility_scripts/compacter.rb'
-# =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
-
-module Bioroebe
-
-class Compacter < ::Bioroebe::CommandlineApplication # === Bioroebe::Compacter
-
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize(
-      i           = nil,
-      run_already = true
-    )
-    register_sigint
-    reset
-    set_input(i)
-    case run_already
-    # ======================================================================= #
-    # === :do_not_ask_for_user_input
-    # ======================================================================= #
-    when :do_not_ask_for_user_input
-      @ask_for_user_input = false
-      run_already = true
-    end
-    run if run_already
-  end
-
-  # ========================================================================= #
-  # === reset                                                     (reset tag)
-  # ========================================================================= #
-  def reset
-    super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
-    # ======================================================================= #
-    # === @ask_for_user_input
-    # ======================================================================= #
-    @ask_for_user_input = true
-  end
-
-  # ========================================================================= #
-  # === set_input
-  # ========================================================================= #
-  def set_input(i = '')
-    i = i.first if i.is_a? Array
-    i = i.to_s.dup if i
-    @input = i
-  end
-
-  # ========================================================================= #
-  # === input?
-  # ========================================================================= #
-  def input?
-    @input
-  end; alias file? input? # === file?
-
-  # ========================================================================= #
-  # === run                                                         (run tag)
-  # ========================================================================= #
-  def run
-    this_file = file?
-    if this_file
-      if File.exist? this_file
-        # =================================================================== #
-        # Tell the user which file we will compact next.
-        # =================================================================== #
-        e "We will now compact the file `#{sfile(this_file)}`."
-        dataset = File.read(this_file)
-        if dataset.start_with? 'ORIGIN'
-          dataset[0,'ORIGIN'.size] = ''
-          dataset.lstrip!
-        elsif dataset.start_with? '>'
-          # ================================================================= #
-          # In this case, chop off the first line completely.
-          # ================================================================= #
-          dataset[0, dataset.index("\n")] = ''
-          dataset.lstrip!
-        end
-        # =================================================================== #
-        # Here we tap into class Bioroebe::SanitizeNucleotideSequence
-        # =================================================================== #
-        require 'bioroebe/nucleotides/sanitize_nucleotide_sequence.rb'
-        dataset = Bioroebe::SanitizeNucleotideSequence[dataset]
-        if @ask_for_user_input
-          e 'We will now store into the same file, but you must'
-          e 'type "'+steelblue('y')+'" to confirm, else we cancel:'
-          user_input = $stdin.gets.chomp
-        else
-          user_input = 'yes'
-        end
-        if user_input.start_with? 'y'
-          e "Now storing into the file #{sfile(this_file)}."
-          write_what_into(dataset, this_file)
-        end
-      else
-        e "The file `#{sfile(this_file)}` does not exist."
-      end
-    else
-      opnn; e 'Please provide an existing file as input.'
-    end
-  end
-
-end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::Compacter.new(ARGV, :do_not_ask_for_user_input)
-end # compacter