RubyGems - bio - Versions diffs - 1.5.2 → 1.6.0.pre.20181210 - Mend

bio 1.5.2 → 1.6.0.pre.20181210

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (93) hide show

checksums.yaml +5 -5
data/.travis.yml +12 -11
data/ChangeLog +14 -3106
data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile} +0 -1
data/KNOWN_ISSUES.rdoc +0 -5
data/README.rdoc +11 -18
data/RELEASE_NOTES.rdoc +34 -291
data/Rakefile +13 -9
data/appveyor.yml +21 -0
data/bioruby.gemspec +7 -78
data/bioruby.gemspec.erb +8 -27
data/doc/ChangeLog-1.5.0 +2919 -0
data/doc/RELEASE_NOTES-1.5.0.rdoc +285 -0
data/doc/Tutorial.rd +6 -108
data/doc/Tutorial.rd.html +19 -98
data/gemfiles/Gemfile.travis-jruby1.8 +3 -5
data/gemfiles/Gemfile.travis-jruby1.9 +0 -3
data/gemfiles/Gemfile.travis-rbx +0 -1
data/gemfiles/Gemfile.travis-ruby1.8 +4 -4
data/gemfiles/Gemfile.travis-ruby1.9 +0 -1
data/gemfiles/prepare-gemspec.rb +4 -0
data/lib/bio.rb +0 -10
data/lib/bio/data/codontable.rb +99 -3
data/lib/bio/io/togows.rb +5 -5
data/lib/bio/version.rb +6 -8
data/sample/test_restriction_enzyme_long.rb +1 -1
data/test/unit/bio/data/test_codontable.rb +3 -0
metadata +11 -77
data/bin/bioruby +0 -47
data/bin/br_biofetch.rb +0 -71
data/bin/br_bioflat.rb +0 -293
data/bin/br_biogetseq.rb +0 -45
data/bin/br_pmfetch.rb +0 -422
data/lib/bio/db/biosql/biosql_to_biosequence.rb +0 -78
data/lib/bio/db/biosql/sequence.rb +0 -444
data/lib/bio/db/phyloxml/phyloxml.xsd +0 -582
data/lib/bio/db/phyloxml/phyloxml_elements.rb +0 -1197
data/lib/bio/db/phyloxml/phyloxml_parser.rb +0 -1001
data/lib/bio/db/phyloxml/phyloxml_writer.rb +0 -227
data/lib/bio/io/biosql/ar-biosql.rb +0 -257
data/lib/bio/io/biosql/biosql.rb +0 -39
data/lib/bio/io/biosql/config/database.yml +0 -21
data/lib/bio/io/sql.rb +0 -79
data/lib/bio/shell.rb +0 -44
data/lib/bio/shell/core.rb +0 -578
data/lib/bio/shell/demo.rb +0 -146
data/lib/bio/shell/interface.rb +0 -217
data/lib/bio/shell/irb.rb +0 -94
data/lib/bio/shell/object.rb +0 -71
data/lib/bio/shell/plugin/blast.rb +0 -42
data/lib/bio/shell/plugin/codon.rb +0 -218
data/lib/bio/shell/plugin/das.rb +0 -58
data/lib/bio/shell/plugin/emboss.rb +0 -23
data/lib/bio/shell/plugin/entry.rb +0 -137
data/lib/bio/shell/plugin/flatfile.rb +0 -101
data/lib/bio/shell/plugin/midi.rb +0 -430
data/lib/bio/shell/plugin/ncbirest.rb +0 -68
data/lib/bio/shell/plugin/obda.rb +0 -45
data/lib/bio/shell/plugin/psort.rb +0 -56
data/lib/bio/shell/plugin/seq.rb +0 -248
data/lib/bio/shell/plugin/togows.rb +0 -40
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +0 -29
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +0 -4
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +0 -27
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +0 -11
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +0 -4
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +0 -7
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +0 -368
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +0 -47
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +0 -144
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +0 -47
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +0 -8
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +0 -10
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +0 -26
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
data/lib/bio/shell/script.rb +0 -25
data/lib/bio/shell/setup.rb +0 -108
data/lib/bio/shell/web.rb +0 -102
data/sample/test_phyloxml_big.rb +0 -205
data/test/data/phyloxml/apaf.xml +0 -666
data/test/data/phyloxml/bcl_2.xml +0 -2097
data/test/data/phyloxml/made_up.xml +0 -144
data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +0 -65
data/test/data/phyloxml/phyloxml_examples.xml +0 -415
data/test/unit/bio/db/biosql/tc_biosql.rb +0 -114
data/test/unit/bio/db/biosql/ts_suite_biosql.rb +0 -8
data/test/unit/bio/db/test_phyloxml.rb +0 -821
data/test/unit/bio/db/test_phyloxml_writer.rb +0 -334
data/test/unit/bio/shell/plugin/test_seq.rb +0 -187
data/test/unit/bio/test_shell.rb +0 -20

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml DELETED

@@ -1,47 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>BioRuby shell on Rails</title>
-<%= stylesheet_link_tag "bioruby.css" %>
-<%= javascript_include_tag :defaults %>
-</head>
-<body>
-<div id="content">
- <div id="side">
-  <div class="title">Project</div>
-  <ul>
-   <li><%= link_to "#{File.basename(project_workdir)}", "file://#{project_workdir}" %>
-  </ul>
-  <div class="title">Functions</div>
-  <ul>
-    <li><%= link_to "Console", :action => "index" %></li>
-    <li><%= link_to "History", :action => "history" %></li>
-    <li><%= link_to "Commands", :action => "commands" %></li>
-  </ul>
-  <div class="title">Local variables</div>
-  <%= render :partial => "variables" %>
-  <br>
-  <a href="http://bioruby.org/"><img src="/images/bioruby/link.gif" border=0></a>
- </div><!-- side -->
- <div id="title">
-  <p class="titletop">BioRuby shell on Rails</p>
-  <p class="titlesub">Web interface for the BioRuby library</p>
- </div><!-- title -->
- <div id="main">
-<%= yield %>
- </div><!-- main -->
-</div><!-- content -->
-</body>
-</html>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb DELETED

@@ -1,144 +0,0 @@
-class BiorubyController < ApplicationController
-  HIDE_METHODS = Object.methods + [ "singleton_method_added" ]
-  HIDE_MODULES = [
-    Base64::Deprecated, Base64, PP::ObjectMixin, Bio::Shell,
-  ]
-  HIDE_MODULES << WEBrick if defined?(WEBrick)
-  HIDE_VARIABLES = [
-    "_", "irb", "_erbout",
-  ]
-  SECURITY_NOTICE = "For security purposes, this functionality is only available to local requests."
-  def index
-    unless local_request?
-      flash[:notice] = SECURITY_NOTICE
-    end
-  end
-  def evaluate
-    if local_request?
-      begin
-        @script = params[:script].strip
-        # write out to history
-        Bio::Shell.store_history(@script)
-        # evaluate ruby script
-        @result = eval(@script, Bio::Shell.cache[:binding])
-        # *TODO* need to handle with output of print/puts/p/pp etc. here
-        @output = nil
-      rescue
-        @result = $!
-        @output = nil
-      end
-    else
-      @result = SECURITY_NOTICE
-      @output = nil
-    end
-    @number = Bio::Shell.cache[:results].store(@script, @result, @output)
-    render :update do |page|
-      render_log(page)
-    end
-  end
-  def list_methods
-    number = params[:number].to_i
-    script, result, output = Bio::Shell.cache[:results].restore(number)
-    @class = result.class
-    @methods = (result.methods - HIDE_METHODS).sort
-    render :update do |page|
-      page.replace_html "methods_#{number}", :partial => "methods"
-      page.visual_effect :toggle_blind, "methods_#{number}", :duration => 0.5
-    end
-  end
-  def list_classes
-    number = params[:number].to_i
-    script, result, output = Bio::Shell.cache[:results].restore(number)
-    class_name = result.class
-    @class = class_name
-    @classes = []
-    loop do
-      @classes.unshift(class_name)
-      if class_name == Object
-        break
-      else
-        class_name = class_name.superclass
-      end
-    end
-    render :update do |page|
-      page.replace_html "classes_#{number}", :partial => "classes"
-      page.visual_effect :toggle_blind, "classes_#{number}", :duration => 0.5
-    end
-  end
-  def list_modules
-    number = params[:number].to_i
-    script, result, output = Bio::Shell.cache[:results].restore(number)
-    @class = result.class
-    @modules = result.class.included_modules - HIDE_MODULES
-    render :update do |page|
-      page.replace_html "modules_#{number}", :partial => "modules"
-      page.visual_effect :toggle_blind, "modules_#{number}", :duration => 0.5
-    end
-  end
-  def reload_script
-    number = params[:number].to_i
-    script, result, output = Bio::Shell.cache[:results].restore(number)
-    render :update do |page|
-      page.replace_html :script, script
-    end
-  end
-  def results
-    if Bio::Shell.cache[:results].number > 0
-      limit = params[:limit].to_i
-      max_num = Bio::Shell.cache[:results].number
-      min_num = [ max_num - limit + 1, 1 ].max
-      min_num = 1 if limit == 0
-      render :update do |page|
-        # delete all existing results in the current DOM for clean up
-        page.select(".log").each do |element|
-          #page.hide element
-          page.remove element
-        end
-        # add selected results to the current DOM
-        min_num.upto(max_num) do |@number|
-          #page.show "log_#{@number}"
-          @script, @result, @output = Bio::Shell.cache[:results].restore(@number)
-          if @script
-            render_log(page)
-          end
-        end
-      end
-    end
-  end
-  def commands
-    @bioruby_commands = Bio::Shell.private_instance_methods.sort
-  end
-  def history
-    @history = File.readlines(Bio::Shell.history_file)
-  end
-end

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb DELETED

@@ -1,47 +0,0 @@
-module BiorubyHelper
-  include Bio::Shell
-  def project_workdir
-    if Bio::Shell.cache[:savedir].match(/\.bioruby$/)
-      Bio::Shell.cache[:workdir]
-    else
-      Bio::Shell.cache[:savedir]
-    end
-  end
-  def have_results
-    Bio::Shell.cache[:results].number > 0
-  end
-  def local_variables
-    eval("local_variables", Bio::Shell.cache[:binding]) -
-      BiorubyController::HIDE_VARIABLES
-  end
-  def render_log(page)
-    page.insert_html :top, :logs, :partial => "log"
-    page.replace_html "variables", :partial => "variables"
-    page.hide "methods_#{@number}"
-    page.hide "classes_#{@number}"
-    page.hide "modules_#{@number}"
-  end
-  def reference_link(class_or_module)
-    name = class_or_module.to_s
-    case name
-    when /Bio::(.+)/
-      path = $1.split('::').join('/')
-      url = "http://bioruby.org/rdoc/classes/Bio/#{path}.html"
-    when /Chem::(.+)/
-      path = $1.split('::').join('/')
-      url = "http://chemruby.org/rdoc/classes/Chem/#{path}.html"
-    else
-      path = name.split('::').join('/')
-      url = "http://www.ruby-doc.org/core/classes/#{path}.html"
-    end
-    return "<a href='#{url}'>#{name}</a>"
-  end
-end

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml DELETED

@@ -1,8 +0,0 @@
-<div id="command">
-<h2>BioRuby shell commands</h2>
-<ul>
-  <% @bioruby_commands.each do |cmd| %>
-  <li><%= cmd %></li>
-  <% end %>
-</ul>
-</div>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml DELETED

@@ -1,10 +0,0 @@
-<div id="history">
-<h2>Command history</h2>
-<% @history.each do |line| %>
-<%   if line[/^# /] %>
-<div class="histtime"><%= line %></div>
-<%   else %>
-<div class="histline"><%= line %></div>
-<%   end %>
-<% end %>
-</div>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml DELETED

@@ -1,26 +0,0 @@
-<div id="console">
- <%- if flash[:notice] -%>
-  <div id="notice"><p><%= flash[:notice] %></p></div><br>
- <%- end -%>
- <% form_remote_tag(:url => {:action => "evaluate"}, :position => "top",
-      :before => %(Element.show('spinner')),
-      :complete => %(Element.hide('spinner'))) do %>
-  <img id="spinner" src="/images/bioruby/spinner.gif" style="display:none">
-  <b>BioRuby script:</b>
-  <br/>
-  <textarea id="script" name="script" rows=10 cols=80></textarea>
-  <br/>
-  <input type="submit" value="Evaluate">
-  <input type="reset" value="Clear">
-  &nbsp;&nbsp;
-  Show [
-  <%= link_to_remote "All",    :url => {:action => "results", :limit => 0} %> |
-  <%= link_to_remote "Last 5", :url => {:action => "results", :limit => 5} %> |
-  <%= link_to_remote "Previous", :url => {:action => "results", :limit => 1} %>
-  ] or <%= link_to "Hide", :action => "index" %> results<br/>
- <% end %>
-</div>
-<div id="logs">
-</div>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif DELETED

Binary file

data/lib/bio/shell/script.rb DELETED

@@ -1,25 +0,0 @@
-#
-# = bio/shell/script.rb - script mode for the BioRuby shell
-#
-# Copyright::   Copyright (C) 2006
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: script.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
-#
-module Bio::Shell
-  class Script
-    def initialize(script)
-      Bio::Shell.cache[:binding] = TOPLEVEL_BINDING
-      Bio::Shell.load_session
-      eval(File.read(script), TOPLEVEL_BINDING)
-      exit
-    end
-  end # Script
-end

data/lib/bio/shell/setup.rb DELETED

@@ -1,108 +0,0 @@
-#
-# = bio/shell/setup.rb - setup initial environment for the BioRuby shell
-#
-# Copyright::   Copyright (C) 2006
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-#
-require 'getoptlong'
-class Bio::Shell::Setup
-  def initialize
-    check_ruby_version
-    # command line options
-    getoptlong
-    # setup working directory
-    savedir = setup_savedir
-    # load configuration and plugins
-    Bio::Shell.configure(savedir)
-    # set default to irb mode
-    Bio::Shell.cache[:mode] = ((defined? @mode) && @mode) || :irb
-    case Bio::Shell.cache[:mode]
-    when :web
-      # setup rails server
-      Bio::Shell::Web.new
-    when :irb
-      # setup irb server
-      Bio::Shell::Irb.new
-    when :script
-      # run bioruby shell script
-      Bio::Shell::Script.new(@script)
-    end
-  end
-  def check_ruby_version
-    if RUBY_VERSION < "1.8.2"
-      raise "BioRuby shell runs on Ruby version >= 1.8.2"
-    end
-  end
-  # command line argument (working directory or bioruby shell script file)
-  def getoptlong
-    opts = GetoptLong.new
-    opts.set_options(
-      [ '--rails',   '-r',  GetoptLong::NO_ARGUMENT ],
-      [ '--web',     '-w',  GetoptLong::NO_ARGUMENT ],
-      [ '--console', '-c',  GetoptLong::NO_ARGUMENT ],
-      [ '--irb',     '-i',  GetoptLong::NO_ARGUMENT ]
-    )
-    opts.each_option do |opt, arg|
-      case opt
-      when /--rails/, /--web/
-        @mode = :web
-      when /--console/, /--irb/
-        @mode = :irb
-      end
-    end
-  end
-  def setup_savedir
-    arg = ARGV.shift
-    # Options after the '--' argument are not parsed by GetoptLong and
-    # are passed to irb or rails.  This hack preserve the first option
-    # when working directory of the project is not given.
-    if arg and arg[/^-/]
-      ARGV.unshift arg
-      arg = nil
-    end
-    if arg.nil?
-      # run in the current directory
-      if File.exist?(Bio::Shell::Core::HISTORY)
-        savedir = Dir.pwd
-      else
-        savedir = File.join(ENV['HOME'].to_s, ".bioruby")
-        install_savedir(savedir)
-      end
-    elsif File.file?(arg)
-      # run file as a bioruby shell script
-      savedir = File.join(File.dirname(arg), "..")
-      @script = arg
-      @mode = :script
-    else
-      # run in new or existing directory
-      if arg[/^#{File::SEPARATOR}/]
-        savedir = arg
-      else
-        savedir = File.join(Dir.pwd, arg)
-      end
-      install_savedir(savedir)
-    end
-    return savedir
-  end
-  def install_savedir(savedir)
-    FileUtils.makedirs(savedir)
-  end
-end # Setup

data/lib/bio/shell/web.rb DELETED

@@ -1,102 +0,0 @@
-#
-# = bio/shell/web.rb - GUI for the BioRuby shell
-#
-# Copyright::   Copyright (C) 2006
-#               Nobuya Tanaka <t@chemruby.org>,
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: web.rb,v 1.5 2007/06/26 08:38:38 k Exp $
-#
-module Bio::Shell
-  class Web
-    def initialize
-      Bio::Shell.cache[:binding] = binding
-      Bio::Shell.cache[:results] ||= Results.new
-      install_rails
-      setup_rails
-      start_rails
-    end
-    private
-    def setup_rails
-      puts
-      puts ">>>"
-      puts ">>>  open http://localhost:3000/bioruby"
-      puts ">>>"
-      puts
-      puts '(You can change the port number by adding "-- -p 4000" option)'
-      puts
-    end
-    def install_rails
-      savedir = Bio::Shell.cache[:savedir]
-      path = File.join(savedir, "script", "generate")
-      unless File.exist?(path)
-        puts "Installing Rails application for BioRuby shell ... "
-        system("rails #{savedir}")
-        puts "done"
-      end
-      path = File.join(savedir, "app", "controllers", "bioruby_controller.rb")
-      unless File.exist?(path)
-        basedir = File.dirname(__FILE__)
-        puts "Installing Rails plugin for BioRuby shell ... "
-        FileUtils.cp_r("#{basedir}/rails/.", savedir)
-        Dir.chdir(savedir) do
-          system("./script/generate bioruby shell")
-        end
-        puts "done"
-      end
-    end
-    def start_rails
-      begin
-        Bio::Shell.cache[:rails] = Thread.new do
-          Dir.chdir(Bio::Shell.cache[:savedir]) do
-            require './config/boot'
-            require 'commands/server'
-          end
-        end
-      end
-    end
-    class Results
-      attr_accessor :number, :script, :result, :output
-      def initialize
-        @number = 0
-        @script = []
-        @result = []
-        @output = []
-      end
-      def store(script, result, output)
-        @number += 1
-        @script[@number] = script
-        @result[@number] = result
-        @output[@number] = output
-        return @number
-      end
-      def restore(number)
-        return @script[number], @result[number], @output[number]
-      end
-    end
-  end
-  private
-  # *TODO* stop irb and start rails?
-  #def web
-  #end
-end