Class: NexusParser::Builder

Inherits:
Object
  • Object
show all
Defined in:
lib/nexus_parser.rb

Overview

constructs the NexusParser

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Builder

Returns a new instance of Builder.



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# File 'lib/nexus_parser.rb', line 124

def initialize
  @nf = NexusParser.new
end

Instance Method Details

#add_note(options = {}) ⇒ Object 



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# File 'lib/nexus_parser.rb', line 245

def add_note(options = {})
  @opt = {
    :text => ''
  }.merge!(options)

  case @opt[:type]

  # Why does mesquite differentiate b/w footnotes and annotations?!, apparently same data structure?
  when 'TEXT' # a footnote
    if @opt[:file]
     @nf.notes << NexusParser::Note.new(@opt)

    elsif  @opt[:taxon] && @opt[:character] # its a cell, parse this case
      @nf.codings[@opt[:taxon].to_i - 1][@opt[:character].to_i - 1].notes = [] if !@nf.codings[@opt[:taxon].to_i - 1][@opt[:character].to_i - 1].notes
      @nf.codings[@opt[:taxon].to_i - 1][@opt[:character].to_i - 1].notes << NexusParser::Note.new(@opt)

    elsif @opt[:taxon] && !@opt[:character]
      @nf.taxa[@opt[:taxon].to_i - 1].notes << NexusParser::Note.new(@opt)

    elsif @opt[:character] && !@opt[:taxon]

      @nf.characters[@opt[:character].to_i - 1].notes << NexusParser::Note.new(@opt)
    end

  when 'AN' # an annotation, rather than a footnote, same dif
    if @opt[:t] && @opt[:c]
      @nf.codings[@opt[:t].to_i - 1][@opt[:c].to_i - 1].notes = [] if !@nf.codings[@opt[:t].to_i - 1][@opt[:c].to_i - 1].notes
      @nf.codings[@opt[:t].to_i - 1][@opt[:c].to_i - 1].notes << NexusParser::Note.new(@opt)
    elsif @opt[:t]
      @nf.taxa[@opt[:t].to_i - 1].notes << NexusParser::Note.new(@opt)
    elsif @opt[:c]
      @nf.characters[@opt[:c].to_i - 1].notes << NexusParser::Note.new(@opt)
    end
  end

end

#add_var(hash) ⇒ Object 



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# File 'lib/nexus_parser.rb', line 162

def add_var(hash)
  hash.keys.each do |k|
    raise "var #{k} has already been set" if @nf.vars[:k]
  end
  @nf.vars.update(hash)
end

#code_row(taxon_index, rowvector) ⇒ Object 



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# File 'lib/nexus_parser.rb', line 138

def code_row(taxon_index, rowvector)

  @nf.characters.each_with_index do |c, i|
    raise(ParseError,
      "Row #{taxon_index} of the matrix is too short") if rowvector[i].nil?

    @nf.codings[taxon_index.to_i] = [] if !@nf.codings[taxon_index.to_i]
    @nf.codings[taxon_index.to_i][i] = NexusParser::Coding.new(:states => rowvector[i])

    # !! we must update states for a given character if the state isn't found (not all states are referenced in description !!

    existing_states = @nf.characters[i].state_labels

    new_states = rowvector[i].class == Array ? rowvector[i].collect{|s| s.to_s} :  [rowvector[i].to_s]
    new_states.delete("?") # we don't add this to the db
    new_states = new_states - existing_states

    new_states.each do |s|
      @nf.characters[i].add_state(:label => s)
    end

  end
end

#create_or_update_states_for_character(i, options) ⇒ Object 



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# File 'lib/nexus_parser.rb', line 223

def create_or_update_states_for_character(i, options)
  options.keys.each do |k|

    if (@nf.characters[i].states != {}) && @nf.characters[i].states[k] # state exists

      ## !! ONLY HANDLES NAME, UPDATE TO HANDLE notes etc. when we get them ##
      update_state(i, :index => k, :name => options[k])

    else # doesn't, create it
      @nf.characters[i].add_state(:label => k.to_s, :name => options[k])
    end
  end
end

#nexus_file ⇒ Object 



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# File 'lib/nexus_parser.rb', line 282

def nexus_file
  @nf
end

#stub_chr ⇒ Object 



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# File 'lib/nexus_parser.rb', line 133

def stub_chr
  @nf.characters.push(NexusParser::Character.new)
  return @nf.characters.size
end

#stub_taxon ⇒ Object 



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# File 'lib/nexus_parser.rb', line 128

def stub_taxon
  @nf.taxa.push(NexusParser::Taxon.new)
  return @nf.taxa.size
end

#update_chr(options = {}) ⇒ Object

legal hash keys are :index, :name, and integers that point to state labels

Raises:



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# File 'lib/nexus_parser.rb', line 178

def update_chr(options = {} )
  @opt = {
    :name => ''
  }.merge!(options)
  return false if !@opt[:index]

  @index = @opt[:index].to_i

  # need to create the characters

  raise(ParseError, "Can't update character of index #{@index}, it doesn't exist! This is a problem parsing the character state labels. Check the indices. It may be for this character \"#{@opt[:name]}\".") if !@nf.characters[@index]

  (@nf.characters[@index].name = @opt[:name]) if @opt[:name]

  @opt.delete(:index)
  @opt.delete(:name)

  # the rest have states
  create_or_update_states_for_character(@index, @opt)
end

#update_chr_name(i, name) ⇒ Object

Raises:



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# File 'lib/nexus_parser.rb', line 199

def update_chr_name(i, name)
  raise(ParseError, "There are #{@nf.characters.count} characters but we're trying to update from row #{i + 1} of the CHARLABELS list - check your NCHAR and/or the length of your list.") if !@nf.characters[i]

  # The CHARLABELS list is unindexed, so users are allowed to use '_' to
  # indicate that a character name is unspecified.
  @nf.characters[i].name = (name == '_' ? '' : name)
end

#update_chr_states(options = {}) ⇒ Object

legal hash keys are :index and integers that point to state labels

Raises:



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# File 'lib/nexus_parser.rb', line 208

def update_chr_states(options = {})
  return false if !options[:index]

  @opt = options

  @index = @opt[:index].to_i

  raise(ParseError, "Can't update character of index #{@index}, it doesn't exist! This is a problem parsing the STATELABELS. Check the indices.") if !@nf.characters[@index]

  @opt.delete(:index)

  # the rest have states
  create_or_update_states_for_character(@index, @opt)
end

#update_state(chr_index, options = {}) ⇒ Object 



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# File 'lib/nexus_parser.rb', line 237

def update_state(chr_index, options = {})
  # only handling name now
  #options.keys.each do |k|
    @nf.characters[chr_index].states[options[:index]].name = options[:name]
      # add notes here
  # end
end

#update_taxon(options = {}) ⇒ Object 



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# File 'lib/nexus_parser.rb', line 169

def update_taxon(options = {})
  @opt = {
    :name => ''
  }.merge!(options)
  return false if !@opt[:index]
  (@nf.taxa[@opt[:index]].name = @opt[:name]) if @opt[:name]
end