Module: ObservationMatricesHelper

Defined in:
app/helpers/observation_matrices_helper.rb

Constant Summary collapse

LABEL_REPLACEMENT = 
{
  '10' => 'A',
  '11' => 'B',
  '12' => 'C',
  '13' => 'D',
  '14' => 'E',
  '15' => 'F',
  '16' => 'G',
  '17' => 'H',
  '18' => 'I',
  '19' => 'J',
  '20' => 'K',
  '21' => 'L',
  '22' => 'M',
  '23' => 'N',
  '24' => 'O',
  '25' => 'P',
  '26' => 'R',
  '27' => 'S',
  '28' => 'T',
  '29' => 'U',
  '30' => 'V',
  '31' => 'W',
  '32' => 'X',
  '33' => 'Y',
  '34' => 'Z',
}.freeze

Instance Method Summary collapse

Instance Method Details

#descriptor_list(observation_matrix) ⇒ Object 



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# File 'app/helpers/observation_matrices_helper.rb', line 136

def descriptor_list(observation_matrix)
  rows = []
  observation_matrix.descriptors.each do |d|
    l = d.name + ': '
    if d.qualitative?
      l << d.character_states.order(:position).collect{|cs| "#{cs.label}: " + cs.name }.join('; ')
    elsif d.presence_absence?
      l << '0: absent; 1: present'
    end
    rows.push l
  end
  rows.join("\n")
end

#keywords_on_addable_column_items ⇒ Object 



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# File 'app/helpers/observation_matrices_helper.rb', line 53

def keywords_on_addable_column_items
  Keyword.joins(:tags).where(project_id: sessions_current_project_id).where(tags: {tag_object_type: 'Descriptor'}).distinct.all
end

#keywords_on_addable_row_items ⇒ Object 



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# File 'app/helpers/observation_matrices_helper.rb', line 49

def keywords_on_addable_row_items
  Keyword.joins(:tags).where(project_id: sessions_current_project_id).where(tags: {tag_object_type: ['Otu', 'CollectionObject']}).distinct.all
end

#max_row_name_width(observation_matrix) ⇒ Object

TODO: This is only used in TNT exports, expand to allow for other export formats



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# File 'app/helpers/observation_matrices_helper.rb', line 61

def max_row_name_width(observation_matrix)
  max = 0

  observation_matrix.observation_matrix_rows.load.each do |r|
    s = observation_matrix_row_label_tnt(r).length
    max = s if max < s
  end
  max + 1
end

#nexus_symbol_list(descriptors) ⇒ String

Returns the list of symbols actually used as character state labels, like 0 1 2 3 4 5 6 7 8 9 A.

Returns:

  • (String) —

    the list of symbols actually used as character state labels, like 0 1 2 3 4 5 6 7 8 9 A



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# File 'app/helpers/observation_matrices_helper.rb', line 153

def nexus_symbol_list(descriptors)
  max = 1
  descriptors.each do |d|
    case d.type
    when 'Descriptor::Qualitative'
      # Assumes non-gap character state labels are sequential starting at 0.
      size = d.has_gap_state? ?
        d.character_states.size - 1 : d.character_states.size
      max = size if size > max
    when 'Descriptor::PresenceAbsence'
      max = 2 if max < 2
    end
  end

  (0..max - 1).to_a
    .map{|i| i > 9 ? LABEL_REPLACEMENT[i.to_s] : i.to_s}.compact.join(' ')
end

#observation_export_value(observation) ⇒ String

Returns the value shown in the cell.

Returns:

  • (String) —

    the value shown in the cell



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# File 'app/helpers/observation_matrices_helper.rb', line 106

def observation_export_value(observation)
  case observation.type
  when 'Observation::Qualitative'
    LABEL_REPLACEMENT[observation.character_state.label].nil? ? observation.character_state.label : LABEL_REPLACEMENT[observation.character_state.label]
  when 'Observation::PresenceAbsence'
    case observation.presence
    when true
      '1'
    when false
      '0'
    when nil
      '?'
    else
      'INTERNAL ERROR'
    end
  when 'Observation::Continuous'
    observation.converted_value.to_s
  when 'Observation::Sample'
    if observation.sample_max && observation.sample_max && observation.sample_max.to_f != observation.sample_min.to_f
      ('%g' % observation.sample_min).to_s + '-' + ('%g' % observation.sample_max).to_s
    elsif observation.sample_min
      ('%g' % observation.sample_min).to_s
    else
      '?'
    end
  else
    '-' # ? not sure
  end
end

#observation_matrices_search_form ⇒ Object 



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# File 'app/helpers/observation_matrices_helper.rb', line 40

def observation_matrices_search_form
  render('/observation_matrices/quick_search_form')
end

#observation_matrix_label(observation_matrix) ⇒ Object 



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# File 'app/helpers/observation_matrices_helper.rb', line 35

def observation_matrix_label(observation_matrix)
  return nil if observation_matrix.nil?
  observation_matrix.name
end

#observation_matrix_link(observation_matrix) ⇒ Object 



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# File 'app/helpers/observation_matrices_helper.rb', line 44

def observation_matrix_link(observation_matrix)
  return nil if observation_matrix.nil?
  link_to(observation_matrix_tag(observation_matrix).html_safe, observation_matrix)
end

#observation_matrix_tag(observation_matrix) ⇒ Object 



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# File 'app/helpers/observation_matrices_helper.rb', line 30

def observation_matrix_tag(observation_matrix)
  return nil if observation_matrix.nil?
  observation_matrix.name
end

#observations_cell_label(observations_hash, descriptor, hash_index, style = :tnt) ⇒ String

Returns the fully formatted cell, handles polymorphisms show states in tnt or nexus format for a ‘cell’ (e.g. [ab]) Mx.print_codings in mx.

Returns:

  • (String) —

    the fully formatted cell, handles polymorphisms show states in tnt or nexus format for a ‘cell’ (e.g. [ab]) Mx.print_codings in mx



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# File 'app/helpers/observation_matrices_helper.rb', line 75

def observations_cell_label(observations_hash, descriptor, hash_index, style = :tnt)

  case observations_hash[descriptor.id][hash_index].size
  when 0
    '?'
  when 1
    o = observations_hash[descriptor.id][hash_index][0]
    s = observation_export_value(o)
    s = LABEL_REPLACEMENT[s].nil? ? s : LABEL_REPLACEMENT[s]

    if s.length > 1 && (style == :nexus || style == :tnt) && o.type == 'Observation::Qualitative'
      "#{s} [WARNING STATE '#{s}' is TOO LARGE FOR PAUP (0-9, A-Z only).]"
    else
      s
    end
  else
    str = observations_hash[descriptor.id][hash_index].collect{|o| observation_export_value(o) }.sort

    case style
    when :csv
      str.join('|')
    when :nexus
      "{#{str.join("")}}"
    else
      "[#{str.join("")}]"
    end
  end
end