Module: Map::Coordinate

Defined in:
app/models/map.rb

Constant Summary collapse

PLATE_DIMENSIONS =
Note:
  • 96 represents a 96-well plate, arranged in 12 columns and 8 rows.
  • 384 represents a 384-well plate, arranged in 24 columns and 16 rows.
  • 16 represents a 16-well Chromium Chip, which has 8 columns and 2 rows. Although a 16-well Chromium Chip does not have 3:2 ratio to be a standard plate, i.e. it has 4:1 ratio, the methods here still apply. Note that the asset shape is a generic one, Shape4x1, although it has been created for the 16-well Chromium Chip.
  • 8 represents a 8-well Chromium Chip, which has 8 columns and 1 row. Note that the asset shape is a generic one, Shape8x1, although it has been created for the 8-well Chromium Chip.

A hash representing the dimensions of different types of plates. The keys are the total number of wells in the plate, and the values are arrays, where the first element is the number of columns and the second element is the number of rows.

Returns:

  • (Hash{Integer => Array<Integer>}) —

    the dimensions of the plates

Hash.new { |_h, _k| [] }.merge(96 => [12, 8], 384 => [24, 16], 16 => [8, 2], 8 => [8, 1])

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Attribute Details

#asset_size ⇒ Integer

Returns the plate size for which the Map corresponds.

Returns:

  • (Integer) —

    the plate size for which the Map corresponds



17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
 
# File 'app/models/map.rb', line 17

module Coordinate
  # TODO: These methods are only valid for standard plates. Moved them here to make that more explicit
  # (even if its not strictly appropriate) They could do with refactoring/removing.

  # A hash representing the dimensions of different types of plates.
  # The keys are the total number of wells in the plate, and the values are
  # arrays, where the first element is the number of columns and the second
  # element is the number of rows.
  #
  # @note
  #   - 96 represents a 96-well plate, arranged in 12 columns and 8 rows.
  #   - 384 represents a 384-well plate, arranged in 24 columns and 16 rows.
  #   - 16 represents a 16-well Chromium Chip, which has 8 columns and 2 rows.
  #     Although a 16-well Chromium Chip does not have 3:2 ratio to be a
  #     standard plate, i.e. it has 4:1 ratio, the methods here still apply.
  #     Note that the asset shape is a generic one, Shape4x1, although it has
  #     been created for the 16-well Chromium Chip.
  #   - 8 represents a 8-well Chromium Chip, which has 8 columns and 1 row.
  #     Note that the asset shape is a generic one, Shape8x1, although it has
  #     been created for the 8-well Chromium Chip.
  # @return [Hash{Integer => Array<Integer>}] the dimensions of the plates
  PLATE_DIMENSIONS = Hash.new { |_h, _k| [] }.merge(96 => [12, 8], 384 => [24, 16], 16 => [8, 2], 8 => [8, 1])

  # Seems to expect row to be zero-indexed but column to be 1 indexed
  def self.location_from_row_and_column(row, column, _ = nil, __ = nil)
    "#{('A'.getbyte(0) + row).chr}#{column}"
  end

  def self.description_to_horizontal_plate_position(well_description, plate_size)
    return nil unless Map.valid_well_description_and_plate_size?(well_description, plate_size)

    split_well = Map.split_well_description(well_description)
    width = plate_width(plate_size)
    return nil if width.nil?

    (width * split_well[:row]) + split_well[:col]
  end

  # e.g. B5 returns 34 for a 96 well plate
  # So 4 columns of 8 rows each, plus 2 for the B row
  def self.well_description_to_by_column_map_index(well_description, plate_size)
    return nil unless Map.valid_well_description_and_plate_size?(well_description, plate_size)

    split_well = Map.split_well_description(well_description)
    length = plate_length(plate_size)
    return nil if length.nil?

    (length * (split_well[:col] - 1)) + split_well[:row] + 1
  end

  # e.g. 23 returns B11 for a 96 well plate
  # So 1 full row of 12, plus 11, to give row B, column 11
  def self.by_row_map_index_to_well_description(well_position, plate_size)
    return nil unless Map.valid_plate_position_and_plate_size?(well_position, plate_size)

    width = plate_width(plate_size)
    return nil if width.nil?

    horizontal_position_to_description(well_position, width)
  end

  # e.g. 23 returns G3 for a 96 well plate
  # So 2 full columns of 8, plus 7, to give row G, column 3
  def self.by_column_map_index_to_well_description(well_position, plate_size)
    return nil unless Map.valid_plate_position_and_plate_size?(well_position, plate_size)

    length = plate_length(plate_size)
    return nil if length.nil?

    vertical_position_to_description(well_position, length)
  end

  def self.descriptions_for_row(row, size)
    (1..plate_width(size)).map { |column| "#{row}#{column}" }
  end

  def self.descriptions_for_column(column, size)
    (0...plate_length(size)).map { |row| Map.location_from_row_and_column(row, column) }
  end

  def self.plate_width(plate_size)
    PLATE_DIMENSIONS[plate_size].first
  end

  def self.plate_length(plate_size)
    PLATE_DIMENSIONS[plate_size].last
  end

  # well number counting by columns, length is the number of rows in the plate
  # e.g. B5 sends this 34 and 8
  def self.vertical_position_to_description(well_position, length)
    desc_letter = (((well_position - 1) % length) + 65).chr
    desc_number = ((well_position - 1) / length) + 1
    (desc_letter + desc_number.to_s)
  end

  def self.horizontal_position_to_description(well_position, width)
    desc_letter = (((well_position - 1) / width) + 65).chr
    desc_number = ((well_position - 1) % width) + 1
    (desc_letter + desc_number.to_s)
  end

  def self.horizontal_to_vertical(well_position, plate_size)
    alternate_position(well_position, plate_size, :width, :length)
  end

  def self.vertical_to_horizontal(well_position, plate_size)
    alternate_position(well_position, plate_size, :length, :width)
  end

  def self.location_from_index(index, size)
    by_row_map_index_to_well_description(index + 1, size)
  end

  class << self
    # Given the well position described in terms of a direction (vertical or horizontal) this function
    # will map it to the alternate positional representation, i.e. a vertical position will be mapped
    # to a horizontal one.  It does this with the divisor and multiplier, which will be reversed for
    # the alternate.
    #
    # NOTE: I don't like this, it just makes things clearer than it was!
    # NOTE: I hate the nil returns but external code would take too long to change this time round
    def alternate_position(well_position, size, *dimensions)
      return nil unless Map.valid_well_position?(well_position)

      divisor, multiplier = dimensions.map { |n| send(:"plate_#{n}", size) }
      return nil if divisor.nil? || multiplier.nil?

      column, row = (well_position - 1).divmod(divisor)
      return nil unless (0...multiplier).cover?(column)
      return nil unless (0...divisor).cover?(row)

      (row * multiplier) + column + 1
    end
    private :alternate_position
  end
end

#column_order ⇒ Integer

Returns zero indexed order of the well when sorted by column.

Returns:

  • (Integer) —

    zero indexed order of the well when sorted by column



17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
 
# File 'app/models/map.rb', line 17

module Coordinate
  # TODO: These methods are only valid for standard plates. Moved them here to make that more explicit
  # (even if its not strictly appropriate) They could do with refactoring/removing.

  # A hash representing the dimensions of different types of plates.
  # The keys are the total number of wells in the plate, and the values are
  # arrays, where the first element is the number of columns and the second
  # element is the number of rows.
  #
  # @note
  #   - 96 represents a 96-well plate, arranged in 12 columns and 8 rows.
  #   - 384 represents a 384-well plate, arranged in 24 columns and 16 rows.
  #   - 16 represents a 16-well Chromium Chip, which has 8 columns and 2 rows.
  #     Although a 16-well Chromium Chip does not have 3:2 ratio to be a
  #     standard plate, i.e. it has 4:1 ratio, the methods here still apply.
  #     Note that the asset shape is a generic one, Shape4x1, although it has
  #     been created for the 16-well Chromium Chip.
  #   - 8 represents a 8-well Chromium Chip, which has 8 columns and 1 row.
  #     Note that the asset shape is a generic one, Shape8x1, although it has
  #     been created for the 8-well Chromium Chip.
  # @return [Hash{Integer => Array<Integer>}] the dimensions of the plates
  PLATE_DIMENSIONS = Hash.new { |_h, _k| [] }.merge(96 => [12, 8], 384 => [24, 16], 16 => [8, 2], 8 => [8, 1])

  # Seems to expect row to be zero-indexed but column to be 1 indexed
  def self.location_from_row_and_column(row, column, _ = nil, __ = nil)
    "#{('A'.getbyte(0) + row).chr}#{column}"
  end

  def self.description_to_horizontal_plate_position(well_description, plate_size)
    return nil unless Map.valid_well_description_and_plate_size?(well_description, plate_size)

    split_well = Map.split_well_description(well_description)
    width = plate_width(plate_size)
    return nil if width.nil?

    (width * split_well[:row]) + split_well[:col]
  end

  # e.g. B5 returns 34 for a 96 well plate
  # So 4 columns of 8 rows each, plus 2 for the B row
  def self.well_description_to_by_column_map_index(well_description, plate_size)
    return nil unless Map.valid_well_description_and_plate_size?(well_description, plate_size)

    split_well = Map.split_well_description(well_description)
    length = plate_length(plate_size)
    return nil if length.nil?

    (length * (split_well[:col] - 1)) + split_well[:row] + 1
  end

  # e.g. 23 returns B11 for a 96 well plate
  # So 1 full row of 12, plus 11, to give row B, column 11
  def self.by_row_map_index_to_well_description(well_position, plate_size)
    return nil unless Map.valid_plate_position_and_plate_size?(well_position, plate_size)

    width = plate_width(plate_size)
    return nil if width.nil?

    horizontal_position_to_description(well_position, width)
  end

  # e.g. 23 returns G3 for a 96 well plate
  # So 2 full columns of 8, plus 7, to give row G, column 3
  def self.by_column_map_index_to_well_description(well_position, plate_size)
    return nil unless Map.valid_plate_position_and_plate_size?(well_position, plate_size)

    length = plate_length(plate_size)
    return nil if length.nil?

    vertical_position_to_description(well_position, length)
  end

  def self.descriptions_for_row(row, size)
    (1..plate_width(size)).map { |column| "#{row}#{column}" }
  end

  def self.descriptions_for_column(column, size)
    (0...plate_length(size)).map { |row| Map.location_from_row_and_column(row, column) }
  end

  def self.plate_width(plate_size)
    PLATE_DIMENSIONS[plate_size].first
  end

  def self.plate_length(plate_size)
    PLATE_DIMENSIONS[plate_size].last
  end

  # well number counting by columns, length is the number of rows in the plate
  # e.g. B5 sends this 34 and 8
  def self.vertical_position_to_description(well_position, length)
    desc_letter = (((well_position - 1) % length) + 65).chr
    desc_number = ((well_position - 1) / length) + 1
    (desc_letter + desc_number.to_s)
  end

  def self.horizontal_position_to_description(well_position, width)
    desc_letter = (((well_position - 1) / width) + 65).chr
    desc_number = ((well_position - 1) % width) + 1
    (desc_letter + desc_number.to_s)
  end

  def self.horizontal_to_vertical(well_position, plate_size)
    alternate_position(well_position, plate_size, :width, :length)
  end

  def self.vertical_to_horizontal(well_position, plate_size)
    alternate_position(well_position, plate_size, :length, :width)
  end

  def self.location_from_index(index, size)
    by_row_map_index_to_well_description(index + 1, size)
  end

  class << self
    # Given the well position described in terms of a direction (vertical or horizontal) this function
    # will map it to the alternate positional representation, i.e. a vertical position will be mapped
    # to a horizontal one.  It does this with the divisor and multiplier, which will be reversed for
    # the alternate.
    #
    # NOTE: I don't like this, it just makes things clearer than it was!
    # NOTE: I hate the nil returns but external code would take too long to change this time round
    def alternate_position(well_position, size, *dimensions)
      return nil unless Map.valid_well_position?(well_position)

      divisor, multiplier = dimensions.map { |n| send(:"plate_#{n}", size) }
      return nil if divisor.nil? || multiplier.nil?

      column, row = (well_position - 1).divmod(divisor)
      return nil unless (0...multiplier).cover?(column)
      return nil unless (0...divisor).cover?(row)

      (row * multiplier) + column + 1
    end
    private :alternate_position
  end
end

#description ⇒ String

Returns the name of the well. In most cases this will be in the along the lines of A1 or H12.

Returns:

  • (String) —

    the name of the well. In most cases this will be in the along the lines of A1 or H12



17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
 
# File 'app/models/map.rb', line 17

module Coordinate
  # TODO: These methods are only valid for standard plates. Moved them here to make that more explicit
  # (even if its not strictly appropriate) They could do with refactoring/removing.

  # A hash representing the dimensions of different types of plates.
  # The keys are the total number of wells in the plate, and the values are
  # arrays, where the first element is the number of columns and the second
  # element is the number of rows.
  #
  # @note
  #   - 96 represents a 96-well plate, arranged in 12 columns and 8 rows.
  #   - 384 represents a 384-well plate, arranged in 24 columns and 16 rows.
  #   - 16 represents a 16-well Chromium Chip, which has 8 columns and 2 rows.
  #     Although a 16-well Chromium Chip does not have 3:2 ratio to be a
  #     standard plate, i.e. it has 4:1 ratio, the methods here still apply.
  #     Note that the asset shape is a generic one, Shape4x1, although it has
  #     been created for the 16-well Chromium Chip.
  #   - 8 represents a 8-well Chromium Chip, which has 8 columns and 1 row.
  #     Note that the asset shape is a generic one, Shape8x1, although it has
  #     been created for the 8-well Chromium Chip.
  # @return [Hash{Integer => Array<Integer>}] the dimensions of the plates
  PLATE_DIMENSIONS = Hash.new { |_h, _k| [] }.merge(96 => [12, 8], 384 => [24, 16], 16 => [8, 2], 8 => [8, 1])

  # Seems to expect row to be zero-indexed but column to be 1 indexed
  def self.location_from_row_and_column(row, column, _ = nil, __ = nil)
    "#{('A'.getbyte(0) + row).chr}#{column}"
  end

  def self.description_to_horizontal_plate_position(well_description, plate_size)
    return nil unless Map.valid_well_description_and_plate_size?(well_description, plate_size)

    split_well = Map.split_well_description(well_description)
    width = plate_width(plate_size)
    return nil if width.nil?

    (width * split_well[:row]) + split_well[:col]
  end

  # e.g. B5 returns 34 for a 96 well plate
  # So 4 columns of 8 rows each, plus 2 for the B row
  def self.well_description_to_by_column_map_index(well_description, plate_size)
    return nil unless Map.valid_well_description_and_plate_size?(well_description, plate_size)

    split_well = Map.split_well_description(well_description)
    length = plate_length(plate_size)
    return nil if length.nil?

    (length * (split_well[:col] - 1)) + split_well[:row] + 1
  end

  # e.g. 23 returns B11 for a 96 well plate
  # So 1 full row of 12, plus 11, to give row B, column 11
  def self.by_row_map_index_to_well_description(well_position, plate_size)
    return nil unless Map.valid_plate_position_and_plate_size?(well_position, plate_size)

    width = plate_width(plate_size)
    return nil if width.nil?

    horizontal_position_to_description(well_position, width)
  end

  # e.g. 23 returns G3 for a 96 well plate
  # So 2 full columns of 8, plus 7, to give row G, column 3
  def self.by_column_map_index_to_well_description(well_position, plate_size)
    return nil unless Map.valid_plate_position_and_plate_size?(well_position, plate_size)

    length = plate_length(plate_size)
    return nil if length.nil?

    vertical_position_to_description(well_position, length)
  end

  def self.descriptions_for_row(row, size)
    (1..plate_width(size)).map { |column| "#{row}#{column}" }
  end

  def self.descriptions_for_column(column, size)
    (0...plate_length(size)).map { |row| Map.location_from_row_and_column(row, column) }
  end

  def self.plate_width(plate_size)
    PLATE_DIMENSIONS[plate_size].first
  end

  def self.plate_length(plate_size)
    PLATE_DIMENSIONS[plate_size].last
  end

  # well number counting by columns, length is the number of rows in the plate
  # e.g. B5 sends this 34 and 8
  def self.vertical_position_to_description(well_position, length)
    desc_letter = (((well_position - 1) % length) + 65).chr
    desc_number = ((well_position - 1) / length) + 1
    (desc_letter + desc_number.to_s)
  end

  def self.horizontal_position_to_description(well_position, width)
    desc_letter = (((well_position - 1) / width) + 65).chr
    desc_number = ((well_position - 1) % width) + 1
    (desc_letter + desc_number.to_s)
  end

  def self.horizontal_to_vertical(well_position, plate_size)
    alternate_position(well_position, plate_size, :width, :length)
  end

  def self.vertical_to_horizontal(well_position, plate_size)
    alternate_position(well_position, plate_size, :length, :width)
  end

  def self.location_from_index(index, size)
    by_row_map_index_to_well_description(index + 1, size)
  end

  class << self
    # Given the well position described in terms of a direction (vertical or horizontal) this function
    # will map it to the alternate positional representation, i.e. a vertical position will be mapped
    # to a horizontal one.  It does this with the divisor and multiplier, which will be reversed for
    # the alternate.
    #
    # NOTE: I don't like this, it just makes things clearer than it was!
    # NOTE: I hate the nil returns but external code would take too long to change this time round
    def alternate_position(well_position, size, *dimensions)
      return nil unless Map.valid_well_position?(well_position)

      divisor, multiplier = dimensions.map { |n| send(:"plate_#{n}", size) }
      return nil if divisor.nil? || multiplier.nil?

      column, row = (well_position - 1).divmod(divisor)
      return nil unless (0...multiplier).cover?(column)
      return nil unless (0...divisor).cover?(row)

      (row * multiplier) + column + 1
    end
    private :alternate_position
  end
end

#row_order ⇒ Integer

Returns zero indexed order of the well when sorted by row.

Returns:

  • (Integer) —

    zero indexed order of the well when sorted by row



17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
 
# File 'app/models/map.rb', line 17

module Coordinate
  # TODO: These methods are only valid for standard plates. Moved them here to make that more explicit
  # (even if its not strictly appropriate) They could do with refactoring/removing.

  # A hash representing the dimensions of different types of plates.
  # The keys are the total number of wells in the plate, and the values are
  # arrays, where the first element is the number of columns and the second
  # element is the number of rows.
  #
  # @note
  #   - 96 represents a 96-well plate, arranged in 12 columns and 8 rows.
  #   - 384 represents a 384-well plate, arranged in 24 columns and 16 rows.
  #   - 16 represents a 16-well Chromium Chip, which has 8 columns and 2 rows.
  #     Although a 16-well Chromium Chip does not have 3:2 ratio to be a
  #     standard plate, i.e. it has 4:1 ratio, the methods here still apply.
  #     Note that the asset shape is a generic one, Shape4x1, although it has
  #     been created for the 16-well Chromium Chip.
  #   - 8 represents a 8-well Chromium Chip, which has 8 columns and 1 row.
  #     Note that the asset shape is a generic one, Shape8x1, although it has
  #     been created for the 8-well Chromium Chip.
  # @return [Hash{Integer => Array<Integer>}] the dimensions of the plates
  PLATE_DIMENSIONS = Hash.new { |_h, _k| [] }.merge(96 => [12, 8], 384 => [24, 16], 16 => [8, 2], 8 => [8, 1])

  # Seems to expect row to be zero-indexed but column to be 1 indexed
  def self.location_from_row_and_column(row, column, _ = nil, __ = nil)
    "#{('A'.getbyte(0) + row).chr}#{column}"
  end

  def self.description_to_horizontal_plate_position(well_description, plate_size)
    return nil unless Map.valid_well_description_and_plate_size?(well_description, plate_size)

    split_well = Map.split_well_description(well_description)
    width = plate_width(plate_size)
    return nil if width.nil?

    (width * split_well[:row]) + split_well[:col]
  end

  # e.g. B5 returns 34 for a 96 well plate
  # So 4 columns of 8 rows each, plus 2 for the B row
  def self.well_description_to_by_column_map_index(well_description, plate_size)
    return nil unless Map.valid_well_description_and_plate_size?(well_description, plate_size)

    split_well = Map.split_well_description(well_description)
    length = plate_length(plate_size)
    return nil if length.nil?

    (length * (split_well[:col] - 1)) + split_well[:row] + 1
  end

  # e.g. 23 returns B11 for a 96 well plate
  # So 1 full row of 12, plus 11, to give row B, column 11
  def self.by_row_map_index_to_well_description(well_position, plate_size)
    return nil unless Map.valid_plate_position_and_plate_size?(well_position, plate_size)

    width = plate_width(plate_size)
    return nil if width.nil?

    horizontal_position_to_description(well_position, width)
  end

  # e.g. 23 returns G3 for a 96 well plate
  # So 2 full columns of 8, plus 7, to give row G, column 3
  def self.by_column_map_index_to_well_description(well_position, plate_size)
    return nil unless Map.valid_plate_position_and_plate_size?(well_position, plate_size)

    length = plate_length(plate_size)
    return nil if length.nil?

    vertical_position_to_description(well_position, length)
  end

  def self.descriptions_for_row(row, size)
    (1..plate_width(size)).map { |column| "#{row}#{column}" }
  end

  def self.descriptions_for_column(column, size)
    (0...plate_length(size)).map { |row| Map.location_from_row_and_column(row, column) }
  end

  def self.plate_width(plate_size)
    PLATE_DIMENSIONS[plate_size].first
  end

  def self.plate_length(plate_size)
    PLATE_DIMENSIONS[plate_size].last
  end

  # well number counting by columns, length is the number of rows in the plate
  # e.g. B5 sends this 34 and 8
  def self.vertical_position_to_description(well_position, length)
    desc_letter = (((well_position - 1) % length) + 65).chr
    desc_number = ((well_position - 1) / length) + 1
    (desc_letter + desc_number.to_s)
  end

  def self.horizontal_position_to_description(well_position, width)
    desc_letter = (((well_position - 1) / width) + 65).chr
    desc_number = ((well_position - 1) % width) + 1
    (desc_letter + desc_number.to_s)
  end

  def self.horizontal_to_vertical(well_position, plate_size)
    alternate_position(well_position, plate_size, :width, :length)
  end

  def self.vertical_to_horizontal(well_position, plate_size)
    alternate_position(well_position, plate_size, :length, :width)
  end

  def self.location_from_index(index, size)
    by_row_map_index_to_well_description(index + 1, size)
  end

  class << self
    # Given the well position described in terms of a direction (vertical or horizontal) this function
    # will map it to the alternate positional representation, i.e. a vertical position will be mapped
    # to a horizontal one.  It does this with the divisor and multiplier, which will be reversed for
    # the alternate.
    #
    # NOTE: I don't like this, it just makes things clearer than it was!
    # NOTE: I hate the nil returns but external code would take too long to change this time round
    def alternate_position(well_position, size, *dimensions)
      return nil unless Map.valid_well_position?(well_position)

      divisor, multiplier = dimensions.map { |n| send(:"plate_#{n}", size) }
      return nil if divisor.nil? || multiplier.nil?

      column, row = (well_position - 1).divmod(divisor)
      return nil unless (0...multiplier).cover?(column)
      return nil unless (0...divisor).cover?(row)

      (row * multiplier) + column + 1
    end
    private :alternate_position
  end
end

Class Method Details

.alternate_position(well_position, size, *dimensions) ⇒ Object

Given the well position described in terms of a direction (vertical or horizontal) this function will map it to the alternate positional representation, i.e. a vertical position will be mapped to a horizontal one. It does this with the divisor and multiplier, which will be reversed for the alternate.

NOTE: I don't like this, it just makes things clearer than it was! NOTE: I hate the nil returns but external code would take too long to change this time round



139
140
141
142
143
144
145
146
147
148
149
150
 
# File 'app/models/map.rb', line 139

def alternate_position(well_position, size, *dimensions)
  return nil unless Map.valid_well_position?(well_position)

  divisor, multiplier = dimensions.map { |n| send(:"plate_#{n}", size) }
  return nil if divisor.nil? || multiplier.nil?

  column, row = (well_position - 1).divmod(divisor)
  return nil unless (0...multiplier).cover?(column)
  return nil unless (0...divisor).cover?(row)

  (row * multiplier) + column + 1
end

.by_column_map_index_to_well_description(well_position, plate_size) ⇒ Object

e.g. 23 returns G3 for a 96 well plate So 2 full columns of 8, plus 7, to give row G, column 3



80
81
82
83
84
85
86
87
 
# File 'app/models/map.rb', line 80

def self.by_column_map_index_to_well_description(well_position, plate_size)
  return nil unless Map.valid_plate_position_and_plate_size?(well_position, plate_size)

  length = plate_length(plate_size)
  return nil if length.nil?

  vertical_position_to_description(well_position, length)
end

.by_row_map_index_to_well_description(well_position, plate_size) ⇒ Object

e.g. 23 returns B11 for a 96 well plate So 1 full row of 12, plus 11, to give row B, column 11



69
70
71
72
73
74
75
76
 
# File 'app/models/map.rb', line 69

def self.by_row_map_index_to_well_description(well_position, plate_size)
  return nil unless Map.valid_plate_position_and_plate_size?(well_position, plate_size)

  width = plate_width(plate_size)
  return nil if width.nil?

  horizontal_position_to_description(well_position, width)
end

.description_to_horizontal_plate_position(well_description, plate_size) ⇒ Object 



45
46
47
48
49
50
51
52
53
 
# File 'app/models/map.rb', line 45

def self.description_to_horizontal_plate_position(well_description, plate_size)
  return nil unless Map.valid_well_description_and_plate_size?(well_description, plate_size)

  split_well = Map.split_well_description(well_description)
  width = plate_width(plate_size)
  return nil if width.nil?

  (width * split_well[:row]) + split_well[:col]
end

.descriptions_for_column(column, size) ⇒ Object 



93
94
95
 
# File 'app/models/map.rb', line 93

def self.descriptions_for_column(column, size)
  (0...plate_length(size)).map { |row| Map.location_from_row_and_column(row, column) }
end

.descriptions_for_row(row, size) ⇒ Object 



89
90
91
 
# File 'app/models/map.rb', line 89

def self.descriptions_for_row(row, size)
  (1..plate_width(size)).map { |column| "#{row}#{column}" }
end

.horizontal_position_to_description(well_position, width) ⇒ Object 



113
114
115
116
117
 
# File 'app/models/map.rb', line 113

def self.horizontal_position_to_description(well_position, width)
  desc_letter = (((well_position - 1) / width) + 65).chr
  desc_number = ((well_position - 1) % width) + 1
  (desc_letter + desc_number.to_s)
end

.horizontal_to_vertical(well_position, plate_size) ⇒ Object 



119
120
121
 
# File 'app/models/map.rb', line 119

def self.horizontal_to_vertical(well_position, plate_size)
  alternate_position(well_position, plate_size, :width, :length)
end

.location_from_index(index, size) ⇒ Object 



127
128
129
 
# File 'app/models/map.rb', line 127

def self.location_from_index(index, size)
  by_row_map_index_to_well_description(index + 1, size)
end

.location_from_row_and_column(row, column, _ = nil, __ = nil) ⇒ Object

Seems to expect row to be zero-indexed but column to be 1 indexed



41
42
43
 
# File 'app/models/map.rb', line 41

def self.location_from_row_and_column(row, column, _ = nil, __ = nil)
  "#{('A'.getbyte(0) + row).chr}#{column}"
end

.plate_length(plate_size) ⇒ Object 



101
102
103
 
# File 'app/models/map.rb', line 101

def self.plate_length(plate_size)
  PLATE_DIMENSIONS[plate_size].last
end

.plate_width(plate_size) ⇒ Object 



97
98
99
 
# File 'app/models/map.rb', line 97

def self.plate_width(plate_size)
  PLATE_DIMENSIONS[plate_size].first
end

.vertical_position_to_description(well_position, length) ⇒ Object

well number counting by columns, length is the number of rows in the plate e.g. B5 sends this 34 and 8



107
108
109
110
111
 
# File 'app/models/map.rb', line 107

def self.vertical_position_to_description(well_position, length)
  desc_letter = (((well_position - 1) % length) + 65).chr
  desc_number = ((well_position - 1) / length) + 1
  (desc_letter + desc_number.to_s)
end

.vertical_to_horizontal(well_position, plate_size) ⇒ Object 



123
124
125
 
# File 'app/models/map.rb', line 123

def self.vertical_to_horizontal(well_position, plate_size)
  alternate_position(well_position, plate_size, :length, :width)
end

.well_description_to_by_column_map_index(well_description, plate_size) ⇒ Object

e.g. B5 returns 34 for a 96 well plate So 4 columns of 8 rows each, plus 2 for the B row



57
58
59
60
61
62
63
64
65
 
# File 'app/models/map.rb', line 57

def self.well_description_to_by_column_map_index(well_description, plate_size)
  return nil unless Map.valid_well_description_and_plate_size?(well_description, plate_size)

  split_well = Map.split_well_description(well_description)
  length = plate_length(plate_size)
  return nil if length.nil?

  (length * (split_well[:col] - 1)) + split_well[:row] + 1
end