Module: TagLayout::InColumnsThenColumns

Defined in:
app/models/tag_layout/in_columns_then_columns.rb

Overview

Lays out the tags so that they are column then column ordered. e.g. a dual index plate with 96 tags in tag group 1 and 4 in tag group 2 is laid out as follows for the first 4 rows/columns on a 384-well plate: 1 2 3 4 etc.

A 1,1 1,3 9,1 9,3 B 1,2 1,4 9,2 9,4 C 2,1 2,3 10,1 10,3 D 2,2 2,4 10,2 10,4 etc. This version is a variation of the tag 2 order used in the InColumnsThenRows layout.

Class Method Summary collapse

Class Method Details

.direction ⇒ Object 



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# File 'app/models/tag_layout/in_columns_then_columns.rb', line 15

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

.tag2_index(row, column, scale, _height, _width) ⇒ Object

Returns the tag index for the secondary tag e.g. 4 tags in group, A1 = 1, B1 = 2, A2 = 3, B2 = 4



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# File 'app/models/tag_layout/in_columns_then_columns.rb', line 36

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

.tag_index(row, column, scale, height, _width) ⇒ Object

Returns the tag index for the primary tag That is the one laid out in columns with four copies of each (scale = 4). The row and column are the indexes of the position, height and width are the plate dimensions.



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# File 'app/models/tag_layout/in_columns_then_columns.rb', line 28

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

.well_order_scope ⇒ Object

We don't rely on well sorting, so lets not worry about it.



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# File 'app/models/tag_layout/in_columns_then_columns.rb', line 21

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end