Class: Utility::NormalisedBinningCalculator

Inherits:
Object
  • Object
show all
Includes:
ActiveModel::Model, CommonDilutionCalculations
Defined in:
app/models/utility/normalised_binning_calculator.rb

Overview

Handles the Computations for Normalised Binning Used by the Normalised Binned Plate and Presenter classes to handle the normalisation, compute the bins and provide helpers on displaying the bins on the child plate.

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#config ⇒ Object (readonly) Originally defined in module CommonDilutionCalculations

Returns the value of attribute config.

Instance Method Details

#compute_presenter_bin_details(plate) ⇒ Object

Used by the plate presenter. Uses the concentration in the well and the plate purpose config to work out the well bin colour and number of PCR cycles.



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# File 'app/models/utility/normalised_binning_calculator.rb', line 27

def compute_presenter_bin_details(plate)
  well_amounts = compute_well_amounts_for_presenter(plate)
  compute_bin_details_by_well(well_amounts)
end

#compute_vol_source_reqd(sample_conc) ⇒ float Originally defined in module CommonDilutionCalculations

Computes the volume of source material required for normalisation based on the sample concentration and attributes from the purpose configuration (target amount and volume, minimum source volume). Includes checks for minimum source volume and rounding for low diluent volumes due to liquid handler robot restrictions.

Parameters:

  • sample_conc (float) —

    The concentration of the source sample in ng/ul

Returns:

  • (float) —

    The volume of the source required in ul.

#compute_well_transfers(parent_plate, filtered_wells) ⇒ Object 



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# File 'app/models/utility/normalised_binning_calculator.rb', line 14

def compute_well_transfers(parent_plate, filtered_wells)
  norm_details = normalisation_details(filtered_wells)
  compute_well_transfers_hash(norm_details, parent_plate.number_of_rows, parent_plate.number_of_columns)
end

#compute_well_transfers_hash(norm_details, number_of_rows, number_of_columns) ⇒ Object 



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# File 'app/models/utility/normalised_binning_calculator.rb', line 19

def compute_well_transfers_hash(norm_details, number_of_rows, number_of_columns)
  conc_bins = concentration_bins(norm_details)
  compression_reqd = compression_required?(conc_bins, number_of_rows, number_of_columns)
  build_transfers_hash(conc_bins, number_of_rows, compression_reqd)
end

#construct_dest_qc_assay_attributes(child_uuid, transfer_hash) ⇒ array Originally defined in module CommonDilutionCalculations

Constructs the qc_assays collection details for use when writing calculated concentrations for the newly created child plate.

Parameters:

  • child_uuid (string) —

    The uuid of the child plate being transferred into.

  • transfer_hash (hash) —

    The transfers hash from which we extract the destination concentrations.

Returns:

  • (array) —

    An array of qc assay details for the child plate, ready to send via Api to sequencescape.

#extract_destination_concentrations(transfer_hash) ⇒ hash Originally defined in module CommonDilutionCalculations

Refactor the transfers hash to give destination concentrations

Parameters:

  • transfer_hash (hash) —

    The transfer details.

Returns:

  • (hash) —

    A refactored hash of well concentrations.

#initialize(config) ⇒ Object Originally defined in module CommonDilutionCalculations

The calculators all use a common configuration structure stored on the plate purpose.

Parameters:

  • config (hash) —

    The relevant section from the plate purpose configuration.

#normalisation_details(wells) ⇒ hash Originally defined in module CommonDilutionCalculations

Creates a hash of well normalisation details for a plate used when generating the well transfers and qc assays.

Parameters:

  • wells (Wells) —

    The source wells being normalised.

Returns:

  • (hash) —

    The well details hash containing calculated normalisation values.