TorsadePredictMethods.hpp

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*/

#ifndef TORSADEPREDICTMETHODS_HPP_
#define TORSADEPREDICTMETHODS_HPP_

#include "ApPredictMethods.hpp"
#include "LinearDiscriminantAnalysis.hpp"

/**
 * This class calls ApPredict to predict action potentials
 * for given ion channel IC50 and Hill data. For a range of
 * concentrations as requested. It then performs a linear
 * discrimanant analysis to predict the Torsade risk category
 * of your drug at each concentration, as per Mirams et al. 2011.
 *
 * Call PrintArguments to see usage.
 */
class TorsadePredictMethods : public ApPredictMethods
{
public:
    /**
     * This constructor does all the work of running the ActionPotential (AP) preDiCT
     * with Torsadogenic risk estimates (TorsadePredict) program
     */
    TorsadePredictMethods();

    /**
     * Run the predictions.
     */
    virtual void Run();

    /**
     * This is a helper method to print out the available arguments.
     *
     * @return available arguments for this class.
     */
    static std::string PrintArguments();

    /**
     * Get the predicted Redfern category for each concentration of this compound.
     *
     * @return The torsade predictions.
     */
    std::vector<unsigned> GetTorsadePredictions();

protected:
    /**
     * Load up the Torsade training data from file.
     * This relies on "paper_drug_data.dat" being present.
     *
     * @return a Linear Discriminant Analysis (LDA) object preloaded with the Grandi APD90 training data.
     */
    LinearDiscriminantAnalysis LoadLdaFromDrugData();

    /**
     * Use the APD data from the current run to
     * call the LDA methods and classify points.
     */
    void MakeTorsadePredictions();

private:
    friend class TestTorsadePredict;

    /** A vector used to store the Torsade predictions (as indexed by Redfern i.e. 0,1,2,3 = cats 2/3/4/5) */
    std::vector<unsigned> mTorsadePredictions;

    /**
     * Write the TdP classification results to HTML table.
     */
    void WriteTorsadeResultsToFile();

};

#endif // TORSADEPREDICTMETHODS_HPP_