#ifndef STDATA_H

#define STDATA_H

#include <QSharedPointer>

#include <QList>

#include <QVector2D>

#include <QVector3D>

#include <QVector4D>

#include <QColor>

#include "data/Gene.h"

#include "data/Spot.h"

#include "viewPages/SettingsWidget.h"

#include "viewRenderer/SelectionEvent.h"

#include <armadillo>

using namespace arma;

class STData

{

public:

typedef QSharedPointer<Spot> SpotObjectType;

typedef QSharedPointer<Gene> GeneObjectType;

typedef QList<SpotObjectType> SpotListType;

typedef QList<GeneObjectType> GeneListType;

struct STDataFrame {

mat counts;

QList<QString> genes;

QList<QString> spots;

};

STData();

~STData();

// Parses the matrix and initialize the size-factors and genes/spots containers

void init(const QString &filename, const QString &spots_coordinates = QString());

// Functions to import/export the data

static STDataFrame read(const QString &filename);

static void save(const QString &filename, const STDataFrame &data);

// Retrieves the original data frame (without filtering using the tresholds)

STDataFrame data() const;

// Returns the spot/gene objects corresponding to the data frame

const GeneListType &genes() const;

const SpotListType &spots() const;

// Rendering functions

void computeRenderingData(SettingsWidget::Rendering &rendering_settings);

const QVector<bool> &renderingVisible() const;

const QVector<QColor> &renderingColors() const;

const QVector<bool> &renderingSelected() const;

const QVector<double> &renderingValues() const;

// to parse a file with spots coordinates old_spot -> new_spot

// It returns a map of old_spots -> new_spots

// It throws exceptions when errors during parsing or empty file

QMap<QString, QString> parseSpotsMap(const QString &spots_file);

// helper slicing functions (assumes the spots and genes lists given are present in the data)

static STDataFrame sliceDataFrameGenes(const STDataFrame &data,

const QList<QString> &spots);

static STDataFrame sliceDataFrameSpots(const STDataFrame &data,

const QList<QString> &genes);

// helper function to filter out a data frame using thresholds

static STDataFrame filterDataFrame(const STDataFrame &data,

const int min_exp_value,

const int min_reads_spot,

const int min_genes_spot,

const int min_spots_gene);

// helper function to merge a list of data frames into one (by common genes)

// the spots (rows) will have the index of the dataset append (1_,2_..)

static STData::STDataFrame aggregate(const QList<STDataFrame> &datasets);

// helper function to get the sum of non zeroes elements (by column, aka gene)

static urowvec computeNonZeroColumns(const mat &matrix, const int min_value = 0);

// helper function to get the sum of non zeroes elements (by row, aka spot)

static ucolvec computeNonZeroRows(const mat &matrix, const int min_value = 0);

// helper function that returns the normalized matrix counts using the rendering settings

static STDataFrame normalizeCounts(const STDataFrame &data,

SettingsWidget::NormalizationMode mode);

// functions to select spots

void clearSelection();

void selectSpots(const SelectionEvent &event);

void selectSpots(const QList<QString> &spots);

void selectSpots(const QList<int> &spots_indexes);

void selectGenes(const QRegExp &regexp, const bool force = true);

void selectGenes(const QList<QString> &genes);

// functions to change spot and gene colors

void loadSpotColors(const QHash<QString, QColor> &colors);

void loadGeneColors(const QHash<QString, QColor> &colors);

// returns the boundaries (min spot and max spot)

const QRectF getBorder() const;

private:

// The matrix with the counts (spots are rows and genes are columns)

STDataFrame m_data;

// store gene/spots objects for the matrix (columns and rows)

// each index in each vector correspond to a row index or column index in the matrix

SpotListType m_spots;

GeneListType m_genes;

// use hash tables for look-ups (spot and gene to matrix index)

// so to not have to search the QLists

QHash<QString, int> m_spot_index;

QHash<QString, int> m_gene_index;

// rendering data

QVector<bool> m_rendering_selected;

QVector<bool> m_rendering_visible;

QVector<QColor> m_rendering_colors;

QVector<double> m_rendering_values;

Q_DISABLE_COPY(STData)

};

#endif // STDATA_H