#include "io.hpp"

#include <algorithm>

#include <boost/tokenizer.hpp>

#include <exception>

#include <fstream>

#include <regex>

#include <unordered_map>

#include "compression.hpp"

using namespace std;

namespace PF = PoissonFactorization;

using Int = PF::Int;

using Float = PF::Float;

using Matrix = PF::Matrix;

using IMatrix = PF::IMatrix;

using Vector = PF::Vector;

Matrix read_matrix(istream &is, const string &separator) {

// TODO improve / factor / simplify implementation

vector<string> row_names, col_names;

Matrix m = read_floats(is, separator, row_names, col_names);

return m;

}

IMatrix vec_of_vec_to_multi_array(const vector<vector<Int>> &v) {

const size_t s1 = v.size();

const size_t s2 = v[0].size();

IMatrix A(s1, s2);

for (size_t i = 0; i < s1; ++i)

for (size_t j = 0; j < s2; ++j)

A(i, j) = v[i][j];

return A;

}

Matrix vec_of_vec_to_multi_array_float(const vector<vector<Float>> &v) {

const size_t s1 = v.size();

const size_t s2 = v[0].size();

Matrix A(s1, s2);

for (size_t i = 0; i < s1; ++i)

for (size_t j = 0; j < s2; ++j)

A(i, j) = v[i][j];

return A;

}

Matrix read_floats(istream &ifs, const string &separator,

vector<string> &row_names, vector<string> &col_names) {

using tokenizer = boost::tokenizer<boost::char_separator<char>>;

boost::char_separator<char> sep(separator.c_str());

vector<vector<Float>> m;

string line;

getline(ifs, line);

tokenizer tok(line, sep);

for (auto token : tok)

col_names.push_back(token.c_str());

while (getline(ifs, line)) {

tok = tokenizer(line, sep);

size_t col = 0;

vector<Float> v;

for (auto token : tok)

if (col++ == 0)

row_names.push_back(token);

else

v.push_back(atof(token.c_str()));

m.push_back(v);

}

auto matrix = vec_of_vec_to_multi_array_float(m);

size_t ncol = matrix.n_cols;

if (ncol == col_names.size())

return matrix;

else if (ncol == col_names.size() - 1) {

vector<string> new_col_names(begin(col_names) + 1, end(col_names));

col_names = new_col_names;

return matrix;

} else

throw std::runtime_error(

"Mismatch between number of columns and number of column labels.");

}

IMatrix read_counts(istream &ifs, const string &separator,

vector<string> &row_names, vector<string> &col_names) {

using tokenizer = boost::tokenizer<boost::char_separator<char>>;

boost::char_separator<char> sep(separator.c_str());

vector<vector<Int>> m;

string line;

getline(ifs, line);

tokenizer tok(line, sep);

for (auto token : tok)

col_names.push_back(token.c_str());

while (getline(ifs, line)) {

tok = tokenizer(line, sep);

size_t col = 0;

vector<Int> v;

for (auto token : tok)

if (col++ == 0)

row_names.push_back(token);

else

v.push_back(atoi(token.c_str()));

m.push_back(v);

}

auto matrix = vec_of_vec_to_multi_array(m);

size_t ncol = matrix.n_cols;

if (ncol == col_names.size())

return matrix;

else if (ncol + 1 == col_names.size()) {

vector<string> new_col_names(begin(col_names) + 1, end(col_names));

col_names = new_col_names;

return matrix;

} else

throw std::runtime_error(

"Mismatch between number of columns and number of column labels.");

}

void print_matrix_head(ostream &os, const Matrix &m, const std::string &label,

size_t n) {

if (label != "")

os << label << std::endl;

size_t X = m.n_rows;

size_t Y = m.n_cols;

for (size_t x = 0; x < std::min<size_t>(X, n); ++x) {

for (size_t y = 0; y < Y; ++y)

os << (y > 0 ? "\t" : "") << m(x, y);

os << std::endl;

}

if (label != "")

os << label << " ";

os << "column sums" << std::endl;

size_t zeros = 0;

for (size_t y = 0; y < Y; ++y) {

double sum = 0;

for (size_t x = 0; x < X; ++x) {

if (m(x, y) == 0)

zeros++;

sum += m(x, y);

}

os << (y > 0 ? "\t" : "") << sum;

}

os << std::endl;

os << "There are " << zeros << " zeros";

if (label != "")

os << " in " << label;

os << ". This corresponds to " << (100.0 * zeros / X / Y) << "%."

<< std::endl;

}