/usr/include/pbseq/pbdata/matrix/MatrixImpl.hpp is in libpbdata-dev 0~20161219-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 | #ifndef _BLASR_MATRIX_IMPL_HPP
#define _BLASR_MATRIX_IMPL_HPP
#include <cassert>
#include <vector>
#include <iostream>
#include <fstream>
#include <stdint.h>
#include "../utils.hpp"
#include "../Types.h"
template<typename T>
void CreateMatrix(VectorIndex rows, int cols, std::vector<T*> matrix) {
matrix.resize(rows);
if (matrix[0]) {delete [] matrix[0]; matrix[0] = NULL;}
matrix[0] = ProtectedNew<T>(rows*cols);
VectorIndex r = 1;
for (r = 1; r < rows; r++) {
matrix[r] = &matrix[cols * r];
}
}
template<typename T>
Matrix<T>::Matrix() {
nRows = 0;
rowsBufferSize = 0;
nCols = 0;
matrixBufferSize = 0;
matrix = NULL;
}
template<typename T>
unsigned int Matrix<T>::size() {
return nRows * nCols;
}
template<typename T>
unsigned int Matrix<T>::GetNCols() {
return nCols;
}
template<typename T>
unsigned int Matrix<T>::GetNRows() {
return nRows;
}
template<typename T>
void Matrix<T>::Resize(VectorIndex nRowsP, VectorIndex nColsP) {
nRows = nRowsP;
nCols = nColsP;
matrixSize = nRows * nCols;
if (nRows * nCols > matrixBufferSize) {
matrixBufferSize = nRows * nCols;
if (nRows > rowsBufferSize) {
if (matrix != NULL) {
delete[] matrix; matrix = NULL;
}
}
if (matrix == NULL) {
matrix = ProtectedNew<T*>(nRows);
}
else {
if (matrix[0] != NULL) {
delete[] matrix[0]; matrix[0] = NULL;
}
}
matrix[0] = ProtectedNew<T>(matrixBufferSize);
VectorIndex rowIndex;
for (rowIndex = 1; rowIndex < nRows; rowIndex++ ){
matrix[rowIndex] = &matrix[0][nCols * rowIndex];
}
}
}
template<typename T>
Matrix<T>::Matrix(VectorIndex nRowsP, VectorIndex nColsP) {
Resize(nRowsP, nColsP);
}
template<typename T>
void Matrix<T>::Reference(Matrix<T> &rhs) {
matrix = rhs.matrix;
}
template<typename T>
void Matrix<T>::Initialize(T value) {
std::fill(&matrix[0][0], &matrix[0][matrixSize], value);
}
template<typename T>
T* Matrix<T>::operator[](VectorIndex rowIndex) {
assert(rowIndex < nRows);
return matrix[rowIndex];
}
template<typename T>
void Matrix<T>::Free() {
if (matrix != NULL) {
if (matrix[0] != NULL) {
delete[] matrix[0];
}
delete[] matrix;
}
matrix = NULL;
}
template<typename T>
void Matrix<T>::Print(std::ofstream &out) {
VectorIndex i;
VectorIndex j;
for (i = 0; i < nRows; i++) {
for (j = 0; j < nCols; j++ ){
out << matrix[i][j] << " ";
}
out << std::endl;
}
}
#endif
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