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#include "config.h"
#include <stdio.h>
#include <stdlib.h>
#include "parasail.h"
#include "parasail/io.h"
#include "parasail/matrices/blosum62.h"
static void print_matrix(const parasail_matrix_t *matrix) {
int i = 0;
int j = 0;
const char *alphabet = NULL;
alphabet = matrix->alphabet;
printf("matrix '%s'\n", matrix->name);
printf(" ");
for (i=0; i<matrix->size; ++i) {
printf("%4c", alphabet[i]);
}
printf("\n");
for (j=0; j<matrix->length; ++j) {
if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
printf("%c ", alphabet[j]);
}
else {
if (matrix->query != NULL) {
printf("%c ", matrix->query[j]);
}
else {
printf("* ");
}
}
for (i=0; i<matrix->size; ++i) {
printf("%4d", matrix->matrix[j*matrix->size + i]);
}
printf("\n");
}
printf("max = %d\n", matrix->max);
printf("min = %d\n", matrix->min);
}
static void print_mapper(const parasail_matrix_t *matrix) {
int i = 0;
const int *mapper = matrix->mapper;
for (i=0; i<256; ++i) {
if (i%16 == 0) printf("\n");
printf("%5d", mapper[i]);
}
printf("\n");
}
int main(int argc, char **argv)
{
parasail_matrix_t *matrix = NULL;
const parasail_matrix_t *internal_matrix = NULL;
parasail_matrix_t *user_matrix = NULL;
parasail_matrix_t *user_matrix_copy = NULL;
const char *pssm_alphabet = "abcdef";
const int pssm_values[] = {
0, 1, 2, 3, 4, 5,
6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23
};
const int pssm_length = 4;
if (argc == 2) {
matrix = parasail_matrix_from_file(argv[1]);
print_matrix(matrix);
print_mapper(matrix);
parasail_matrix_free(matrix);
}
else {
printf("missing matrix file argument, skipping that part of the test\n");
}
print_matrix(¶sail_blosum62);
print_mapper(¶sail_blosum62);
internal_matrix = parasail_matrix_lookup("blosum62");
if (NULL == internal_matrix) {
fprintf(stderr, "matrix lookup failed");
exit(EXIT_FAILURE);
}
user_matrix = parasail_matrix_create("ACGT", 2, -1);
if (NULL == user_matrix) {
fprintf(stderr, "matrix create failed");
exit(EXIT_FAILURE);
}
print_matrix(user_matrix);
print_mapper(user_matrix);
parasail_matrix_free(user_matrix);
user_matrix = parasail_matrix_create_case_sensitive("AcgT", 2, -1);
if (NULL == user_matrix) {
fprintf(stderr, "matrix create failed");
exit(EXIT_FAILURE);
}
print_matrix(user_matrix);
print_mapper(user_matrix);
parasail_matrix_free(user_matrix);
user_matrix = parasail_matrix_create_case_sensitive("ACGTacgt", 2, -1);
if (NULL == user_matrix) {
fprintf(stderr, "matrix create failed");
exit(EXIT_FAILURE);
}
print_matrix(user_matrix);
print_mapper(user_matrix);
parasail_matrix_free(user_matrix);
user_matrix = parasail_matrix_copy(internal_matrix);
if (NULL == user_matrix) {
fprintf(stderr, "matrix copy failed");
exit(EXIT_FAILURE);
}
parasail_matrix_set_value(user_matrix, 10, 10, 100);
if (100 != user_matrix->max) {
fprintf(stderr, "matrix set value failed");
exit(EXIT_FAILURE);
}
parasail_matrix_free(user_matrix);
user_matrix = parasail_matrix_pssm_create(
pssm_alphabet,
pssm_values,
pssm_length);
if (NULL == user_matrix) {
fprintf(stderr, "pssm matrix create failed");
exit(EXIT_FAILURE);
}
print_matrix(user_matrix);
print_mapper(user_matrix);
user_matrix_copy = parasail_matrix_copy(user_matrix);
if (NULL == user_matrix_copy) {
fprintf(stderr, "pssm matrix copy failed");
exit(EXIT_FAILURE);
}
parasail_matrix_free(user_matrix);
print_matrix(user_matrix_copy);
print_mapper(user_matrix_copy);
parasail_matrix_free(user_matrix_copy);
user_matrix = parasail_matrix_convert_square_to_pssm(internal_matrix, "asdf", 4);
print_matrix(user_matrix);
print_mapper(user_matrix);
parasail_matrix_free(user_matrix);
print_matrix(internal_matrix);
return 0;
}
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