input_parser.c

#include "input_parser.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>

//function to free input data 

void free_input_data(input_data* d) {
  for (size_t i = 0; i < d->number_of_species; ++i) {
    free(d->names[i]);
  }

  free(d->names);
  free(d->matrix);
  free(d);
}


//read newick tree string from empirical input example files 

char* read_newk_tree(const char* newk_file) {
  FILE *f = fopen(newk_file, "rb");

  if (f == NULL) {
    return NULL;
  }

  fseek(f, 0, SEEK_END);
  long fsize = ftell(f);
  fseek(f, 0, SEEK_SET);  //same as rewind(f);

  if (fsize < 0) {
    fclose(f);
    return NULL;
  }

  char *string = malloc((size_t)fsize + 1);

  if (string != NULL) {
    fread(string, (size_t)fsize, 1, f);
    string[(size_t)fsize] = 0;
  }

  fclose(f);

  return string;
}


//parse input data from input example files 

input_data* parse_input_data(const char* data_file) {
  FILE *f = fopen(data_file, "rb");

  if (f == NULL) {
    return NULL;
  }

  input_data* result = (input_data*)malloc(sizeof(input_data));

  char input_buffer[256];

  if (result != NULL) {
    fscanf(f, "%zu %zu", &(result->number_of_species), &(result->number_of_partitions));

    result->matrix = (unsigned char*)malloc(sizeof(unsigned char) * result->number_of_species * result->number_of_partitions);
    result->names = (char**)malloc(sizeof(char*) * result->number_of_species);

    for (size_t s = 0; s < result->number_of_species; ++s) {
      for (size_t p = 0; p < result->number_of_partitions; ++p) {
	fscanf(f, "%1hhu", &result->matrix[s * result->number_of_partitions + p]);
      }

      // discard one (whitespace)
      fgetc(f);

      fgets(input_buffer, 256, f);
      size_t len = strlen(input_buffer);
      if (len < 255) {
	result->names[s] = malloc(sizeof(char) * len);
	strncpy(result->names[s], input_buffer, len);
	// replace newline by NULL
	result->names[s][len-1] = 0;
      } else {
	assert(0);
      }
    }
  }

  fclose(f);

  return result;
}