nodefinderc.h

#define _GNU_SOURCE

#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>

/* ===================================================================== */
/* Options you may want to change*/
/* ===================================================================== */
/* The maximum line numbers for calibration configs (default: 500) */
#define MAX_CONFIG_LINE_LEN 500

/* The length of insertion point display.
 * For example, default value (20):
 *           |      -> 20 <-     ||     -> 20 <-     |
 * [Insert]:  b,c)>0.05<0.07,(d,e)))>0.1<0.2,(f,g))>0.
 * [Insert]:                   ->||<-
 * [Insert]:                 Insert Here
 */
#define CALI_DISPLAY_HALF_WIDTH 20

/* The max size of ancestor insertion point list. (default: 400) */
#define MAX_INDEX_LIST_NUM 400

/* ===================================================================== */
/* Options generally don't need to be changed*/
/* ===================================================================== */

/* NodeFinder version */
#define NODEFINDERC_VERSION "1.1.7"

/* Symbol used for comment lines. Lines starts with this will be ignored.
 * (defualt: '#')*/
#define COMMENT_SYMBOL '#'

/* The max whitespaces number used in gen_blank_str() function to
 * get a string consists of whitespaces only. (default: 200) */
#define MAX_WHITESPACES_NUM 200

/* The buffer multiple size used by add_cali() and modify_exists_cali() fucntion
 * for adding calibration string. (default: 2) */
#define MULTIPLE_OF_BUFSIZE 2


const char *BAR = "=======================================================================\n";
const char *THIN_BAR = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n";

struct Calibration {
    char *name_a;
    char *name_b;
    char *cali_info;
};


/**************************** FUNCTIONS ************************************/


// print functions
void print_array(const int arr[], int size);

void print_cali_struct(size_t cali_num, struct Calibration *calis[cali_num]);

void printcali(struct Calibration cali);


// Utils functions
void gen_blank_str(char **blank_str, size_t whitespace_num);

char *make_str_clean(char *input);

char *stripchar(char *str, const char c);

size_t countchar(const char *s, const char c);

size_t get_index_of_substring(const char *srcstr, const char *substr);

void reverse_array(int arr[], int start, int end);

char *sliced_string(const char *str, int start, int end);

char **split_by_delim(const char *str, const char *delim, size_t *num_tokens);

char *concat_three_str(const size_t bufsize, const char *str1,
                       const char *str2, const char *str3);

char *read_whole_str(const char *filename);

void write_str_to_file(const char *filename, const char *out_str);


// NodeFinder functions
void print_version();

void get_insertion_list(const char *treestr, int *insertion_list, int *list_num, int indexnow);

int get_index_of_tmrca(const char *treestr, const char *name_a, const char *name_b);

char *get_exists_cali(const char *right_part);

char *find_non_cali_pointer(const char *right_part);

char *add_cali(const char *treestr, int index_of_tmrca, const char *cali_info);

char *modify_exists_cali(const char *treestr, int index_of_tmrca, const char *cali_info);

char *single_cali(char *treestr, struct Calibration *cali);

char *multi_cali(char *clean_str, int cali_num, struct Calibration *calis[cali_num]);

size_t read_config_lines(const char *config_file_name, char *valid_config_lines[]);

void parse_config(char *valid_config_lines[], size_t valid_line_num,
                  struct Calibration *calis[valid_line_num]);

void show_help_message();

int argparser(int argc, char **argv,
              char **infile_value,
              char **outfile_value,
              char **config_file_value);