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

#define MAX_LINE_LENGTH 1024 // Adjust line length as needed

void printStats(int uid, long long length, long long A_count, long long T_count, long long G_count, long long C_count, FILE *output) {
    long long total_count = A_count + T_count + G_count + C_count;
    fprintf(output, "Total statistics for %d chromosomes\n\n", uid);
    fprintf(output, "Length: %lld\n", length);
    fprintf(output, "Nucleotide frequencies:\n");
    fprintf(output, "A: % 10lld % 5.2f%%\n", A_count, ((double)A_count / total_count) * 100);
    fprintf(output, "T: % 10lld % 5.2f%%\n", T_count, ((double)T_count / total_count) * 100);
    fprintf(output, "G: % 10lld % 5.2f%%\n", G_count, ((double)G_count / total_count) * 100);
    fprintf(output, "C: % 10lld % 5.2f%%\n", C_count, ((double)C_count / total_count) * 100);
    fprintf(output, "GC content:    %.2f%%\n\n", ((double)(G_count + C_count) / total_count) * 100);
}

void printFileContent_fgetc_putchar_rewind(FILE *file) {
    int c;
    rewind(file); // reset the file position
    while ((c = fgetc(file)) != EOF) {
        putchar(c);
    }
    printf("\n");
}

void printFileContent_fgetc_putchar_fseek(FILE *file) {
    fseek(file, 0, SEEK_SET); // Set the file position indicator to the beginning of the file
    int c;
    while ((c = fgetc(file)) != EOF) {
        putchar(c);
    }
    printf("\n");
}
void printFileContent_getc_printf(FILE *f)
{
    int c;
    while ((c = getc(f)) != EOF){
            printf("%c",c);
        }
    printf("\n");
}

void printFileContent_fread_buffer(FILE *file) {
    fseek(file, 0, SEEK_SET); // Set the file position indicator to the beginning of the file

    char buffer[MAX_LINE_LENGTH];
    size_t bytesRead;

    while ((bytesRead = fread(buffer, 1, MAX_LINE_LENGTH, file)) > 0) {
        fwrite(buffer, 1, bytesRead, stdout); // Print buffer content to stdout
    }

    printf("\n");
}

void printFileContent_fgets_printf(FILE *file) {
    fseek(file, 0, SEEK_SET); // Set the file position indicator to the beginning of the file

    char line[MAX_LINE_LENGTH];

    while (fgets(line, MAX_LINE_LENGTH, file) != NULL) {
        printf("%s", line); // Print each line to stdout
    }

    printf("\n");
}

void printFileContent_getc_putchar(FILE *file) {
    fseek(file, 0, SEEK_SET); // Set the file position indicator to the beginning of the file

    int c;
    while ((c = getc(file)) != EOF) {
        putchar(c); // Print each character to stdout
    }

    printf("\n");
}

void processFasta(FILE *fasta, FILE *output) {
    char *line = NULL;
    int chromosome_cunter = 0;
    size_t len = 0;
    ssize_t read;
    char *currentUID = NULL;
    long long A_count = 0, T_count = 0, G_count = 0, C_count = 0, length = 0;
    long long A_global_count = 0, T_global_count = 0, G_global_count = 0, C_global_count = 0, length_global = 0;
    while ((read = getline(&line, &len, fasta)) != -1) {
        if (line[0] == '>') {
            if (currentUID != NULL) {
                printf("Processing chromosome: %s\n", currentUID);
                //printStats(currentUID, length, A_count, T_count, G_count, C_count, output);
                free(currentUID);
                chromosome_cunter += 1;
                length_global += length;
                A_global_count += A_count;
                T_global_count += T_count;
                G_global_count += G_count;
                C_global_count += C_count;

                A_count = T_count = G_count = C_count = length = 0;
            }
            currentUID = strdup(line + 1); // Skip '>'
            char *end = strchr(currentUID, ' ');
            if (end != NULL) {
                *end = '\0'; // Terminate at the first space
            }
        } else {
            //size_t line_length = strlen(line);             //alternatively use strlen() function from string.h
            //for (size_t i = 0; i < line_length; i++) {
            for (int i = 0; line[i] != '\0' && line[i] != '\n'; i++) {
                char c = toupper(line[i]);
                if (isalpha(c)) {
                    length++;
                    if      (c == 'A') A_count++;
                    else if (c == 'T') T_count++;
                    else if (c == 'G') G_count++;
                    else if (c == 'C') C_count++;
                }
            }
        }
    }
    free(currentUID);
    //do not forget about last one
    chromosome_cunter += 1;
    length_global += length;
    A_global_count += A_count;
    T_global_count += T_count;
    G_global_count += G_count;
    C_global_count += C_count;

    printf("Processed %d chromosomes:\n\n", chromosome_cunter);
    printStats(chromosome_cunter, length_global, A_global_count, T_global_count, G_global_count, C_global_count, output);
    free(line);
}


int main() {
    FILE *fasta = fopen("/home/lukaskoz/tmp/lab7_wdi/chm13v2.0.fa", "r");
    //FILE *fasta = fopen("/home/lukaskoz/tmp/lab7_wdi/chm13v2.0.fa_5M", "r"); //5M contains 2 chromosomes only
    FILE *output = fopen("/home/lukaskoz/tmp/lab7_wdi/genome_stats_short.txt", "w");

    if (fasta == NULL || output == NULL) {
        perror("Error opening files");
        return 1;
    }

    processFasta(fasta, output);

    fclose(fasta);
    fclose(output);

    // Display output file content
    FILE *outputFile = fopen("/home/lukaskoz/tmp/lab7_wdi/genome_stats_short.txt", "r");
    if (outputFile == NULL) {
        perror("Error opening output file");
        return 1;
    }

    printf("\n\n=============================================\n\nContent of output file:\n\n");

    printFileContent_fgetc_putchar_fseek(outputFile);
    //printFileContent_fgetc_putchar_rewind(outputFile);
    //printFileContent_fgets_printf(outputFile);
    //printFileContent_fread_buffer(outputFile);
    //printFileContent_getc_printf(outputFile);
    //printFileContent_getc_putchar(outputFile);
    fclose(outputFile);

    return 0;
}