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2D Array incorrectly printing

I'm having a problem correctly printing out a 2D array for the traveling salesman problem. I'm getting my input from a text file using input redirection. The file contains cities and arcs with the distance between the cities. Here is a small example.

c 1
c 2
a 1 2 1400

After setting up my array and plotting the distance between the cities I use a nested for loop to print out the array but it looks like this.

    0       1       2       3       4       5

    1       0       1400    1800    4000    3500

    2       1       0       0       3400    3600

    3       1800    1200    0       2300    0

    4       4000    3400    2300    0       2100

    5       3500    3600    0       2100    0

EDIT: I want to make it appear like this

    0       1       2       3       4       5

    1       0       1400    1800    4000    3500

    2       1400    0       1200    3400    3600

    3       1800    1200    0       2300    2700

    4       4000    3400    2300    0       2100

    5       3500    3600    2700    2100    0

I tried manipulating the for loop different ways but I can't seem to figure out where my problem is in the loop or if it's somewhere else in my code.

// Sets up the array
int CityArray [6][6] = { {0, 0, 0, 0, 0, 0},
                         {0, 0, 0, 0, 0, 0},
                         {0, 0, 0, 0, 0, 0},
                         {0, 0, 0, 0, 0, 0},
                         {0, 0, 0, 0, 0, 0},
                         {0, 0, 0, 0, 0, 0}
                       };

int main(void) // Takes in a variable number of arguments
{
    // Sets a string input for the city
    char Cbuffer[32];
    char *b = Cbuffer;
    size_t cbufsize = 32;
    size_t cinput;

    // Other vairables
    int x = 1; // used to go through the array
    int n1, n2, n3, n4, cost; // variables to store the value pulled the cost from the arc

    // Reads in the city and sets the prices for each arc
    while((cinput = getline(&b, &cbufsize, stdin)) != -1)
    {
        if (Cbuffer[0] == 'c')
        {
            // Stores the last element as a digit to CityArray
            if (Cbuffer[2] >= '0' && Cbuffer[2] <= '9')
            {
                CityArray[x][0] = Cbuffer[2] - '0';
                int z = CityArray[x][0];
                // Flips it
                CityArray[0][x] = Cbuffer[2] - '0';
                z = CityArray[0][x];
                // printf("CityArray[%d] is '%d' \n", x, z);
                x++;
            }
        }
        else if (Cbuffer[0] == 'a')
        {
            int y = 1;
            // I know this looks ugly but it's the only way I could think of getting the prices
            if ((Cbuffer[6] >= '0' && Cbuffer[6] <= '9') && (Cbuffer[7] >= '0' && Cbuffer[7] <= '9') &&
                    (Cbuffer[8] >= '0' && Cbuffer[8] <= '9') && (Cbuffer[9] >= '0' && Cbuffer[9] <= '9'))
            {
                for (x = 1; x < 6; x++)
                {
                    for (y; y < 6; y++)
                    {   // converts the char to a int
                        n1 = CityArray[x][6] = Cbuffer[6] - '0';
                        n2 = CityArray[x][7] = Cbuffer[7] - '0';
                        n3 = CityArray[x][8] = Cbuffer[8] - '0';
                        n4 = CityArray[x][9] = Cbuffer[9] - '0';
                    }
                } // sets all converted ints to = cost
                cost = (n1 * 1000) + (n2 * 100) + (n3 * 10) + (n4 * 1);
                x++;
            }
            // Checks where the arc is located and plots the distance of the trip
            if (Cbuffer[2] == '1')
            {
                if (Cbuffer[4] == '2')
                {
                    CityArray[1][2] = cost;
                    CityArray[2][1] = cost;
                }
                else if (Cbuffer[4] == '3')
                {
                    CityArray[1][3] = cost;
                    CityArray[3][1] = cost;
                }
                else if (Cbuffer[4] == '4')
                {
                    CityArray[1][4] = cost;
                    CityArray[4][1] = cost;
                }
                else if (Cbuffer[4] == '5')
                {
                    CityArray[1][5] = cost;
                    CityArray[5][1] = cost;
                }
            }
            else if (Cbuffer[2] == '2')
            {
                if (Cbuffer[4] == '3')
                {
                    CityArray[2][3] = cost;
                    CityArray[3][2] = cost;
                }
                else if (Cbuffer[4] == '4')
                {
                    CityArray[2][4] = cost;
                    CityArray[4][2] = cost;
                }
                else if (Cbuffer[4] == '5')
                {
                    CityArray[2][5] = cost;
                    CityArray[5][2] = cost;
                }
            }
            else if (Cbuffer[2] == '3')
            {
                if (Cbuffer[4] == '4')
                {
                    CityArray[3][4] = cost;
                    CityArray[4][3] = cost;
                }
            else if (Cbuffer[4] == '5')
            {
                    CityArray[4][5] = cost;
                    CityArray[5][4] = cost;
                }
            }
            else if (Cbuffer[2] == '4')
            {
                if (Cbuffer[4] == '5')
                {
                    CityArray[4][5] = cost;
                    CityArray[5][4] = cost;
                }
            }
        }   
    }

    // Prints the array
    int i, j;
    printf("\n\nThe cost list is:\n\n");
    for(i = 0; i < 6;i ++)
    {
        printf("\n\n");
        for(j = 0; j < 6; j++)
        {
            printf("\t%d", CityArray[i][j]);
        }
        printf("\n");
    }

    return 0;
}

Your problem is here:

            for (x = 1; x < 6; x++)
            {
                for (y; y < 6; y++)
                {   // converts the char to a int
                    n1 = CityArray[x][6] = Cbuffer[6] - '0';
                    n2 = CityArray[x][7] = Cbuffer[7] - '0';
                    n3 = CityArray[x][8] = Cbuffer[8] - '0';
                    n4 = CityArray[x][9] = Cbuffer[9] - '0';
                }
            } // sets all converted ints to = cost
            cost = (n1 * 1000) + (n2 * 100) + (n3 * 10) + (n4 * 1);
            x++;

First, you don't need loops here; looping here means just that you will do the conversion several times. (It's worse, actually: Because you don't initialise y you may not do the conversion at all. If you activate warnings, you'll get someting along the lines of "statement with no effect" for the standaone y .)

Second, you store the converted digits in CityArray[x][6 ... 9] , but indices of 6 and beyond are out of bounds. That's undefined behaviour. In practice, you overwrite the data for the next city.

Third, you shouldn't use x as a looping variable and as a variable to hold the numer of cities. The loop will overwrite the data. (But that problem goes away when you remove the loops.)

Just do:

            n1 = Cbuffer[6] - '0';
            n2 = Cbuffer[7] - '0';
            n3 = Cbuffer[8] - '0';
            n4 = Cbuffer[9] - '0';

            cost = (n1 * 1000) + (n2 * 100) + (n3 * 10) + (n4 * 1);

The code still has many problems. In particular, the parsing of the cities and distances is very restricted. What happens if the cost for a city isn't a four digit number? And what happens if the first city has a greater number than the second city?

You can also use the conversion from ASCII to a single-digit integer for the cities:

        int from = Cbuffer[2] - '0';
        int dest = Cbuffer[4] - '0';

        CityArray[from][dest] = cost;
        CityArray[dest][from] = cost;

This will get rid of a lot of code. Instead of hard-coding all possibilities, your energy is better spent in writing meaningful error messages, for example if a city's id is out of bounds.

You should also consider using the standard approaches to parsing the input. getline in combination with scanf may be a good approach.

Edit : Below is an example implementation of the input. It can take at most 10 cities, identified by a single character which may be a digit. It doesn't have any restrictions of the exact format of the c and a lines and also keeps track of the number of actual cities in the variable ncitiy . It accepts blank lines and lines starting with a # as non-commands.

Despite the heavy error checking, this program is a bit shorter than yours. Here goes:

#define _GNU_SOURCE

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

#define MAX 10


int find(int array[], int n, int x)
{
    for (int i = 0; i < n; i++) {
        if (array[i] == x) return i;
    }

    return -1;
}

int main(void)
{
    int cost[10][10] = {{0}};       // cost matrix
    int id[MAX];                    // city id; can be any character
    int ncity = 0;                  // number of cities

    char *line = NULL;
    size_t nline = 0;
    int error = 0;

    while (getline(&line, &nline, stdin) != -1) {
        char c1, c2;
        int c;

        if (sscanf(line, " c %c", &c1) == 1) {
            if (find(id, ncity, c1) != -1) {
                fprintf(stderr, "Duplicate city id %c.\n", c1);
                error = 1;
                break;
            } else if (ncity >= MAX) {
                fprintf(stderr, "Maximum number of cities exceeded\n");
                error = 1;
                break;
            } else {
                id[ncity++] = c1;
            }
            continue;
        }

        if (sscanf(line, " a %c %c %d\n", &c1, &c2, &c) == 3) {
            int from = find(id, ncity, c1);
            int dest = find(id, ncity, c2);

            if (from < 0) {
                fprintf(stderr, "Unknown city id %c.\n", c1);
                error = 1;
                break;
            }

            if (dest < 0) {
                fprintf(stderr, "Unknown city id %c.\n", c2);
                error = 1;
                break;
            }

            cost[from][dest] = c;
            cost[dest][from] = c;

            continue;
        }

        if (sscanf(line, " %c", &c1) == 1 && c1 != '#') {
            fprintf(stderr, "Unknown command: %s", line);
            error = 1;
            break;
        }
    }

    free(line);

    if (error) {
        fprintf(stderr, "Errors in input. Aborting.\n");
        exit(1);
    }

    printf("%8s", "");
    for (int j = 0; j < ncity; j++) {
        printf("%8c", id[j]);
    }
    puts("");

    for(int i = 0; i < ncity; i ++)
    {
        printf("%8c", id[i]);
        for (int j = 0; j < ncity; j++) {
            printf("%8d", cost[i][j]);
        }
        puts("");
    }
    puts("");

    return 0;
}

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