trouble with creating two dimensional array from file

Question

I have some troubles with parsing matrix file. It looks sth like this:

#  Matrix made by matblas from blosum62.iij 
#  * column uses minimum score 
#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units 
#  Blocks Database = /data/blocks_5.0/blocks.dat 
#  Cluster Percentage: >= 62 
#  Entropy =  0.6979, Expected =  -0.5209 
  A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  * 
A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -4 
R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -4 
N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -4 
D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -4 
C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 
Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -4 
E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -4 
H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -4 
I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -4 
L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -4 
K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -4 
M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -4 
F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -4 
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -4 
S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -4 
T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -4 
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -4 
Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -4 
V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -4 
B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -4 
Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -4 
* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1

It is a part of bigger program, but first I want to check it separately before putting it into a class. So my code looks like this:

#include <iostream>
#include <fstream>
#include <string>

using namespace std;

char readfile(char * file)
{
    int lines, cols;
    char matrix[30][30];
    ifstream ifs(file, ios::in);
    ifs.precision(2);
    ifs.setf(ios::fixed, ios::showpoint);
    ifs >> matrix[lines][cols];
    while(!ifs.eof())
    {
        string linijka;
        getline(ifs, linijka);
        if (linijka[0] != '#')
        {
            for (lines = 0; lines < 30; lines++)
            {
                for (cols = 0; cols < 30; cols++)
                {
                    return matrix[lines][cols];
                }
            }
        }
    } 

    ifs.close();
}

int main(int argc, char * argv[1])
{
    cout << "Matrix:\n" << readfile(argv[1]) << endl;
    return 0;
}

Everything is compiled without errors. Unfortuntely matrix is empty. After executing it I receive sth like that:

mateusz@viking:$ ./matpars submat/BLOSUM62.txt 
Matrix:

I need it to get mark from cell eg [T][G].

Any ideas? I'll be very thankfully. ;-)

Answer 1

Your code has a fundamental problem in it: as soon as it reaches that return statement, the function will end, and the rest of your file won't be parsed.

This is why you're not seeing anything; it's printing out the first character in the first line of your file ONLY, and that happens to be the blank space before the first A column marker.

EDIT : Actually, looking closer, it appears there's a more significant problem. You seem to be expecting that first ifs >> matrix line to load the entire file into the array for you, which it cannot do.

You seem to be a beginning programmer. To be honest, I'd recommend you start out with an easier language than C++, such as Python or Ruby.

Answer 2

There are several problems. As has already been mentionned, you return from the middle of the nested loop: certainly not what you want to do. Also, before the loop, you read into matrix[lines][cols]: this is undefined behavior, since you've never initialized lines and cols. (Typically, you wouldn't even define them until in the for, eg: for ( int lines = 0; lines < 30; ++ lines ) for ( int cols = 0; cols < 30; ++ cols ) .) Still, the line is syntactically valid, and reads the first non-blank char from the input (in your case, the initial #). And writes it somewhere, although it's anybody's guess where.

Some additional comments: -- The argument to readfile should be char const*, and not char*. Or even std::string const&.

-- I'm not sure what you're trying to read into the matrix: where do the 30 come from in its definition? And shouldn't it be "int matrix[x][x]", or something along those lines. Or more likely: "std::vector >".

-- You're reading integers (or as written, a single char); precision has no effect. It also has no effect on input.

-- And what is "ifs.setf(ios::fixed, ios::showpoint)" supposed to do. (As it happens, it almost certainly sets the floating point format to its default---and not to fixed---, although I think the behavior is formally undefined.) Not that it matters; these flags also have no effect on input.

-- The "while(!ifs.eof())" is also certainly wrong. The expression ifs.eof() is only reliable after an input operation has failed.

In addition, you'll need some special handling for the first non-comment line, and some special handling for the first character in each line.

-- James Kanze

Answer 3

I get the feeling this is homework, so I don't want to solve it outright for you. :-) However, to help you along, here's a Python implementation written in a C++ish style:

#!/usr/bin/python

import sys

def readfile(fname):
  # A dynamic array; a similar thing in C++ is vector<int>.
  # If you want a two-dimensional dynamic array in C++, it's a vector< vector<int> >
  # It's not as efficient as a fixed-size C-style array, but much more convenient!
  mat = []
  fh = file(fname)

  for line in fh: # Read through the file line by line
    cells = line.split() # This is an array of all the items in this line

    # Skip blank lines, and comment lines that start with the hash symbol
    if len(cells) == 0 or cells[0] == '#':
      continue 

    # Skip lines that end with * (lets us avoid the column titles line)
    if cells[len(cells)-1] == "*":
      continue

    # Add a row to the matrix, in C++ it would be something like mat.push_back(vector<int>())
    mat.append([])

    # Add all the items except the first one as numbers
    for i in range(1, len(cells)): # Equivalent to C++'s "for (int i = 1; i < cells.size; ++i) { }"
      mat[len(mat)-1].append(int(cells[i]))

  fh.close()
  return mat

mat = readfile(sys.argv[1])
print "Cell at 3,4 is %u" % mat[3][4]