Transpose string[][] input file

Hi
I'd like to know why my program does not apply the transpose method.
Input is like
C0,F0,D0,E0,G0,B0
C1,F1,D1,E1,G1,B1
C2,F2,D2,E2,G2,B2
C3,F3,D3,E3,G3,B3
C4,F4,D4,E4,G4,B4
C5,F5,D5,E5,G5,B5

I want output like
C0
C1
C2
C3
C4
C5
F0
F1
etc.

The commas are handled by the .split(",")

Here is the program:
import java.io.*;
import java.util.*;

public class SwapIO {

public static String[][] transpose(String [][] a) {
int r = a.length;
int c = a[r-1].length;
String [][] t = new String[c][r];
for(int i = 0; i < r; ++i) {
for(int j = 0; j < c; ++j) {
t[j][i] = a[i][j];
}
}
return t;

}

public static void main(String[] args) {
// TODO Auto-generated method stub
FileOutputStream out; // declare a file output object
PrintStream p; // declare a print stream object

try
{
// Create a new file output stream
// connected to "myfile.txt"
File file = new File(args[0]);
String fileName= file.getName();
int len = fileName.length();
StringBuffer sb = new StringBuffer(fileName);
sb.replace(len-4,len,".hr");
out = new FileOutputStream(sb.toString());

// Connect print stream to the output stream
p = new PrintStream( out );

// p.println ("This is written to a file");
Scanner sc = null;
try {
sc = new Scanner(new DataInputStream(new FileInputStream(args[0])));
} catch (FileNotFoundException e) {
e.printStackTrace();
}

try {
// Scanner input = new Scanner(new File("array.txt"));
Scanner input = new Scanner(new DataInputStream(new FileInputStream(args[0])));
int m = count(args[0]);
int n = count(args[0]);
int place;
int string;
String[][] a = new String[m][n];
// while (input.hasNextLine()) {

for (int i = 0; i < m; i++) {
for (int j = 0; j < n; j++) {
try{// System.out.println("number is ");

String txt = input.next();
String[] tmp = txt.split(",");
String[][] proxies = new String[m][n];
String[][] chords = new String[count(args[0])][count(args[0])];

for(int ii = 0; ii<tmp.length; ii=ii+1){
String[] proxy = tmp[ii].split(",");
for(int k = 0; k<proxy.length; k++){
proxies[ii][k] = proxy[k];
System.out.println(proxies[ii][k]);

// for( place = 0 ; place < proxy.length ; place++ ){
// for( string = 0 ; string < proxy.length ; string++ ){
// proxies[k][ii] = proxies[ii][k];
chords = transpose(proxies);//why does it not apply transpose?

p.println(chords[k][ii]);
// }
// }

}

}

// System.out.println("number is "+ str[i][j]);
}
catch (java.util.NoSuchElementException e) {
// e.printStackTrace();
}
}
} //print the input matrix
System.out.println("The input sorted matrix is : ");
for (int i = 0; i < m; i++) {
for (int j = 0; j < n; j++) {
String[][] chords = new String[count(args[0])][count(args[0])];

for( place = 0 ; place < n ; place++ ){
for( string = 0 ; string < n ; string++ ){
chords[n - 1 - place][string] = a[string][place];
}
}
System.out.println(chords[i][j]);
// p.println(chords[i][j]);
}
}
// }
} catch (Exception e) {
e.printStackTrace();
}
}
catch (Exception e)
{
System.err.println ("Error writing to file");
}
}

public static int count(String filename) throws IOException {
InputStream is = new BufferedInputStream(new FileInputStream(filename));
try {
byte[] c = new byte[1024];
int count = 0;
int readChars = 0;
while ((readChars = is.read(c)) != -1) {
for (int i = 0; i < readChars; ++i) {
if (c[i] == '\n')
++count;
}
}
return count;
} finally {
is.close();
}
}

public static final boolean stringToBoolean(String r) {

if (r.equals("0")) {return false;}

r = r.toLowerCase();

if (r.equals("false")) {return false;}

if (r.equals("f")) {return false;}

if (r.equals("none")) {return false;}

if (r.equals("not")) {return false;}

if (r.equals("no")) {return false;}

if (r.equals("n")) {return false;}

if (r.equals("zero")) {return false;}

if (r.equals("z")) {return false;}

else {return true;}

}

public static void shln(String s) {

System.out.println(s);

}

public static void show(String s) {

System.out.print(s);

}

}