[FIXED] I am getting 2 outputs for extremely long strings

Issue

I have a program that involves parsing strings that represent nucleotides.

When I use a small nucleotide string (basically, a small DNA strand) i.e. 'input' is small enough, I get one output:

However, when I use a loooooooooooooooong string. e.g. 10000 nucleotides long (which I actually use) , I end up with 2 outputs :O

http://i.stack.imgur.com/A39um.png http://i.stack.imgur.com/JnNcG.png

Source code: I only added the functions that I was actually using in the main class.

public static void main (String args[])
{
    String input = "Blah Blah";
    System.out.println(translate(input));
}

public static String codon (String codon_input)
/* Returns the amino acid alphabet corresponding to entered codon 
   (3 nucleotide string) in String format. */        
{
    if (codon_input.substring(0,2).equals("GC"))
    {
        return "A";
    }
    else if (codon_input.equals("UGU") || codon_input.equals("UGC"))
    {
        return "C";
    }
    else if (codon_input.equals("GAU") || codon_input.equals("GAC"))
    {
        return "D";
    }
    else if (codon_input.equals("GAA") || codon_input.equals("GAG"))
    {
        return "E";
    }
    else if (codon_input.equals("UUU") || codon_input.equals("UUC"))
    {
        return "F";
    }
    else if (codon_input.substring(0,2).equals("GG"))
    {
        return "G";
    }
    else if (codon_input.equals("CAU") || codon_input.equals("CAC"))
    {
        return "H";
    }
    else if (codon_input.substring(0,2).equals("AU") && !codon_input.equals("AUG"))
    {
        return "I";
    }
    else if (codon_input.equals("AAA") || codon_input.equals("AAG"))
    {
        return "K";
    }
    else if (codon_input.substring(0,2).equals("CU") || codon_input.equals("UUA") || codon_input.equals("UUG"))
    {
        return "L";
    }
    else if (codon_input.equals("AUG"))
    {
        return "M";
    }
    else if (codon_input.equals("AAU") || codon_input.equals("AAC"))
    {
        return "N";
    }
    else if (codon_input.substring(0,2).equals("CC"))
    {
        return "P";
    }
    else if (codon_input.equals("CAA") || codon_input.equals("CAG"))
    {
        return "Q";
    }
    else if (codon_input.substring(0,2).equals("CG") || codon_input.equals("AGA") || codon_input.equals("AGG"))
    {
        return "R";
    }
    else if (codon_input.substring(0,2).equals("UC") || codon_input.equals("AGU") || codon_input.equals("AGC"))
    {
        return "S";
    }
    else if (codon_input.substring(0,2).equals("AC"))
    {
        return "T";
    }
    else if (codon_input.substring(0,2).equals("GU"))
    {
        return "V";
    }
    else if (codon_input.equals("UGG"))
    {
        return "W";
    }
    else if (codon_input.equals("UAU") || codon_input.equals("UAC"))
    {
        return "Y";
    }
    else if (codon_input.equals("UAA") || codon_input.equals("UAG") || codon_input.equals("UGA"))
    {
        return "Stop";
    }
    return "-";
}

public static String translate (String tran_input)
/* Converts an RNA strand into an amino acid strand using codon() */
{
    String tran_output = "";
    int tran_length = tran_input.length();
    int tran_cursor = 0;
    while (tran_cursor < tran_length - 2)
    {
        if (codon(tran_input.substring(tran_cursor, tran_cursor + 3)).equals("Stop"))
        {
            return tran_output;
        }
        else
        {
            tran_output = tran_output + codon(tran_input.substring(tran_cursor, tran_cursor + 3));
        }
        tran_cursor = tran_cursor + 3;
    }
    return tran_output;
}

Solution

The console can only have so many characters in one line. According to another post mac can have 2047 (I don't know what it is on netbeans). Therefore, I think your console is just moving to the next line because it is so long. I would suggest just outputting to a file.

Answered By - Anthony Dito
Answer Checked By - Timothy Miller (JavaFixing Admin)