Bioinformatics program with useless code

[ApacheOmega]

I wrote this program and I thought i was pretty sure that everything would check out but when I run it, it doesn't print out the final cout<< and I cant really figure out why. I know its probably something small but I just cant put my finger on it. its supposed to translate the RNA input into protein output but it wont budge. I just need to know what I'm doing wrong. All it does is print the RNA sequence but i need it to print the Amino acid equivalent to what ever codon is created ex.UUU=Phenylalanine if you have any incite please let me know
Thank You!!!

here's my code

#include<iostream>
#include <string>
using namespace std;

int main()
{
	
	int numberOfCodons;
	int rnaLength;
	int beginIndex;
	int endIndex;
	int i,j,k;
	string codons[64] = {"UUU","UUC","UUA","UUG","UCU","UCC","UCA","UCG","UAU","UAC","UAA","UAG","UGU","UGC","UGA","UGG", 
						 "CUU","CUC","CUA","CUG","CCU","CCC","CCA","CCG","CAU","CAC","CAA","CAG","CGU","CGC","CGA","CGG",
						 "AUU","AUC","AUA","AUG","ACU","ACC","ACA","ACG","AAU","AAC","AAA","AAG","AGU","AGC","AGA","AGG",
						 "GUU","GUC","GUA","GUG","GCU","GCC","GCA","GCG","GAU","GAC","GAA","GAG","GGU","GGC","GGA","GGG"};
	string aminoAcids[64]={"Phenylalanine","Phenylalanine","Leucine","Leucine", "Serine","Serine","Serine","Serine","Tyrosine","Tyrosine", "Stop","Stop", "Cysteine","Cysteine","Stop", "Tryptophan",
						   "Leucine","Leucine","Leucine","Leucine","Proline","Proline","Proline","Proline","Histidine","Histidine","Glutamine","Glutamine","Arginine","Arginine","Arginine","Arginine",
						   "Isoleucine","Isoleucine","Isoleucine","Methionine","Threonine","Threonine","Threonine","Threonine","Asparagine","Asparagine","Lysine","Lysine","Serineine","Serineine","Arginine","Arginine",
							"Valine","Valine","Valine","Valine","Alanine","Alanine","Alanine","Alanine","Aspartate","Aspartate","Glutamate","Glutamate","Glycine","Glycine","Glycine","Glycine"};
	string codon=" ";
	string protein=" ";
	string RNA;
	cout<<"   To begin translation    "<<endl;
	cout<<"Please enter RNA sequence: "<<endl;
	cin>>RNA;
	cout<<endl;
	rnaLength=RNA.length();
	for(int i=0; i<RNA.length(); i+=3){
    
    cout<<RNA[i];
	if(i+1 < RNA.length())
        cout<<RNA[i+1];
	if(i+2 < RNA.length())
        cout<<RNA[i+2];
		cout<<" ";
}
	cout<<endl;
	numberOfCodons=rnaLength/3;
	beginIndex=0;
	cout<<"Total Number Of codons are: "<<numberOfCodons<<endl;
	for (i=0; i<numberOfCodons;i++)
	{
		beginIndex=beginIndex;
		endIndex=beginIndex+2;
		for(j=beginIndex;j<endIndex;j++)
		{
			codon.append(string(1,RNA[j]));
		//cout<<" ";
		//cout<<codon<<endl;
		
		}
	for (k=0;k<64;k++)
	{///////////this if statement is not working----------------------------
		if(codon==codons[k])
		{
			protein.append(aminoAcids[k]);
			
		
		}
		
	
	}
beginIndex=beginIndex+3;

	}
//heres the problem right here----------------------------
	cout<<protein<<endl;
	
	system("PAUSE");
		return 0;
}

if i say
if(codon<codons[k])
it will print the whole array I just need the corresponding protein or Amino Acid

[helios]

What's the value of codon at line 55?

By the way, the loop on line 46 is very ugly. It can be replaced with

codon.append(RNA.substr(beginIndex,endIndex-beginIndex));

or with

codon.append(RNA.begin()+beginIndex,RNA.begin()+endIndex);

Also note that RNA[endIndex] is not appended to codon, because the for condition is j<endIndex, so codon.size()==2 (actually, there's probably another bug which makes this last statement false. I can't say for sure if it's a bug because I don't know what you're trying to accomplish).

[ApacheOmega]

the value can be what ever is imputed (oh that cin at line 26 shouldn't be commented out)
thanks for the tip also i know i gotta get better with my loops

[helios]

the value can be what ever is imputed

Well, no. While its value certainly does depend on the user's input, it's not directly entered by the user.