Thread: Getting an ArrayIndexOutOfBoundsException

SO this is for a homework assignment. And if you look at my previous posts you will see that I am not asking for help and I have done this work by myself. That being said I have one single error left to fix on this code, and I can not firgure out why it is giving me this error

import java.util.Scanner;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
 
public class Parser {
 
	public static int countEntries(String filename) throws IOException{
		int numEntries = 0;
		Scanner lineScanner = new Scanner(new File(filename));
		while(lineScanner.hasNextLine())
		     if (lineScanner.nextLine().startsWith("//"))
		     	numEntries++;
		return numEntries;
	}
 
	public static String[][] parse(String filename) throws IOException {
 
		String[][] data = new String[2][countEntries(filename)];
	    Scanner lineScanner = new Scanner(new File(filename));	
	    boolean foundAC = false;	// True when AC line is encountered
	    boolean foundSQ = false;	// True when SQ line is encountered
	    String sequence="";			// accumulates the sequence
	    String accession = "";		// stores the primary accession
	    int n = 0;
 
	    while(lineScanner.hasNextLine( )){
	     	String line = lineScanner.nextLine();
	     	String[] tokens = line.split(" ");
	     	String s = tokens[0];
 
	     	if (s.startsWith("//")){
	     		data[0][n] = accession;
	     		data[1][n] = sequence;
	     		foundAC = foundSQ = false;
	     		sequence = "";
	     		n++;
	     	}
	     	else if (foundSQ){
	     		sequence += line.replace(" ", "");
	     	}
	     	else if (s.equals("AC") && !foundAC){
	     			foundAC = true;
	     			accession = line.substring(5, line.length()-1).split(";")[0];
	     	}
	     	else if (s.equals("SQ")){
	     		foundSQ = true;
	     	}
	    }
	    lineScanner.close();
	    return data;
	}
 
 
	public static void main(String[] args) throws IOException {
		String[][] data = parse(args[0]);
		FileWriter output = new FileWriter(new File(args[1]));
		for (int i = 0; i < data[0].length; i++)
			output.write(">"+data[0][i]+"\n"+data[1][i]+"\n");
		output.close();
	}
 
}

That is the entire project. It is designed to read in a file, find certain values inside the file and save thoose into an array, and then write that array into a new file. However I am getting a Indexoutofbounds error on line 56 which is this

public static void main(String[] args) throws IOException {
	THIS LINE HERE------------->	String[][] data = parse(args[0]);
		FileWriter output = new FileWriter(new File(args[1]));
		for (int i = 0; i < data[0].length; i++)
			output.write(">"+data[0][i]+"\n"+data[1][i]+"\n");
		output.close();

Any and all help as to why I am getting this would be great

What do you mean? I am passing a file title "uniprotFile" into the program under the command line if that is what you mean. Could you elaborate on your question more

I figured it out. I wasn't spelling the things right in the command prompt (because of the hard coding)

and for those of you who helped me with the original model of this code i fixed that version as well. These codes do the same thing but written differently

import java.util.*;
import java.io.*;
 
public class Parser 
{
	    public static void main(String[] args) throws IOException
	    {	
	    	PrintWriter out = new PrintWriter("fastaFile");
	    	String[][] extractedInfo = extract_info();
		int n = count_entries();
 
	    	for(int i = 0; i < n; i++)
	    	{
			out.write("<"+extractedInfo[i][1]+"\n"+extractedInfo[i][0]+"\n");
	    	}
 		out.close();	        
	    }
 
 
	    public static String[][] extract_info() throws IOException 
	    {
		String[][] extractedData = new String[count_entries()][2];
	    	File uniprot = new File ("uniprotFile");
	    	Scanner uniprotScanner = new Scanner (uniprot);
	    	int i = 0;
	    	boolean foundAC = false;
		boolean SQMode = false;
		String sequence = "";
 
	    	while (uniprotScanner.hasNextLine())
	    	{
	    		String currentLine = uniprotScanner.nextLine();
	    		String[] tokens = currentLine.split(" ");
 
	    		if ( tokens [0].equals("AC") && !foundAC )
	    		{
	    			extractedData[i][1] = tokens[3];
	    			foundAC = true;
	    		}
	    			else if (tokens [0].equals("SQ") && !SQMode)
	    			{
	    				SQMode = true;
	    			}
	    				else if (currentLine.startsWith("//"))
	    				{
	    					SQMode = foundAC = false;
	    					extractedData[i][0] = sequence; 
	    					sequence = "";
	    					i++;
	    				}	
	    					else if (SQMode)
	    					{
	    						sequence += currentLine.replaceAll(" ", "");
	    					}	    			    		
	    	}	
	    	return extractedData;
	    }
 
	    public static int count_entries() throws IOException
	    {
	    	int entriesCount = 0;
	    	File uniprot = new File ("uniprotFile");
	    	Scanner uniprotScanner = new Scanner (uniprot);
	    while (uniprotScanner.hasNextLine())
	    { 
	    	String currentLine = uniprotScanner.nextLine();
	    	String[] tokens = currentLine.split(" ");
 
	    	if (tokens [0].equals("//"))
	    	{
	    		entriesCount++;
	    	} 
	    }
	    return entriesCount;
	    }
 }

THanks for all the help. Assignment two is due monday so expect some posts here in a day or so.

Thanks again