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Thread: Getting an ArrayIndexOutOfBoundsException

  1. #1
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    Default 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

  2. #2
    Super Moderator helloworld922's Avatar
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    Default Re: Getting an ArrayIndexOutOfBoundsException

    Looks like you're not passing any command-line arguments to your program. What command are you using to run the program?

  3. #3
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    Default Re: Getting an ArrayIndexOutOfBoundsException

    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

  4. #4
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    Default Re: Getting an ArrayIndexOutOfBoundsException

    If you're passing command-line args correctly then that's not the problem. Do you have the full debug stack trace?

  5. #5
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    Default Re: Getting an ArrayIndexOutOfBoundsException

    Quote Originally Posted by NewbieJavaProgrammer View Post
    ...I am passing a file title "uniprotFile" into the program...
    Try something like the following at the beginning of main():
        public static void main(String[] args) throws IOException {
            System.out.printf("Number of args = %d\n", args.length);
            System.out.printf("args[0]: %s\n", args[0]);
            String[][] data = parse(args[0]);

    It would help us understand your problem (maybe) if you can paste all output and error messages into your response. Don't abbreviate. Don't paraphrase.


    Cheers!

    Z
    Last edited by Zaphod_b; September 26th, 2012 at 03:09 PM.

  6. #6
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    Default Re: Getting an ArrayIndexOutOfBoundsException

    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

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