Cannot read a file when running program from commandline, but it works from Eclipse

I have a simple java program that runs fine in eclipse but cannot find the .txt files I read from and write to when r开发者_JAVA百科un from command line. I tried changing the permissions of the files but because they run in eclipse it seems that is not the issue. I'm not experienced in reading from files in Java. But I think it is a path issue or something. Can anyone help me fix my script or whatever so it works?

I get a bunch of these:

java.io.FileNotFoundException: helloState.txt (No such file or directory)
    at java.io.FileInputStream.open(Native Method)
    at java.io.FileInputStream.<init>(FileInputStream.java:106)
    at bot.FileRead.readByLine(FileRead.java:33)
    at bot.BuildStates.buildStates(BuildStates.java:16)
    at bot.Kate.main(Kate.java:98)

My file structure is as follows CS317_A4/src/myPackage/(class and source files)

My text files are in the CS317_A4 directory and my script is in the src directory (I can't seem to run the program from the CS317_A4 directory

Here is my script for running the program:

#!/bin/bash

set classpath=
java -cp .:.. bot.Kate

Here is how I open the file:

public LinkedList<String> readByLine(String filename) {

    File file = new File(filename);
    FileInputStream fis = null;
    BufferedInputStream bis = null;
    BufferedReader br = null;
    String in;
    LinkedList<String> fileLines = new LinkedList<String>();


    try {
        fis = new FileInputStream(file);
        bis = new BufferedInputStream(fis);
        br = new BufferedReader(new FileReader(file));


        while(br.ready()){
            /* read the line from the text file */
            in = br.readLine();

            /* if the line is empty stop reading */
            if(in.isEmpty()){
                break;
            }
            /* add the line to the linked list */
            fileLines.add(in);

        }

        /* dispose all the resources after using them. */
        fis.close();
        bis.close();

    } catch (FileNotFoundException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }

    return fileLines;

}

Try to start it from the directory that's above src. As classpath, use src.