/*****************************************************
 Amino Acid Preference Toolkit in Java
 Pathogen Project
 Department of Computer Science and Engineering
 University of South Carolina
 Columbia, SC 29208
 Contact Email: rose@cse.sc.edu
*****************************************************/

import java.io.*;
import java.util.*;

public class SequenceReader
{

    int length;
    String header;

    public SequenceReader()
    {
	length = 0;
	header = null;
    }

    public String parseFastaFile(String inputFileName)
    {
	
	BufferedReader bufferedReader;
	String line;
	StringBuffer stringBuffer = new StringBuffer("");
	
	try
	    {

		bufferedReader = new BufferedReader(new FileReader(inputFileName));
		while ((line = bufferedReader.readLine()) != null)
		    {
			if (!line.startsWith(">"))
			    {
				line = line.trim();
				stringBuffer.append(line);
			    }
			else if (line.startsWith(">"))
			    {
				header = line;
			    }
		    }

		length = stringBuffer.length();
		bufferedReader.close();
	    }
	
	catch (Exception exception)
	    {
		System.out.println(exception);
		exception.printStackTrace();
	    }	

	return stringBuffer.toString();
    }

    public int getLength()
    {
	return length;
    }
    
    public String getHeader()
    {
	return header;
    }

    
}