// Class: DNASeqReader
//
// Author: Pamela Cutter & Alyce Brady
//
// Created November 19, 2006

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;

/**
 * This class contains code to read DNA sequence data in from
 * a file.  It should be extended to read sequences from files
 * with different formats.
 * 
 * @author Alyce Brady
 * @author Pamela Cutter
 * @version Nov 19, 2006
 */
public class DNASeqReader 
{
    private BufferedReader reader = null;
    private int lineCounter = 0;

    /** Constructs an object that can read a DNA sequence string from the
     *  given file.
     */
    public DNASeqReader(String filename) 
    {
        // Get an object that can read from the file.
        try
        {
            this.reader = new BufferedReader(new FileReader(filename));
        } catch (IOException e)
        {
            System.err.println("Cannot open file "+filename+" for reading");
        }
    }

    /** Reads in the sequence string for a single DNA sequence.  The sequence
     *  is assumed to be presented as groups of space-separated nucleotide
     *  blocks, spanning 1 or more lines.  For example, the following would
     *  be a valid single-line sequence:
     *      ctccaccaaa ctttgagagt cactacaaaa acattcacga tcgcttcact
     *      @param numLines    the number of lines containing this sequence
     *      @throws IOException
     */
    public String readSequenceString(int numLines) throws IOException
    {
        String seq="";      // Will contain complete nucleotide sequence
        for ( int seqLine = 0; seqLine < numLines; seqLine++ )
        {
            // Read a line and find the individual items.
            String nextLine = this.reader.readLine();
            String[] items = nextLine.split(" ");

            // Concatenate all the blocks on this line.
            for (int i = 0; i< items.length; i++) 
                seq += items[i];
        }

        return seq;
    }

    /** Reads a line of data from the file specified in the constructor.
     *      @return the line read in from the file
     *      @throws IOException
     */
    protected String readLine() throws IOException
    {
        String nextLine = this.reader.readLine();
        lineCounter++;
        return nextLine;
    }

    /** Returns the line number of the most recently read-in line.  The
     *  first line to be read in is line number 1.
     */
    public int getLineNumber()
    {
        return lineCounter;
    }
}