package compbio.data.sequence;

import java.io.File;
import java.io.FileNotFoundException;
import java.util.Iterator;
import java.util.Scanner;

import compbio.util.Util;

/**
 * Reads files with FASTA formatted sequences. All the information in the FASTA
 * header is preserved including trailing white spaces. All the white spaces are
 * removed from the sequence.
 * 
 * Examples of the correct input:
 * 
 * <pre>
 * 
 * >zedpshvyzg
 * GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
 * 
 * >xovkactesa
 * CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
 * FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
 * FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
 * DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
 * 
 * >ntazzewyvv
 * CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
 * EASINM	AQQWRSLPPSRIMKLNG	HGCDCMHSHMEAD	DTKQSGIKGTFWNG	HDAQWLCRWG	
 * EFITEA	WWGRWGAITFFHAH	ENKNEIQECSDQNLKE	SRTTCEIID   TCHLFTRHLDGW 
 *   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    
 *   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   
 *   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
 * 
 *    > 12 d t y wi 		k	jbke  	
 *   KLSHHDCD
 *    N
 *     H
 *     HSKCTEPHCGNSHQMLHRDP
 *     CCDQCQSWEAENWCASMRKAILF
 * 
 * </pre>
 * 
 * @author Peter Troshin
 * @version 1.0 April 2011
 * 
 */
public class FastaReader implements Iterator<FastaSequence> {

	private final Scanner input;

	/**
	 * Header data can contain non-ASCII symbols and read in UTF8
	 * 
	 * @param input
	 *            the file containing the list of FASTA formatted sequences to
	 *            read from
	 * @throws FileNotFoundException
	 *             if the input file is not found
	 * @throws IllegalStateException
	 *             if the close method was called on this instance
	 * 
	 */
	public FastaReader(final String inputFile) throws FileNotFoundException {
		input = new Scanner(new File(inputFile), "UTF8");
		input.useDelimiter("\\s*>");
		Runtime.getRuntime().addShutdownHook(new Thread() {

			@Override
			public void run() {
				if (input != null) {
					input.close();
				}
			}
		});
	}
	/**
	 * {@inheritDoc}
	 * 
	 * @throws IllegalStateException
	 *             if the close method was called on this instance
	 */
	@Override
	public boolean hasNext() {
		return input.hasNext();
	}

	/**
	 * Reads the next FastaSequence from the input
	 * 
	 * @throws AssertionError
	 *             if the header or the sequence is missing
	 * @throws IllegalStateException
	 *             if the close method was called on this instance
	 */
	@Override
	public FastaSequence next() {
		return FastaReader.toFastaSequence(input.next());
	}

	/**
	 * Not implemented
	 */
	@Override
	public void remove() {
		throw new UnsupportedOperationException();
	}

	/**
	 * Call this method to close the connection to the input file if you want to
	 * free up the resources. The connection will be closed on the JVM shutdown
	 * if this method was not called explicitly. No further reading on this
	 * instance of the FastaReader will be possible after calling this method.
	 */
	public void close() {
		input.close();
	}

	private static FastaSequence toFastaSequence(final String singleFastaEntry) {
		final Scanner sc = new Scanner(singleFastaEntry);
		// Use new line delimiter
		sc.useDelimiter("\n");
		if (!sc.hasNext()) {
			throw new AssertionError(
					"The FASTA sequence must contain the header information"
							+ " separated by the new line from the sequence. Given sequence does not appear to "
							+ "contain the header! Given data:\n "
							+ singleFastaEntry);
		}
		String header = sc.next();
		// Get rid of the new line chars (should cover common cases)
		header = header.replaceAll("\n", "").replaceAll("\r", "");

		sc.useDelimiter("\\s*");
		final StringBuilder sb = new StringBuilder();
		while (sc.hasNext()) {
			sb.append(sc.next().trim());
		}
		final String sequence = sb.toString();
		if (Util.isEmpty(sequence)) {
			throw new AssertionError(
					"Empty sequences are not allowed! Please make sure the "
							+ " data is in the FASTA format! Given data:\n "
							+ singleFastaEntry);
		}
		return new FastaSequence(header, sequence);
	}
}