package jalview.io;

import static org.junit.Assert.*;
import jalview.io.TCoffeeScoreFile.Block;
import jalview.io.TCoffeeScoreFile.Header;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.StringReader;
import java.util.List;

import javax.xml.parsers.ParserConfigurationException;

import org.junit.Test;
import org.xml.sax.SAXException;

import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;

public class TCoffeeScoreFileTest {

	final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
        final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
	
	@Test
	public void testReadHeader() throws IOException, FileNotFoundException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed {

	        TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
	        assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
		Header header = scoreFile.header;
		assertNotNull(header);
		assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
		assertEquals( 90, header.score );
		assertEquals( 89, header.getScoreFor("1PHT") );
		assertEquals( 90, header.getScoreFor("1BB9") );
		assertEquals( 94, header.getScoreFor("1UHC") );
		assertEquals( 94, header.getScoreFor("1YCS") );
		assertEquals( 93, header.getScoreFor("1OOT") );
		assertEquals( 94, header.getScoreFor("1ABO") );
		assertEquals( 94, header.getScoreFor("1FYN") );
		assertEquals( 94, header.getScoreFor("1QCF") );
		assertEquals( 90, header.getScoreFor("cons") );
	}
	
	
	@Test
	public void testWrongFile() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed {
	    try {
		TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
		assertFalse(result.isValid());
	    } catch (IOException x)
	    {
	      assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
	    }
	} 

	@Test
	public void testHeightAndWidth() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed {
		TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
		assertTrue(result.isValid());
		assertEquals( 8, result.getHeight() );
		assertEquals( 83, result.getWidth() );
	} 	
	
	@Test
	public void testReadBlock( ) throws IOException {
		
		String BLOCK = "\n" +
				"\n" +
				"\n" +
				"1PHT   999999999999999999999999998762112222543211112134\n" +
				"1BB9   99999999999999999999999999987-------4322----2234  \n" +
				"1UHC   99999999999999999999999999987-------5321----2246\n" +
				"1YCS   99999999999999999999999999986-------4321----1-35\n" +
				"1OOT   999999999999999999999999999861-------3------1135  \n" +
				"1ABO   99999999999999999999999999986-------422-------34\n" +
				"1FYN   99999999999999999999999999985-------32--------35\n" +
				"1QCF   99999999999999999999999999974-------2---------24\n" +
				"cons   999999999999999999999999999851000110321100001134\n" +
				"\n" +
				"\n";
		FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
		Block block = TCoffeeScoreFile.readBlock(source, 0);

                assertNotNull(block);
		assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
		assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
		assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
		assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
		assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
		assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
		assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
		assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
		assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
	}

	@Test
	public void testParse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed {

		TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);

		assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
		assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
		assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
		assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
		assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
		assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
		assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
		assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
		assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );		
	}

	
	@Test
	public void testGetAsList() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed {
		
          TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
          assertTrue(parser.getWarningMessage(),parser.isValid());
		List<String> scores = parser.getScoresList();
		assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
		assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
		assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
		assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
		assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
		assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
		assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
		assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
		assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );		
		
	} 
	
	
	@Test
	public void testGetAsArray() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed {
		
          TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
          assertTrue(parser.getWarningMessage(),parser.isValid());
		byte[][] scores = parser.getScoresArray();
	
		assertEquals( 9, scores[0][0] );
		assertEquals( 9, scores[1][0] );
		assertEquals( 9, scores[2][0] );
		assertEquals( 9, scores[3][0] );
		assertEquals( 9, scores[4][0] );
		assertEquals( 9, scores[5][0] );
		assertEquals( 9, scores[6][0] );
		assertEquals( 9, scores[7][0] );
		assertEquals( 9, scores[8][0] );
		
		assertEquals( 5, scores[0][36] );
		assertEquals( 4, scores[1][36] );
		assertEquals( 5, scores[2][36] );
		assertEquals( 4, scores[3][36] );
		assertEquals( -1, scores[4][36] );
		assertEquals( 4, scores[5][36] );
		assertEquals( 3, scores[6][36] );
		assertEquals( 2, scores[7][36] );
		assertEquals( 3, scores[8][36] );
		
	} 
	
	
	
}