import jaligner.Alignment;
import jaligner.Sequence;
import jaligner.SmithWatermanGotoh;
import jaligner.formats.Pair;
import jaligner.matrix.MatrixLoader;
import jaligner.util.SequenceParser;

import java.io.IOException;
import java.io.InputStream;
import java.util.logging.Level;
import java.util.logging.Logger;

public class Example {
	
	private static final String SAMPLE_SEQUENCE_P35_HUMAN = "jaligner/example/sequences/p53_human.fasta";
	private static final String SAMPLE_SEQUENCE_P35_MOUSE = "jaligner/example/sequences/p53_mouse.fasta";

	private static final Logger logger = Logger.getLogger(Example.class.getName());
	
	public static void main(String[] args) {
        try {
        	
		Sequence s1 = SequenceParser.parse(loadP53Human());  
		Sequence s2 = SequenceParser.parse(loadP53Mouse());
	        
	        Alignment alignment = SmithWatermanGotoh.align(s1, s2, MatrixLoader.load("BLOSUM62"), 10f, 0.5f);
	        
	        System.out.println ( alignment.getSummary() );
	        System.out.println ( new Pair().format(alignment) );


	        
        } catch (Exception e) {
        	logger.log(Level.SEVERE, "Failed running example: " + e.getMessage(), e);
        }
    }



	
	/**
	 * 
	 * @param path location of the sequence
	 * @return sequence string
	 * @throws IOException
	 */
	private static String loadSampleSequence(String path) throws IOException {
		InputStream inputStream = Example.class.getClassLoader().getResourceAsStream(path);
        StringBuffer buffer = new StringBuffer();
        int ch;
        while ((ch = inputStream.read()) != -1) {
            buffer.append((char)ch);
        }
        return buffer.toString();
	}
	
	/**
	 * 
	 * @return sequence string
	 * @throws IOException
	 */
	public static String loadP53Human( ) throws IOException {
		return loadSampleSequence(SAMPLE_SEQUENCE_P35_HUMAN);
	}

	/**
	 * 
	 * @return sequence string
	 * @throws IOException
	 */
	public static String loadP53Mouse( ) throws IOException {
		return loadSampleSequence(SAMPLE_SEQUENCE_P35_MOUSE);
	}
}