// score matrix class for QUASAR format matrices
// (class from ProgPrakt WS 05/06)


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



/**
 * A scoring system including a substitution matrix and a secondary structure matrix
 */


public class ScoreMatrix {
	
	// primary
	private float[][] scores;
	
	/**
	 * Return score for a pair of amino acids AND a pair of 
	 * 
	 * @param AA1		first amino acid
	 * @param AA2		second amino acid
	 * @param SEC1		first secondary structure char
	 * @param SEC2		second secondary structure char
	 * @return
	 */
	public float getScore(byte AA1, byte AA2) {
		// weight scores and return
		return scores[AA1][AA2] ;
	}
	
	
	// read & parse amino acid matrix file
	
	public ScoreMatrix (String file) throws  IOException {
		
		BufferedReader reader = new BufferedReader(new FileReader(file));
				
		byte[] aaOrder=null;
		int numAAs;
		
		// parse, line-by-line
		String line;
		int curMatrixLine=0;
		while ((line = reader.readLine()) != null) {
			// find ROWINDEX (determine AA order in this mat)
			if (line.length() > 8 && line.toLowerCase().substring(0,8).equals("rowindex")) {
				String split[] = splitByWhitespaces(line);
				numAAs = split[1].length();
				aaOrder = new byte[numAAs];
				// create scoring array
				scores = new float[numAAs][numAAs];
				// decode the AA order sequence
				for (int i=0; i<numAAs; i++) 
					aaOrder[i] = AAMapping.mapAAToNum((byte)split[1].charAt(i));
			}
			// find MATRIX line (scoring information)
			if (line.length() > 8 && line.toLowerCase().substring(0,6).equals("matrix")) {
				// splitup line
				String split[] = splitByWhitespaces(line);
				
				curMatrixLine++;
				for (int i=1; i<=curMatrixLine; i++) {
					// translate indices
					int trans1 = aaOrder[i-1];
					int trans2 = aaOrder[curMatrixLine-1];
					scores[trans1][trans2] = Float.parseFloat(split[i]);
					scores[trans2][trans1] = scores[trans1][trans2];
								
				}				
			}		
		}
		
		reader.close();
		
	}
	
	
	
	/**
	 * Split up a string by whitespaces... the inefficient way
	 * 
	 * @param input	the input string
	 * @return
	 */
	public static String[] splitByWhitespaces(String input) {
		// split up by whitespaces
		String[] splitUp = input.split(" ");
		// create container
		Vector<String> vec = new Vector<String>();
		
		for (int i=0; i<splitUp.length; i++) {
			if (!splitUp[i].trim().equals("")) {
				vec.add(splitUp[i]);
			}
		}
		
		return (String[])vec.toArray(new String[0]);
		
	}
	
}