AminoAcidModel.java

package statalign.model.subst.plugins;

import java.awt.Color;

import statalign.io.RawSequences;
import statalign.model.subst.RecognitionError;
import statalign.model.subst.SubstitutionModel;

/**
 * Common superclass for amino acid substitution models.
 * 
 * @author novak
 */
public abstract class AminoAcidModel extends SubstitutionModel {
	
	public static final String type = "protein";
	
	static final String magentaCharacters = "RHK";
	static final String     redCharacters = "AVFPMILW";
	static final String    blueCharacters = "DE";
	static final String   greenCharacters = "STYCNGQ";
	
	static final Color char2color[] = new Color[255];
	
	static {
		int i;
		for(i = 0; i < 255; i++)
			char2color[i] = Color.LIGHT_GRAY;
		for(i = 0; i < magentaCharacters.length(); i++)
			char2color[magentaCharacters.charAt(i)] = Color.MAGENTA;
		for(i = 0; i < redCharacters.length(); i++)
			char2color[redCharacters.charAt(i)] = Color.RED;
		for(i = 0; i < blueCharacters.length(); i++)
			char2color[blueCharacters.charAt(i)] = Color.BLUE;
		for(i = 0; i < greenCharacters.length(); i++)
			char2color[greenCharacters.charAt(i)] = Color.GREEN;
	}

	/**
	 * Returns the color of a character.
	 * 
	 * Magenta characters are 'RHK', red characters are 'AVFPMILW',
	 * blue characters are 'DE' and green characters are 'STYCNGQ'.
	 */
	@Override
	public Color getColor(char c) {
		return char2color[c];		// 'cause speed matters...
	}

	/**
	 * Dummy function with the possibility of further developments.
	 */
	@Override
	public String print() {
		return "";
	}

	/**
	 * Empty method provided for models with no parameters (the evolutionary time
	 * is represented in the edge lengths).
	 */
	@Override
	public void restoreParameter() {
	}

	/**
	 * It does nothing and returns 0, i.e log-probability 1.
	 */
	@Override
	public double sampleParameter() {
		return 0.0;
	}

	/**
	 * This function decides if the model can accept the input sequences.
	 */
	@Override
	public double acceptable(RawSequences r) {
		int[] count = new int[alphabet.length];
		String accept = new String(alphabet).toUpperCase()+"BZJX";	// accept ambiguous amino acids
		for(int i = 0; i < r.size(); i++){
			String sequence = r.getSequence(i);
			for(int j = 0; j < sequence.length(); j++){
				char ch = sequence.charAt(j);
				if(ch != '-' && ch != ' ') {
					int k = accept.indexOf(Character.toUpperCase(ch));
					if(k == -1) {
						throw new RecognitionError(getMenuName()+" cannot be used with the current sequences because they contain the character '"+ch+"'!\n");
					} else if(k < alphabet.length) {
						count[k] = 1;
					}
				}
			}
		}
		int sum = 0;
		for(int i = 0; i < count.length; i++){
			sum += count[i];
		}
		return (double)sum/(double)count.length + 0.1;
	}

	/**
	 * Returns the most likely character given the Felsentein likelihood array. 
	 */
	@Override
	public char mostLikely(double[] seq) {
		// "ARNDCQEGHILKMFPSTWYV";		// plus ambiguous: BZJX

		double max = 0.0;
		char character = '*';
		for(int i = 0; i < seq.length; i++){
			if(seq[i] > max){
				character =  alphabet[i];
				max = seq[i];
			}
		}
		if(character == 'A' && seq[0] == seq[1]) // X: any
			character = 'X';
		else if(character == 'N' && seq[2] == seq[3]) // B: N or D
			character = 'B';
		else if(character == 'Q' && seq[5] == seq[6]) // Z: E or Q
			character = 'Z';
		else if(character == 'L' && seq[10] == seq[11]) // J: L or K
			character = 'J';
		return character;
	}
}