// AminoAcidTable.java
//
//
// Copyright 2004, Ethan Bolker and Bogdan Calota

package edu.umb.cs.eb.folding;

import java.util.Iterator;

/**
 * Model a table of AminoAcids.
 * Serves too as a table factory.
 */
public abstract class AminoAcidTable
{
    public static final String STANDARD = "standard";
    public static final String VIRTUAL  = "virtual";
    private static StandardTable standardTable = null;
    private static VirtualTable virtualTable = null;

    /**
     * The table factory.
     *
     * @param tableName the name of the table.
     *
     * @return the table, null if no table with that name.
     */
    public static AminoAcidTable makeTable( String tableName ) 
	throws FoldingException
    {
	if (tableName.equalsIgnoreCase("standard")) {
	    if (standardTable == null) {
		standardTable = new StandardTable();
	    }
	    return standardTable;
	}
	if (tableName.equalsIgnoreCase("virtual")) {
	    if (virtualTable == null) {
		virtualTable = new VirtualTable();
	    }
	    return virtualTable;
	}
	throw new FoldingException("no AminoAcid  named " + tableName);
    }

    /**
     * Add an AminoAcid to the table, with its frequency.
     *
     * @param a the AminoAcid to add.
     * @param probability how likely is that AminoAcid?
     *
     * @throws FoldingException if operation not allowed.
     */
    public abstract void add( AminoAcid a, double probability )
	throws FoldingException;

    /**
     * Add an AminoAcid to the table.
     *
     * @param a the AminoAcid to add.
     *
     * @throws FoldingException if operation not allowed.
     */
    public abstract void add( AminoAcid a )
	throws FoldingException;

    /**
     * Choose a random sequence of AminoAcids from this table.
     *
     * @param length the length of the desired sequence.
     * @param seed a seed for the random number generator.
     */
    public abstract AminoAcid[] getRandom( int length, int seed );

    /**
     * A bound on the absolute value of the energy of
     * AminoAcids in the table.
     *
     * @return the bound.
     */
    public abstract double getMaxEnergy();

    /**
     * Retrieve an acid from the table.
     *
     * @param name the name of the acid.
     * 
     * @return the acid, null if none.
     */
    public abstract AminoAcid get( String name )
	throws FoldingException;

    /**
     * A constant between 0 and 1 that leads to good contrast
     * when normalized hydrophobic index determines color in a 
     * folding on a grid.
     *
     * Default is 0.5;
     *
     * @return the constant.
     */
    public float getContrastScaler()
    {
	return (float)0.5;
    }

    /**
     * Enable iteration over the keys in the table.
     *
     * @return an Iterator.
     *
     * @throws FoldingException if no Iterator available.
     */
    public Iterator getIterator() 
	throws FoldingException
    {
	throw new FoldingException("no iterator available");
    }

    /**
     *  Returns the name of this AminoAcidTable
     *
     * @return a String
     */
    public abstract String getName();

    /**
     *  Unit testing
     */
    public static void main( String[] args )
    {
	AminoAcidTable t = null;
	try {
	    t = AminoAcidTable.makeTable("standard");
	}
	catch(FoldingException e) {}
	AminoAcid[] list = t.getRandom(15, 999);
	for (int i = 0; i < list.length; i++ ) {
	    System.out.print(list[i] + " ");
	}
	System.out.println();
    }
}