//
//  BCScoreMatrix.m
//  BioCocoa
//
//  Created by Philipp Seibel on 10.03.05.
//  Copyright (c) 2003-2009 The BioCocoa Project.
//  All rights reserved.
//
//  Redistribution and use in source and binary forms, with or without
//  modification, are permitted provided that the following conditions
//  are met:
//  1. Redistributions of source code must retain the above copyright
//  notice, this list of conditions and the following disclaimer.
//  2. Redistributions in binary form must reproduce the above copyright
//  notice, this list of conditions and the following disclaimer in the
//  documentation and/or other materials provided with the distribution.
//  3. The name of the author may not be used to endorse or promote products
//  derived from this software without specific prior written permission.
//
//  THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
//  IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
//  OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
//  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
//  INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
//  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
//  DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
//  THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
//  (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
//  THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

#import "BCScoreMatrix.h"


@implementation BCScoreMatrix

- (id)initWithSymbolSet:(BCSymbolSet *)symbolSet matrix:(int *)aMatrix {
	self = [super init];
	if ( self ) {
		symbols = [symbolSet allSymbols];
		symbolCount = [symbols count];
		
		scoreMatrix = (int *)malloc( sizeof( int ) * 128 * 128 );
		memcpy( scoreMatrix, aMatrix, sizeof( int ) * 128 * 128 );
	}
	return self;
}

- (BOOL)containsSymbol:(BCSymbol *)aSymbol {
	return [symbols containsObject: aSymbol];
}

- (int)substituteSymbol:(BCSymbol *)symbolA forSymbol:(BCSymbol *)symbolB {
	if ( ![self containsSymbol:symbolA] || ![self containsSymbol:symbolB] ) {
		// handle wrong symbols !!!
	}
	
	char idxA = [symbolA symbolChar];
	char idxB = [symbolB symbolChar];
	
	return [self substituteChar:idxA forChar:idxB];
}

- (int)substituteChar:(char)charA forChar:(char)charB {
	return scoreMatrix[ charA * 128 + charB ];
}

- (void)dealloc {
	[symbols release];
	[super dealloc];
}

@end
