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//
// 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
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