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//
// BCToolComplement.m
// BioCocoa
//
// Created by Koen van der Drift on 11/19/04.
// 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 "BCToolComplement.h"
#import "BCSequence.h"
#import "BCSymbol.h"
#import "BCNucleotide.h"
#import "BCFoundationDefines.h"
#import "BCInternal.h"
@implementation BCToolComplement
-(id) initWithSequence:(BCSequence *)list
{
if ( (self = [super initWithSequence:list]) )
{
[self setReverse: NO];
}
return self;
}
+ (BCToolComplement *) complementToolWithSequence: (BCSequence *) list
{
BCToolComplement *complementTool = [[BCToolComplement alloc] initWithSequence: list];
return [complementTool autorelease];
}
- (void)setReverse: (BOOL)value
{
reverse = value;
}
- (BCSequence *) sequenceComplement
{
BCNucleotide *symbol;
NSArray *symbolArray;
NSMutableArray *theComplement;
DECLARE_INDEX(loopCounter);
int theLimit, newLocation;
BCSymbol *symbolComplement;
// if it's a protein, we return the same sequence.
// why a negative test here? It could also be BCSequenceTypeCodon or BCSequenceTypeOther.
// maybe we should test for BCSequenceTypeProtein ?
if ( [sequence sequenceType] != BCSequenceTypeDNA && [sequence sequenceType] != BCSequenceTypeRNA )
return [[sequence copy] autorelease];
symbolArray = [[self sequence] symbolArray];
theComplement = [NSMutableArray array];
theLimit = [symbolArray count];
for ( loopCounter = 0 ; loopCounter < theLimit ; loopCounter++ )
{
symbol = (id)ARRAY_GET_VALUE_AT_INDEX(symbolArray, loopCounter);
symbolComplement = [symbol complement];
if ( symbolComplement != nil )
{
newLocation = ( reverse == NO ? loopCounter : 0 );
ARRAY_INSERT_VALUE_AT_INDEX(theComplement, newLocation, symbolComplement);
}
}
return [BCSequence sequenceWithSymbolArray: theComplement symbolSet: [[self sequence] symbolSet]];
}
@end
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