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// BCSequenceAlignment.h
// BioCocoa
//
// Created by Philipp Seibel on 09.03.05.
// 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.
/*!
@header
@abstract Provides alignment of sequences.
*/
#import <Foundation/Foundation.h>
#import "BCSequence.h"
#import "BCScoreMatrix.h"
@class BCSymbolSet, BCAnnotation;
/*!
@class BCSequenceAlignment
@abstract Represents an alignment of BCSequences
@discussion
*/
@interface BCSequenceAlignment : NSObject {
NSArray *sequenceArray;
}
- (id)initWithSequenceArray:(NSArray *)theSequenceArray;
@end
/*!
@category BCSequenceAlignment(AlignmentQuerying)
@abstract Obtain sequence alignment information
*/
@interface BCSequenceAlignment ( AlignmentQuerying )
/*!
@method sequenceAtIndex:
@abstract obtaining the BCSequence at the given index
@discussion
*/
- (BCSequence *)sequenceAtIndex:(unsigned int)aIndex;
/*!
@method alignmentInRange:
@abstract returns a subalignment
@discussion
*/
- (BCSequenceAlignment *)alignmentInRange:(NSRange)aRange;
/*!
@method symbolsForColumnAtIndex:
@abstract returns a NSArray containing the symbols at the given alignment column
@discussion
*/
- (NSArray *)symbolsForColumnAtIndex:(unsigned int)aColumn;
/*!
@method length
@abstract obtaining the length of the alignment
@discussion
*/
- (unsigned int)length;
- (unsigned int)sequenceCount;
/*!
@method symbolSet
@abstract obtaining the BCSymbolSet corresponding to the aligned BCSequences
@discussion
*/
- (BCSymbolSet *)symbolSet;
@end
/*!
@category BCSequenceAlignment(AlignmentAnnotation)
@abstract sequence alignment annotations
*/
@interface BCSequenceAlignment ( AlignmentAnnotation )
/*!
@method annotationForKey:
@abstract obtaining the BCAnnotation for the given key
@discussion
*/
- (BCAnnotation *)annotationForKey:(NSString *)theKey;
@end
/*!
@category BCSequenceAlignment(PairwiseAlignment)
@abstract perform pairwise sequence alignment
*/
@interface BCSequenceAlignment ( PairwiseAlignment )
/*!
@method needlemanWunschAlignmentWithSequences:properties:
@abstract perform Needleman-Wunsch pairwise sequence alignment
@discussion
*/
+ (BCSequenceAlignment *)needlemanWunschAlignmentWithSequences:(NSArray *)theSequences properties:(NSDictionary *)properties;
/*!
@method smithWatermanAlignmentWithSequences:properties:
@abstract perform Smith-Waterman pairwise sequence alignment
@discussion
*/
+ (BCSequenceAlignment *)smithWatermanAlignmentWithSequences:(NSArray *)theSequences properties:(NSDictionary *)properties;
@end
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