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// BCSuffixArray.h
// BioCocoa
//
// Created by Scott Christley on 7/20/07.
// 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.
//
/*
Hybrid suffix-array builder, written by Sean Quinlan and Sean Doward,
distributed under the Lucent Public License Version 1.02.
Copyright (C) 2003, Lucent Technologies Inc. and others. All Rights Reserved.
*/
/*!
@header
@abstract Create and manage suffix arrays for sequence data.
*/
#import <Foundation/Foundation.h>
@class BCSequence;
@class BCSequenceArray;
@class BCMCP;
/*!
@class BCSuffixArray
@abstract Class that manages a suffix array for a sequence.
@discussion A suffix array is a data structure containing all of the suffix
* strings for a sequence in sorted order. It is useful for doing fast, simple
* string searches and comparison operations. In constrast to a suffix tree,
* the suffix array is easily stored on disk for large sequences like whole genomes.
*/
@interface BCSuffixArray : NSObject {
BCSequenceArray *sequenceArray;
BCSequenceArray *reverseComplementArray;
NSMutableDictionary *metaDict;
NSString *dirPath;
NSString *tmpFile;
unsigned char *memSequence;
int numOfSuffixes;
int *suffixArray;
BOOL inMemory;
long long maxMemoryUsage;
int memoryState;
BOOL softMask;
}
- (BOOL)constructFromSequence:(BCSequence *)aSequence strand:(NSString *)aStrand;
- (BOOL)constructFromSequenceArray:(BCSequenceArray *)anArray strand:(NSString *)aStrand;
- (BOOL)constructFromSequenceFile:(NSString *)aPath strand:(NSString *)aStrand;
- initWithContentsOfFile:(NSString *)aPath forSequence:(BCSequence *)aSequence inMemory:(BOOL)aFlag;
- initWithContentsOfFile:(NSString *)aPath forSequenceArray:(BCSequenceArray *)anArray
inMemory:(BOOL)aFlag;
- initWithContentsOfFile:(NSString *)aPath inMemory:(BOOL)aFlag;
- (BOOL)writeToFile:(NSString *)aPath withMasking:(BOOL)aFlag;
- (FILE *)getFILE;
- (int)numberOfSequences;
- (int)numOfSuffixes;
- (const int *)suffixArray;
- (unsigned char *)memoryForSequence:(int)aNum;
- (BCSequenceArray *)sequenceArray;
- (BCSequenceArray *)reverseComplementArray;
- (NSDictionary *)metaDictionary;
- (BOOL)softMask;
- (void)setSoftMask: (BOOL)aFlag;
- (void)dumpSuffixArray;
- (void)dumpSuffixArrayForSequence:(int)aSeq position:(int)aPos length:(int)aLen;
@end
/*!
@class BCSuffixArrayUnionEnumerator
@abstract Provides an enumeration of the suffix strings for the union of a set of suffix arrays.
@discussion Performs an on-the-fly (online) union of a set of suffix arrays with an enumeration of
* the suffixes in sorted order. Each time -nextSuffixPosition is called, the enumerator moves to
* the next suffix in the union; returns NO when the enumeration is at the end. If enumeration is at
* the end, calling -nextSuffixPosition again will restart the enumeration back at the beginning.
* Puts the current suffix position, sequence index and suffix array index into the parameters, pass
* NULL for any parameters not wanted.
*/
@interface BCSuffixArrayUnionEnumerator : NSObject
{
NSArray *suffixArrays;
int *suffixPositions;
int *suffixSequences;
FILE **arrayFiles;
BOOL *eofFlags;
BCSequenceArray **saSeqs;
BCSequenceArray **saRevs;
int currentSuffix;
BCSuffixArray *currentArray;
}
- initWithSuffixArrays:(NSArray *)arrays;
- (BOOL)nextSuffixPosition:(int *)aPos sequence:(int *)aSeq suffixArray:(int *)anArray;
- (NSArray *)suffixArrays;
@end
#define BCSUFFIXARRAY_TERM_CHAR '#'
|