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// BCMCP.h
// BioCocoa
//
// Created by Scott Christley on 7/24/07.
// 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.
#import <Foundation/Foundation.h>
@class BCSuffixArray;
@class BCSequenceArray;
@class BCCachedSequenceFile;
@interface BCMCP : NSObject {
NSMutableDictionary *metaDict;
NSMutableArray *sequenceToMeta;
BOOL inMemory;
// in memory sequences
BCSequenceArray *sequenceArray;
BCSequenceArray *reverseComplementArray;
// cached sequences
NSMutableArray *cachedFiles;
}
+ (BOOL)mcpToFile:(NSString *)aPath suffixArray:(BCSuffixArray *)oneArray
withSuffixArray:(BCSuffixArray *)otherArray lowerBound:(int)lowerBound;
- (BOOL)intersectToFile:(NSString *)aPath withMCP:(BCMCP *)anMCP;
- (BOOL)unionToFile:(NSString *)aPath withMCP:(BCMCP *)anMCP;
- (BOOL)trimToFile:(NSString *)aPath;
- initWithContentsOfFile:(NSString *)aPath inMemory:(BOOL)aFlag;
- (BOOL)isInMemory;
- (BCSequenceArray *)sequenceArray;
- (BCSequenceArray *)reverseComplementArray;
- (NSDictionary *)metaDictionary;
- (NSArray *)sequenceToMeta;
- (NSArray *)cachedFiles;
- (BOOL)writeToFile:(NSString *)aPath;
- (FILE *)getFILE;
- (void)summaryFormatWithMinimumLength:(int)minLength;
- (void)fastaFormatWithMinimumLength:(int)minLength;
- (void)tableFormatWithMinimumLength:(int)minLength;
@end
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