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// BCCachedSequenceFile.h
// BioCocoa
//
// Created by Scott Christley on 9/10/07.
// 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>
//
// Cached sequences
//
// For handling very large sequence files,
// we do not want to read in all of sequence
// data into memory; instead we parse the file
// and pull out meta-data. Working with the
// sequence data is handled by a specific cached
// sequence class which reads data from the file
// when needed.
//
@interface BCCachedSequenceFile : NSObject {
NSString *sequenceFile;
NSMutableDictionary *sequenceInfo;
NSMutableArray *sequenceList;
FILE *fileHandle;
int currentSequenceNumber;
NSDictionary *currentSequence;
}
+ readCachedFileUsingPath:(NSString *)filePath;
// overridden by file format specific subclasses
- initWithContentsOfFile:(NSString *)filePath;
- (unsigned)numberOfSequences;
- (NSDictionary *)infoForSequence:(NSString *)seqID;
- (NSDictionary *)infoForSequenceNumber:(int)seqNum;
- (char)symbolAtPosition:(unsigned long long)aPos forSequence:(NSString *)seqID;
- (char)symbolAtPosition:(unsigned long long)aPos forSequenceNumber:(int)seqNum;
- (int)symbols:(char *)aBuffer atPosition:(unsigned long long)aPos ofLength:(unsigned)aLen forSequenceNumber:(int)seqNum;
- (int)symbols:(char *)aBuffer atPosition:(unsigned long long)aPos ofLength:(unsigned)aLen forSequence:(NSString *)seqID;
- (void)closeFileHandle;
@end
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