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// BCSequenceReader.h
// BioCocoa
//
// Created by Koen van der Drift on 10/16/04.
// 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 <Foundation/Foundation.h>
@class BCSequence;
@class BCSequenceArray;
typedef struct strider_header
{
char versionNb;
char type;
char topology;
char reserved1;
int reserved2;
int reserved3;
int reserved4;
char reserved5;
char filler1;
short filler2;
int filler3;
int reserved6;
int nLength;
int nMinus;
int reserved7;
int reserved8;
int reserved9;
int reserved10;
int reserved11;
char reserved12[32];
short reserved13;
short filler4;
char reserved14;
char reserved15;
char reserved16;
char filler5;
int com_length;
int reserved17;
int filler6;
int filler7;
}STRIDER_HEADER;
typedef struct gck_header
{
int unknown1;
int unknown2;
int unknown3;
int unknown4;
int unknown5;
int unknown6;
int unknown7;
int nLength;
}GCK_HEADER;
typedef struct macvector_header
{
char seqType; // 0: nucleic, else: protein
char empty1;
char empty2;
char topology; // 0: linear, else: circular
char empty3;
char empty4;
char ntType; // 1: RNA, else: DNA
char empty5;
char month; // 1-12
char day; // 1-31
char year; // 0-255 + 1900
int empty6;
int nSegments; // always 1. Total number of sequences, BTW
int totalLength; // equal to sequence length (nSegments = 1)
int segNo; // Number of segment (always 1?)
int seqLength; // this segment length
int seqBytes; // this segment length again (???)
}MACVECTOR_HEADER;
//
// File formats
//
typedef enum _BCFileFormat {
BCFastaFileFormat,
BCSwissProtFileFormat,
BCPDBFileFormat,
BCNCBIFileFormat,
BCClustalFileFormat,
BCStriderFileFormat,
BCGCKFileFormat,
BCMacVectorFileFormat,
BCGDEFFileFormat,
BCPirFileFormat,
BCMSFFileFormat,
BCPhylipFileFormat,
BCNonaFileFormat,
BCHenningFileFormat,
BCFASTQFileFormat
} BCFileFormat;
@interface BCSequenceReader : NSObject {
}
- (BCSequenceArray *)readFileUsingText:(NSString *)textFile;
- (BCSequenceArray *)readFileUsingData:(NSData *)dataFile;
- (BCSequenceArray *)readFileUsingPath:(NSString *)filePath;
- (BCSequenceArray *)readFileUsingPath:(NSString *)filePath format:(BCFileFormat)aFormat;
- (BCSequenceArray *)readFastaFile:(NSString *)textFile;
- (BCSequenceArray *)readSwissProtFile:(NSString *)textFile;
- (BCSequenceArray *)readPDBFile:(NSString *)textFile;
- (BCSequenceArray *)readNCBIFile:(NSString *)textFile;
- (BCSequenceArray *)readClustalFile:(NSString *)textFile;
- (BCSequenceArray *)readStriderFile:(NSString *)textFile;
- (BCSequenceArray *)readGCKFile:(NSString *)textFile;
- (BCSequenceArray *)readMacVectorFile:(NSString *)textFile;
- (BCSequenceArray *)readGDEFile:(NSString *)entryString;
- (BCSequenceArray *)readPirFile:(NSString *)entryString;
- (BCSequenceArray *)readMSFFile:(NSString *)entryString;
- (BCSequenceArray *)readPhylipFile:(NSString *)entryString;
- (BCSequenceArray *)readRawFile:(NSString *)entryString;
- (BCSequenceArray *)readFASTQFile:(NSString *)textFile;
//- (BCSequenceArray *)readNonaFile:(NSString *)entryString;
//- (BCSequenceArray *)readHennigFile:(NSString *)entryString;
@end
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