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//
// BCSequenceWriter.m
// BioCocoa
//
// Created by Koen van der Drift on 8/12/06.
// 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 "BCSequenceWriter.h"
#import "BCSequenceArray.h"
#import "BCSequence.h"
@implementation BCSequenceWriter
- (NSString *)writeFastaFile:(BCSequenceArray *)sequenceArray
{
int i;
BCSequence *aSequence;
NSString *sequenceString;
NSString *sequenceIdentifier;
NSMutableString *result = [NSMutableString string];
[result setString: @""];
for (i = 0; i < [sequenceArray count]; i++)
{
aSequence = [sequenceArray sequenceAtIndex: i];
sequenceString = [aSequence sequenceString];
if ([aSequence annotations] != nil)
{
sequenceIdentifier = (NSString *) [aSequence annotationForKey: @">"];
[result appendString: @"> "];
[result appendString: sequenceIdentifier];
[result appendString: @"\r"];
}
[result appendString: sequenceString];
}
return result;
}
@end
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