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//
// BCCachedSequenceFile.m
// 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 "BCCachedSequenceFile.h"
#import "BCCachedFastaFile.h"
@implementation BCCachedSequenceFile
+ readCachedFileUsingPath:(NSString *)filePath
{
id result = nil;
NSFileHandle *seqFile = [NSFileHandle fileHandleForReadingAtPath: filePath];
if (!seqFile) {
NSLog(@"Could not open file: %@\n", filePath);
return nil;
}
// determine file type by reading some data
NSData *someData = [seqFile readDataOfLength: 10000];
NSString *entryString = [[NSString alloc] initWithData: someData encoding: NSASCIIStringEncoding]; // or NSUTF8StringEncoding ?
[seqFile closeFile];
// TODO: currently only handle FASTA
if ([entryString hasPrefix:@">"]) {
result = [[BCCachedFastaFile alloc] initWithContentsOfFile: filePath];
} else {
NSLog(@"Unsupported cached sequence file type.\n");
return nil;
}
return result;
}
- initWithContentsOfFile:(NSString *)filePath
{
[super init];
sequenceFile = filePath;
fileHandle = NULL;
sequenceInfo = [NSMutableDictionary new];
sequenceList = [NSMutableArray new];
currentSequenceNumber = -1;
currentSequence = nil;
return self;
}
- (void)dealloc
{
if (fileHandle) fclose(fileHandle);
if (sequenceInfo) [sequenceInfo release];
if (sequenceList) [sequenceList release];
[super dealloc];
}
- (unsigned)numberOfSequences { return [sequenceList count]; }
- (NSDictionary *)infoForSequence:(NSString *)seqID { return [sequenceInfo objectForKey: seqID]; }
- (NSDictionary *)infoForSequenceNumber:(int)seqNum { return [sequenceList objectAtIndex: seqNum]; }
- (char)symbolAtPosition:(unsigned long long)aPos forSequence:(NSString *)seqID
{
char c = 0;
[self symbols: &c atPosition: aPos ofLength: 1 forSequence: seqID];
return c;
}
- (char)symbolAtPosition:(unsigned long long)aPos forSequenceNumber:(int)seqNum
{
char c = 0;
[self symbols: &c atPosition: aPos ofLength: 1 forSequenceNumber: seqNum];
return c;
}
- (int)symbols:(char *)aBuffer atPosition:(unsigned long long)aPos ofLength:(unsigned)aLen forSequenceNumber:(int)seqNum
{
return 0;
}
- (int)symbols:(char *)aBuffer atPosition:(unsigned long long)aPos ofLength:(unsigned)aLen forSequence:(NSString *)seqID
{
return 0;
}
- (void)closeFileHandle
{
if (fileHandle) fclose(fileHandle);
fileHandle = NULL;
currentSequenceNumber = -1;
currentSequence = nil;
}
@end
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