[Biococoa-dev] Even more on sequence formats

[Koen van der Drift]

On Apr 11, 2006, at 6:46 AM, Alexander Griekspoor wrote:

> - (NSDictionary *)readFile:(NSString *)textFile
> {
>     NSMutableDictionary *theContents;
>     NSString *lineBreak;
> 	
> 	// BINARY
> 	// Strider?
>     if([NSHFSTypeOfFile(textFile) isEqualToString: @"'xDNA'"]){
>
> 		theContents =  (NSMutableDictionary*) [self  
> readStriderFile:textFile];
>
> 	// GCK?
> 	}else if([NSHFSTypeOfFile(textFile) isEqualToString: @"'GCKc'"] ||  
> [NSHFSTypeOfFile(textFile) isEqualToString: @"'GCKs'"]){
> 		
> 		theContents =  (NSMutableDictionary*) [self readGCKFile:textFile];
> 		
> 	// TEXT
> 	}else {
> 		NSMutableString *sequenceFile;
> 		
> 		// EXDNA
> 		if([[textFile pathExtension]isEqualToString:@"exdna"])
> 			sequenceFile = [NSMutableString stringWithContentsOfFile:  
> [textFile stringByAppendingPathComponent: @"sequence.txt"]];
> 		else
> 			sequenceFile = [NSMutableString stringWithContentsOfFile:textFile];
> 		
>


With these new great additions, I was wondering if we should slightly  
rethink the methods in BCSequenceReader. Right now we have

- (BCSequenceArray *)readFileUsingPath:(NSString *)filePath
{
	return nil;	// TODO
}

- (BCSequenceArray *)readFileUsingData:(NSData *)dataFile
{
	NSString	*entryString = [[NSString alloc] initWithData: dataFile  
encoding:NSASCIIStringEncoding];

	return [self readFileUsingText: [entryString autorelease]];
}

and

- (BCSequenceArray *)readFileUsingText:(NSString *)entryString
{
...
}

The last one contains all the actual code. So maybe we should factor  
out the code with NSHFSTypeOfFile and the exdna part to  
readFileUsingPath, and let that method call in turn  
readFileUsingText, which actually deals with a contentstring. This  
will allow users to either pass a path, or the contents of a file or  
a data object.

What do you guys think?

cheeers,

- Koen.