[Biococoa-dev] biococoa svn and everything

[Koen van der Drift]

Hi Scott,

>> I noticed you did a lot of updates recently with these class -  
>> this is great. Form your comments in the code I have a hard time  
>> understanding what exactly a suffix array is (I'm an analytical  
>> chemist that mainly works with proteins, so pardon my  
>> ignorance ;-)  Maybe you could add some more info in the source  
>> code to help better understand these classes?
>
> Definitely!  I noticed that there is a documentation setup similar  
> to how javadoc works, so I will eventually add those comments.

We actually use HeaderDoc: http://bioinformatics.org/biococoa/wiki/ 
pmwiki.php?n=Main.UsingHeaderDoc


> I tend to be an iterative programmer, trying out a design then  
> tweaking it until it converges on a best setup, so I think I'm  
> getting there and once I do I will document more thoroughly.  The  
> suffix array is a nifty data structure, it essentially holds all of  
> the strings in a sequence in sorted order, making it quick to  
> search for exact string matches.

Ok, ignorant question #2, isn't a sequence just one (1) string?  
Again, this is from someone who works with proteins ;-)

>
>> Another question I have is why you are using calls such as fopen,  
>> fread, etc instead of the methods that Obj-C and Cocoa provide for  
>> I/O. Mind you, I am just trying to understand the code, it's no  
>> criticism at all.
>
> I presume you mean NSFileHandle?  I was actually thinking of using  
> it, the current code which uses fopen, fread, etc is from the  
> original code for my standalone programs.  The main reason why I  
> didn't switch over is that NSFileHandle can only return data with  
> NSData, and the type of programs which use suffix arrays and etc do  
> alot of file reading, which would mean lots and lots of NSData  
> objects being created and released.  If only NSFileHandle could put  
> the data directly into a buffer provided by the user, or an  
> existing NSMutableData, that would be perfect.

A quick search in cocoabuilder.com gave the following snippet:

   NSMutableData *data = [NSMutableData data];
   NSData *someData;
   NSFileHandle *readHandle = [[aTask standardOutput]   
fileHandleForReading];

   while ((someData = [readHandle availableData]) && [someData  
length]) {
     [data appendData:someData];  // Or, if possible, process the  
data here
   }


would that help?

cheers,

- Koen.