[Biococoa-dev] biococoa svn and everything

[Koen van der Drift]

On Sep 12, 2007, at 4:35 PM, Scott Christley wrote:

> BCSuffixArray, implements a suffix array data structure, a memory  
> efficient structure that allows for string matching operations.
>
> BCMCP, this uses BCSuffixArray and BCCachedSequenceFile to perform  
> the ultraconserved analysis which is essentially looking for  
> longest common substrings across the whole genome for multiple  
> organisms.


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?

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.


cheers,

- Koen.