[Biococoa-dev] biococoa svn and everything
Koen van der Drift
kvddrift at earthlink.net
Wed Sep 26 20:53:44 EDT 2007
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
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.
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