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Brian's changes on July 7

Jul 8, 2009 at 6:53 AM

Hi all.

I updated the code tonight so be sure to do 'svn update' before you start coding. I fixed the problems that changing to using the argv entailed. Should be working like normal again.

Also, for the argv stuff, we will eventually be passing in multiple searches to be run in parallel so we may have to read from a file for a list of the strings we want to match. If somebody wants to add the following small piece that would be good:

-- Permutations --

We need to search all four permutations of a search string like I showed in the powerpoint file. For example, if somebody wants to search for the first string below,  we also need to search the other permutations (#2...#4):

CCCAATTGGG <-- #1: Original search
GGGTTAACCC <-- #2: Reverse of #1
GGGTTAACCC <-- #3: Derived secondary DNA strand from #1 (A<->T and C<->G)
CCCAATTGGG <-- #4: Reverse of #3

So if someone could write a little function to create the other three permutations and also search for them, that would be great.

In the code right before the line below, we could generate the other three strings and then search the tree for them also.

  searchTree(head, level, searchstring);

Thanks, Brian