Work+100612

All of the blast comparisons between motif group 0 and motif group 1 (PMRE and HEE) have been performed. Now I need to add the results to a table.

code removed 100612 dot 1435

removed some code if(useful_tools.isMatchofRegEx(current_line, ".+?\\|(.+?)\\|(.+)?")) {

removed a method from MotifPeptideAnalysis

Alright I've refactored a lot of code, and now I ran it to make a table from the blast results for items 10-12. I then ran the match counting part of the program as well. This part seems to be taking quite some time (just with the table rows from 3 blast results (there were a total of about 1000 rows)). I'm beginning to think that this program as I'm pursuing it with the current computer hardware capabilities may not be practical. It may take too long to accomplish what I want to accomplish.

removed code "C:\kurt\storage\CIM Research Folder\DR\2012\10-6-12\code\potentially duplicated code in detmine match method.txt" This code that I thought was duplicated was actually slightly different, and I added it back.

I'll probably take a break from this coding project for a little while. As of right now I'm leaving off by testing the blast comparison class again since everything was moved around. I am also testing the add info to table method and the determine matches method.

I'm also just trying to generate the table with info from all 20,000 large fasta file blast result files since this will take some time to compute. While trying to do this, Java reported an out of memory error so it looks like I may have to change how the program executes this portion of the code.