%ribostralNoGUI.m   %By Ali Mokdad - BGSU - Copyright 2006

% This is the script version of Ribostral. 

% Follow the following instructions to analyze your data:
% To change the program preferences run the GUI "Preferences".

% There are 5 variables to change so that the program analyzes YOUR files:

% 1-ChosenDomains   :
%This is an array variable, such as [1 2 3] or [1 2] or just 1. 
%It tells the program what domains need to be analyzed in case your Fasta
%file has more than one domain (see the manual for more information about
%this option, and also on how to write KnownFastaFilenames.xls). If you do
%not have your FASTA file encoded in KnownFastaFilenames.xls just use 1. 

% 2-FastaPath       :
%This is the pathname of your fasta file. Note: It must end with the file
%separator character (\ or / depending on your system).

% 3-FastaFilename   :
%This is the fasta filename with extension (without path).

% 4-PositionPath    :
%This is the pathname of your Positions Excel file that defines basepairs
%or other base combinations. Note: It must end with the file separator
%character (\ or / depending on your system).

% 5-PositionList    :
%This is the Positions Excel filename with extension (without path).



% clear
% clc
mPath
load Preferences

% % ChosenDomains = [1];
ChosenDomains = [1 2 3];

FastaPath='C:\AliRes_UCSF\_MatlabWork\MATLAB programs\Alignment_Analysis\FASTA_alignments\';
FastaFilename='23S_ABE_2004_UNIQUE.mat';    %'5S_ABE_2004.mat';
mGetFasta

PositionPath='C:\AliRes_UCSF\_MatlabWork\MATLAB programs\Alignment_Analysis\NT_lists\';
PositionList='rr0033_23S_BPlist_All.xls';   %'5S_Archaea_Hm_AllClasses_MANUAL_ALI.xls';
mGetPositions

Rounding = 10^(Rounding);
for Percentages=0:1
    mMutualCounter_IF
end
fprintf('%s\n','Run "Preferences" to change program defaults');
