% File created by GUI      

% Directory to store the output from a simulation run.
% An empty matrix here will use a directory called 'output'
% under the parameters directory.
% Otherwise input the entire path to the (already present) output directory.

%plot_info.output_directory = [];

% This next setting chooses a default name for the output file.
% A dialogue after starting the program will allow the user to chooose a
% different specific file name for the output data within the above folder.
% '.mat' will be appended to the specified file name.

%output_filename = 'default_out';


% stores data for these compounds in data_cmpds(:,i)
% time data is always saved in data_time(:)
monitor_cmpds = {
          'ATP';
          'GTP';
          'Prod_A';
          'AA_C';
          'AA_E';
          'Sub_A';
          'Sub_B';
          'CTP';
          'T7_RNAp';
          'T7_P';
          'geneA_mRNA';
          'Rib_s';
          'Rib_l';
          'Rib_s_geneA_mRNA';
          'Pro_A';
          'Prot';
          'RNase';
          'UTP';
          'Pi';
          'PPi';
          'T7_RNAp_T7_P';
          'AA_A';
          'AA_Q';
          };

% which compounds to plot.  each plot_cmpds{number} is in the same figure window.
% can use plot_cmpds = {'all'} if you want each monitor_cmpds to be in own
% figure window
% each compound to be plotted must also be monitored
plot_cmpds{1} = {'T7_RNAp' };
plot_cmpds{2} = {'T7_P' };
plot_cmpds{3} = {'geneA_mRNA' };
plot_cmpds{4} = {'Rib_s' };
plot_cmpds{5} = {'Rib_l' };
plot_cmpds{6} = {'Rib_s_geneA_mRNA' };
plot_cmpds{7} = {'Pro_A' };
plot_cmpds{8} = {'Prot' };
plot_cmpds{9} = {'RNase' };
plot_cmpds{10} = {'Prod_A' };
plot_cmpds{11} = {'ATP' };
plot_cmpds{12} = {'GTP' };
plot_cmpds{13} = {'CTP' };
plot_cmpds{14} = {'UTP' };
plot_cmpds{15} = {'Pi' };
plot_cmpds{16} = {'PPi' };
plot_cmpds{17} = {'AA_C' };
plot_cmpds{18} = {'AA_E' };
plot_cmpds{19} = {'T7_RNAp_T7_P' };
plot_cmpds{20} = {'AA_A' };
plot_cmpds{21} = {'AA_Q' };
plot_cmpds{22} = {'Sub_A' };
plot_cmpds{23} = {'Sub_B' };

eventlog_flag = 0; 
eventlog_maxelements = 100000;

snapshot_interval = 5; 
% a zero means it won't even save snapshots, not implemented yet

plot_interval = 4000;
% if positive, the snapshots will be shown on the screen at plot_interval intervals
%     (or as close to plot_interval as monitor_interval (which can vary) allows)
% if zero, plots will be shown at every monitor_interval
% if negative 1, no plots will be displayed on the screen during the run(s)






output_filename = 'Foy'; 
