% txtl_protein_sfGFP.m - protein information for sfGFP
% VS, 4 March 2013


% Written by Richard Murray, 9 Sep 2012
%
% Copyright (c) 2012 by California Institute of Technology
% All rights reserved.
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% modification, are permitted provided that the following conditions are
% met:
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%   1. Redistributions of source code must retain the above copyright
%      notice, this list of conditions and the following disclaimer.
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%      documentation and/or other materials provided with the distribution.
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%   3. The name of the author may not be used to endorse or promote products 
%      derived from this software without specific prior written permission.
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% THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
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function varargout = txtl_protein_sfGFP(mode, tube, protein, varargin)

paramObj = txtl_component_config('sfGFP');

%%%%%%%%%%%%%%%%%%% DRIVER MODE: Setup Species %%%%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmp(mode.add_dna_driver, 'Setup Species')
    
    geneData = varargin{1};
    
    defaultBasePairs = {'deGFP','lva','terminator';...
        paramObj.Gene_Length,paramObj.LVA_tag_Length,paramObj.Terminator_Length};
    geneData = txtl_setup_default_basepair_length(tube,geneData,...
        defaultBasePairs);
    
    varargout{1} = geneData;
    
    coreSpecies = {[protein.Name '*']};
    % empty cellarray for amount => zero amount
    txtl_addspecies(tube, coreSpecies, cell(1,size(coreSpecies,2)), 'Internal');
 
%%%%%%%%%%%%%%%%%%% DRIVER MODE: Setup Reactions %%%%%%%%%%%%%%%%%%%%%%%%%%    
elseif strcmp(mode.add_dna_driver, 'Setup Reactions')

    % Set up the maturation reaction
    txtl_addreaction(tube,['[' protein.Name '] -> [' protein.Name '*]'],...
     'MassAction',{'TXTL_PROT_deGFP_MATURATION',paramObj.Protein_Maturation});
    
%%%%%%%%%%%%%%%%%%% DRIVER MODE: error handling %%%%%%%%%%%%%%%%%%%%%%%%%%% 
else
    error('txtltoolbox:txtl_protein_sfGFP:undefinedmode', ...
      'The possible modes are ''Setup Species'' and ''Setup Reactions''.');
end



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