standardizeModelFieldOrder

 standardizeModelFieldOrder
   Orders fields of RAVEN model structure as specified at
   https://github.com/SysBioChalmers/RAVEN/wiki/RAVEN-Model-Structure

   Input: model           model structure, either RAVEN or COBRA format

   Output: orderedModel   model structure with ordered fields

   The model fields themselves are not changed, only the order is
   modified. For changing model fields between RAVEN and COBRA format, use
   ravenCobraWrapper().

   Usage: orderedModel=standardizeModelFieldOrder(model)

0001 function orderedModel=standardizeModelFieldOrder(model)
0002 % standardizeModelFieldOrder
0003 %   Orders fields of RAVEN model structure as specified at
0004 %   https://github.com/SysBioChalmers/RAVEN/wiki/RAVEN-Model-Structure
0005 %
0006 %   Input: model           model structure, either RAVEN or COBRA format
0007 %
0008 %   Output: orderedModel   model structure with ordered fields
0009 %
0010 %   The model fields themselves are not changed, only the order is
0011 %   modified. For changing model fields between RAVEN and COBRA format, use
0012 %   ravenCobraWrapper().
0013 %
0014 %   Usage: orderedModel=standardizeModelFieldOrder(model)
0015 
0016 ravenPath=findRAVENroot();
0017 
0018 if ~isfield(model,'rules') % Check if model is RAVEN
0019     fid = fopen(fullfile(ravenPath,'struct_conversion','orderRavenFields.csv'));
0020     fields = textscan(fid,'%s','Delimiter',',','HeaderLines',0);
0021     fields = fields{1};
0022     fclose(fid);
0023 else % If model is COBRA
0024     fid = fopen(fullfile(ravenPath,'struct_conversion','COBRA_structure_fields.csv')); % Taken from https://github.com/opencobra/cobratoolbox/blob/develop/src/base/io/definitions/COBRA_structure_fields.csv
0025     fields = textscan(fid,repmat('%s',1,15),'Delimiter','\t','HeaderLines',1);
0026     fields = fields{1};
0027     fclose(fid);
0028 end
0029 
0030 modelfields = fieldnames(model);
0031 order = fields(ismember(fields(:,1),modelfields));
0032 remainingOrder = sort(setdiff(modelfields,order));
0033 overallOrder = [columnVector(order);columnVector(remainingOrder)];
0034 orderedModel = orderfields(model,overallOrder);
0035 end
0036 
0037 function vecT = columnVector(vec)
0038 % Converts a vector to a column vector
0039 %
0040 % USAGE:
0041 %
0042 %   vecT = columnVector(vec)
0043 %
0044 % INPUT:
0045 %   vec:     a vector
0046 %
0047 % OUTPUT:
0048 %   vecT:    a column vector
0049 %
0050 % .. Authors:
0051 %     - Original file: Markus Herrgard
0052 %     - Minor changes: Laurent Heirendt January 2017
0053 %     - Copied from COBRA Toolbox May 2022
0054 
0055 [n, m] = size(vec);
0056 
0057 if (m ~= 1 && n < m) || n == 1
0058     vecT = vec';
0059 else
0060     vecT = vec;
0061 end
0062 end