Home > RAVEN > printModel.m

printModel

PURPOSE ^

printModel

SYNOPSIS ^

function printModel(model,rxnList,outputString,outputFile,metaboliteList)

DESCRIPTION ^

 printModel
   Prints reactions to the screen or to a file

   model           a model structure
   rxnList         either a cell array of reaction IDs, a logical vector 
                   with the same number of elements as reactions in the model,
                   or a vector of indexes to remove (opt, default
                   model.rxns)
   outputString    a string that specifies the output of each reaction (opt,
                   default '%rxnID (%rxnName)\n\t%eqn [%lower %upper]\n')
   outputFile      a file to save the print-out to (opt, default is output to
                   the command window)
   metaboliteList  cell array of metabolite names. Only reactions
                   involving any of these metabolites will be 
                   printed (opt)

   The following codes are available for user-defined output strings:

   %rxnID      reaction ID
   %rxnName    reaction name
   %lower      lower bound
   %upper      upper bound
   %obj        objective coefficient
   %eqn        equation
   %element    equation using the metabolite formulas rather than
               metabolite names
   %unbalanced "(*)" if the reaction is unbalanced and "(-)" if it could not
               be parsed
   %lumped     equation where the elemental compositions for the left/right
               hand sides are lumped

   NOTE: This is just a wrapper function around printFluxes. It is
           intended to be used when there is no flux distribution.

   Usage: printModel(model,rxnList,outputString,outputFile,metaboliteList)

   Rasmus Agren, 2013-02-20

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function printModel(model,rxnList,outputString,outputFile,metaboliteList)
0002 % printModel
0003 %   Prints reactions to the screen or to a file
0004 %
0005 %   model           a model structure
0006 %   rxnList         either a cell array of reaction IDs, a logical vector
0007 %                   with the same number of elements as reactions in the model,
0008 %                   or a vector of indexes to remove (opt, default
0009 %                   model.rxns)
0010 %   outputString    a string that specifies the output of each reaction (opt,
0011 %                   default '%rxnID (%rxnName)\n\t%eqn [%lower %upper]\n')
0012 %   outputFile      a file to save the print-out to (opt, default is output to
0013 %                   the command window)
0014 %   metaboliteList  cell array of metabolite names. Only reactions
0015 %                   involving any of these metabolites will be
0016 %                   printed (opt)
0017 %
0018 %   The following codes are available for user-defined output strings:
0019 %
0020 %   %rxnID      reaction ID
0021 %   %rxnName    reaction name
0022 %   %lower      lower bound
0023 %   %upper      upper bound
0024 %   %obj        objective coefficient
0025 %   %eqn        equation
0026 %   %element    equation using the metabolite formulas rather than
0027 %               metabolite names
0028 %   %unbalanced "(*)" if the reaction is unbalanced and "(-)" if it could not
0029 %               be parsed
0030 %   %lumped     equation where the elemental compositions for the left/right
0031 %               hand sides are lumped
0032 %
0033 %   NOTE: This is just a wrapper function around printFluxes. It is
0034 %           intended to be used when there is no flux distribution.
0035 %
0036 %   Usage: printModel(model,rxnList,outputString,outputFile,metaboliteList)
0037 %
0038 %   Rasmus Agren, 2013-02-20
0039 %
0040 
0041 if nargin<2
0042     rxnList=model.rxns;
0043 end
0044 if isempty(rxnList)
0045     rxnList=model.rxns;
0046 end
0047 if nargin<3
0048     outputString='%rxnID (%rxnName)\n\t%eqn [%lower %upper]\n';
0049 end
0050 if isempty(outputString)
0051     outputString='%rxnID (%rxnName)\n\t%eqn [%lower %upper]\n';
0052 end
0053 if nargin<4
0054     outputFile=[];
0055 end
0056 if nargin<5
0057     metaboliteList=[];
0058 end
0059 
0060 I=getIndexes(model,rxnList,'rxns',true)*1.00; %To convert it to "fluxes"
0061 
0062 if ~isempty(metaboliteList)
0063     printFluxes(model, I, false, 0.1, outputFile,outputString,metaboliteList);
0064 else
0065     printFluxes(model, I, false, 0.1, outputFile,outputString);
0066 end

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