0001 function initCobraToolbox
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0021 pth=which('initCobraToolbox.m');
0022 CBTDIR = pth(1:end-(length('initCobraToolbox.m')+1));
0023 path(path,[CBTDIR, filesep, 'external']);
0024 addpath_recurse(CBTDIR,{'.svn','obsolete','m2html','docs','src','stow'});
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0033 CobraLPSolver = 'tomlab_cplex';
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0037 if isunix
0038 addpath('/usr/local/lib/');
0039 end
0040 CobraLPSolvers = { 'gurobi5', 'gurobi', 'tomlab_cplex', 'glpk', 'mosek', 'cplx' };
0041 for CobraLPSolver = CobraLPSolvers
0042 LPsolverOK = changeCobraSolver(char(CobraLPSolver));
0043 if LPsolverOK
0044 fprintf('LP solver set to %s successful\n',char(CobraLPSolver));
0045 break;
0046 end
0047 end
0048 if ~LPsolverOK
0049 fprintf('LP solver set failed\n');
0050 end
0051
0052
0053
0054 for CobraMILPSolver = { 'gurobi5', 'gurobi', 'tomlab_cplex', 'glpk' }
0055 MILPsolverOK = changeCobraSolver(char(CobraMILPSolver),'MILP');
0056 if MILPsolverOK
0057 fprintf('MILP solver set to %s successful\n',char(CobraMILPSolver));
0058 break;
0059 end
0060 end
0061 if ~MILPsolverOK
0062 fprintf('MILP solver set failed\n');
0063 end
0064
0065
0066 for CobraQPSolver = {'gurobi5', 'gurobi', 'tomlab_cplex', 'qpng' }
0067 QPsolverOK = changeCobraSolver(char(CobraQPSolver),'QP');
0068 if QPsolverOK
0069 fprintf('QP solver set to %s successful\n',char(CobraQPSolver));
0070 break;
0071 end
0072 end
0073 if ~QPsolverOK
0074 fprintf('QP solver set failed\n');
0075 end
0076
0077 for CobraMIQPSolver = {'gurobi5', 'gurobi' 'tomlab_cplex'}
0078 MIQPsolverOK = changeCobraSolver(char(CobraMIQPSolver),'MIQP');
0079 if MIQPsolverOK
0080 fprintf('MIQP solver set to %s successful\n',char(CobraMIQPSolver));
0081 break;
0082 end
0083 end
0084 if ~MIQPsolverOK
0085 fprintf('MIQP solver set failed\n');
0086 end
0087
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0090
0091 CbMapOutput = 'svg';
0092 CbMapOutputOK = changeCbMapOutput(CbMapOutput);
0093 if CbMapOutputOK
0094 fprintf('CB map output set to %s successful\n',CbMapOutput);
0095 else
0096 fprintf('Cb map output set failed\n');
0097 end
0098
0099
0100
0101 changeOK = changeCobraSolverParams('LP','objTol',1e-6);
0102
0103
0104 if (~exist('TranslateSBML'))
0105 warning('SBML Toolbox not in Matlab path: COBRA Toolbox will be unable to read SBML files');
0106 end