TCAPIEXPORT
tc_matrix tc_steadyStateScan(const char * param, double start, double end, int numSteps)
{
if (_tc_steadyStateScan)
return _tc_steadyStateScan(param, start, end, numSteps);
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_getSteadyState()
{
if (_tc_getSteadyState)
return _tc_getSteadyState();
return tc_createMatrix(0,0);
}
*/ TCAPIEXPORT
tc_matrix tc_getNumbers(tc_strings labels)
{
if (_tc_getNumbers)
return _tc_getNumbers(labels);
return tc_createMatrix(0,0);
}
*/ TCAPIEXPORT
tc_matrix tc_getStoichiometry(tc_items A)
{
if (_tc_getStoichiometry)
return _tc_getStoichiometry(A);
return tc_createMatrix(0,0);
}
*/ TCAPIEXPORT
tc_matrix tc_getPos(tc_items items)
{
if (_tc_getPos)
return _tc_getPos(items);
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_getUnscaledConcentrationCC()
{
if (_tc_getUnscaledConcentrationCC)
return _tc_getUnscaledConcentrationCC();
return tc_createMatrix(0,0);
}
/*!
\brief get a value from its full name
\ingroup Data
*/
TCAPIEXPORT
tc_matrix tc_getNumericalValueUsingRegexp(const char* name)
{
if (_tc_getNumericalValueUsingRegexp)
return _tc_getNumericalValueUsingRegexp(name);
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_reducedStoichiometry()
{
if (_tc_reducedStoichiometry)
return _tc_reducedStoichiometry();
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_getUnscaledElasticities()
{
if (_tc_getUnscaledElasticities)
return _tc_getUnscaledElasticities();
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_getScaledFluxCC()
{
if (_tc_getScaledFluxCC)
return _tc_getScaledFluxCC();
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_getJacobian()
{
if (_tc_getJacobian)
return _tc_getJacobian();
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_simulateStochastic(double startTime, double endTime, int numSteps)
{
if (_tc_simulateStochastic)
return _tc_simulateStochastic(startTime, endTime, numSteps);
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_simulateTauLeap(double startTime, double endTime, int numSteps)
{
if (_tc_simulateTauLeap)
return _tc_simulateTauLeap(startTime, endTime, numSteps);
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_optimize(const char * s)
{
if (_tc_optimize)
return _tc_optimize(s);
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_KMatrix()
{
if (_tc_KMatrix)
return _tc_KMatrix();
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_elementaryFluxModes()
{
if (_tc_elementaryFluxModes)
return _tc_elementaryFluxModes();
return tc_createMatrix(0,0);
}
*/ TCAPIEXPORT
tc_matrix tc_getNumericalData(long item,const char* data)
{
if (_tc_getNumericalData)
return _tc_getNumericalData(item,data);
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_getEigenvalues()
{
if (_tc_getEigenvalues)
return _tc_getEigenvalues();
return tc_createMatrix(0,0);
}
TCAPIEXPORT
tc_matrix tc_steadyStateScan2D(const char * param1, double start1, double end1, int numSteps1,
const char * param2, double start2, double end2, int numSteps2)
{
if (_tc_steadyStateScan2D)
return _tc_steadyStateScan2D(param1, start1, end1, numSteps1, param1, start2, end2, numSteps2);
return tc_createMatrix(0,0);
}
// eigenvalues
void eigen(copasi_model model, const char* param)
{
int i, j,k;
double p;
FILE * outfile;
tc_matrix ss;
tc_matrix output;
//steady states
for (i=0; i < 100; ++i)
{
p = (double)(i + 1)/10.0;
k = cSetValue( model, param, p );
if (k)
printf("calculating steady state for %s = %lf\n",param, p);
ss = cGetEigenvalues(model);
//ss = cGetSteadyState(model);
if (i == 0)
{
output = tc_createMatrix(100, ss.rows+1);
tc_setColumnName(output, 0, param);
for (j=0; j < output.cols; ++j)
tc_setColumnName(output, j+1, tc_getRowName(ss, j));
}
tc_setMatrixValue(output, i, 0, p);
for (j=0; j < output.cols; ++j)
tc_setMatrixValue(output, i, j+1, tc_getMatrixValue(ss, j, 0));
tc_deleteMatrix(ss);
}
//output
tc_printMatrixToFile("output.tab", output);
printf("\noutput.tab contains the final output\n\n");
tc_deleteMatrix(output);
}
void run(tc_matrix input)
{
double start = 0.0, end = 50.0;
double dt = 0.1, time = 100.0;
int doStochastic = 0;
int selection = 0, index = 0, sz = 0, rateplot = 0, slider = 1;
tc_items A, B;
const char * param;
FILE * out;
tc_matrix params, initVals, allParams, N;
char * runfuncInput = "tc_matrix input";
char * runfunc = "";
int i;
if (input.cols > 0)
{
if (input.rows > 0)
selectedItemsOnly = selection = (int)tc_getMatrixValue(input,0,0);
if (input.rows > 1)
doStochastic = (int)(tc_getMatrixValue(input,1,0) > 0);
if (input.rows > 2)
index = tc_getMatrixValue(input,2,0);
if (input.rows > 3)
start = tc_getMatrixValue(input,3,0);
if (input.rows > 4)
end = tc_getMatrixValue(input,4,0);
if (input.rows > 5)
dt = tc_getMatrixValue(input,5,0);
if (input.rows > 6)
time = tc_getMatrixValue(input,6,0);
if (input.rows > 7)
rateplot = tc_getMatrixValue(input,7,0);
if (input.rows > 8)
slider = tc_getMatrixValue(input,8,0);
}
if (slider == 0)
slider = 1;
else
slider = 0;
if (selection > 0)
{
A = tc_selectedItems();
if (tc_getItem(A,0) == 0)
{
tc_deleteItemsArray(A);
A = tc_allItems();
}
}
else
{
A = tc_allItems();
}
sz = (int)((end - start) / dt);
if (tc_getItem(A,0) != 0)
{
tc_writeModel( "timet", A );
}
else
{
tc_deleteItemsArray(A);
return;
}
if (index < 0)
{
tc_print("steady state: no variable selected\0");
tc_deleteItemsArray(A);
return;
}
param = tc_getString(allNames,index); //the parameter to vary
strcpy(selected_var,param);
if (slider)
{
params = tc_getParameters(A);
N = tc_getStoichiometry(A);
B = tc_findItems(N.rownames);
tc_deleteMatrix(N);
initVals = tc_getInitialValues(B);
allParams = tc_createMatrix(initVals.rows+params.rows,2);
for (i=0; i < params.rows; ++i)
{
tc_setRowName(allParams,i, tc_getRowName(params,i));
tc_setMatrixValue(allParams,i,0,tc_getMatrixValue(params,i,0)/10.0);
tc_setMatrixValue(allParams,i,1, 2*tc_getMatrixValue(params,i,0) - tc_getMatrixValue(allParams,i,0));
}
for (i=0; i < initVals.rows; ++i)
{
tc_setRowName(allParams,i+params.rows, tc_getRowName(initVals,i));
tc_setMatrixValue(allParams,i+params.rows,0,tc_getMatrixValue(initVals,i,0)/10.0);
tc_setMatrixValue(allParams,i+params.rows,1, 2*tc_getMatrixValue(initVals,i,0) - tc_getMatrixValue(allParams,i+params.rows,0));
}
tc_deleteMatrix(initVals);
tc_deleteMatrix(params);
tc_deleteItemsArray(B);
runfunc = runfuncInput;
}
tc_deleteItemsArray(A);
out = fopen("timet.c","a");
fprintf( out , "\
#include \"TC_api.h\"\n#include \"cvodesim.h\"\n#include \"ssa.h\"\n\
TCAPIEXPORT void run(%s) \n\
{\n initMTrand();\n tc_matrix dat;\n int i,j;\n", runfunc );
fprintf( out, "\
dat.rows = (int)((%lf-%lf)/%lf);\n\
double * y, * y0, *y1;\n\
TCmodel * model = (TCmodel*)malloc(sizeof(TCmodel));\n\
(*model) = TC_initial_model;\n\
if (%i) \n\
{\n\
dat.cols = 1+TCreactions;\n\
dat.colnames = tc_createStringsArray(TCreactions);\n\
for(i=0; i<TCreactions; ++i) dat.colnames.strings[1+i] = TCreactionnames[i];\n\
}\n\
else\n\
{\n\
