void loadAllNames()
{
int i,len;
tc_matrix params, N;
tc_items A = tc_createItemsArray(0);
if (selectedItemsOnly)
A = tc_selectedItems();
if (A.length < 1 || !tc_getItem(A,0))
A = tc_allItems();
tc_deleteStringsArray(allNames);
if (tc_getItem(A,0))
{
params = tc_getParameters(A);
N = tc_getStoichiometry(A);
len = N.rows;
allNames = tc_createStringsArray(len+params.rows);
for (i=0; i < params.rows; ++i)
tc_setString(allNames,i,tc_getRowName(params,i));
for (i=0; i < len; ++i)
tc_setString(allNames,i+params.rows,tc_getRowName(N,i));
params.rownames = tc_createStringsArray(0);
tc_deleteMatrix(params);
tc_deleteMatrix(N);
tc_deleteItemsArray(A);
}
}
*/ TCAPIEXPORT
tc_strings tc_getTextDataNames(long o)
{
if (_tc_getTextDataNames)
return _tc_getTextDataNames(o);
return tc_createStringsArray(0);
}
*/ TCAPIEXPORT
tc_strings tc_getUniqueNames(tc_items items)
{
if (_tc_getUniqueNames)
return _tc_getUniqueNames(items);
return tc_createStringsArray(0);
}
*/ TCAPIEXPORT
tc_strings tc_getRates(tc_items A)
{
if (_tc_getRates)
return _tc_getRates(A);
return tc_createStringsArray(0);
}
TCAPIEXPORT
tc_strings tc_listOfPossibleModels(long item)
{
if (_tc_listOfPossibleModels)
return _tc_listOfPossibleModels(item);
return tc_createStringsArray(0);
}
TCAPIEXPORT tc_matrix tc_createMatrix(int rows, int cols)
{
int i;
tc_matrix M;
M.rows = rows;
M.cols = cols;
M.colnames = tc_createStringsArray(cols);
M.rownames = tc_createStringsArray(rows);
if (rows > 0 && cols > 0)
{
M.values = (double*)malloc( rows * cols * sizeof(double) );
for (i=0; i < (rows*cols); ++i)
M.values[i] = 0.0;
}
else
M.values = 0;
return M;
}
TCAPIEXPORT tc_table tc_createTable(int rows, int cols)
{
int i;
tc_table M;
M.rows = rows;
M.cols = cols;
M.colnames = tc_createStringsArray(cols);
M.rownames = tc_createStringsArray(rows);
if (rows > 0 && cols > 0)
{
M.strings = (char**)malloc( rows * cols * sizeof(char*) );
for (i=0; i < (rows*cols); ++i)
M.strings[i] = 0;
}
else
M.strings = 0;
return M;
}
TCAPIEXPORT void tc_main()
{
allNames = tc_createStringsArray(0);
strcpy(selected_var,"\0");
//add function to menu. args : function, name, description, category, icon file, target part/connection family, in functions list?, in context menu?
tc_addFunction(&setup, "Values at time=T0", "uses repeated simulation to compute state of system at the given time", "Parameter scan", "steadystate.png", "", 1, 0, 0);
tc_callback(&callback);
tc_callWhenExiting(&unload);
}
void run()
{
tc_items selected = tc_selectedItems();
long p;
tc_items C;
int i, j, k, N = 0;
tc_items js, tfs, parts;
tc_strings names, jnames;
tc_matrix m;
p = tc_getItem(selected,0);
if (p == 0) return;
//if (! tc_isA(p,"Regulator")) return;
C = tc_getConnections(p);
//count the number of repressors/activators
for (i=0; i < C.length; ++i)
{
if (tc_isA(tc_getItem(C,i),"Binding"))
{
++N;
}
}
js = tc_createItemsArray(N);
//get kon,koff,and trans.reg. connections
j = 0;
for (i=0; i < C.length; ++i)
{
if (tc_isA(tc_getItem(C,i),"Binding"))
{
tc_setItem(js,j, tc_getItem(C,i));
++j;
}
}
//get the repressors/activators names
tfs = tc_createItemsArray(N+1);
tc_setItem(tfs,0,p);
k = 1;
for (i=0; i < C.length; ++i)
{
if (tc_isA(tc_getItem(C,i),"Binding"))
{
parts = tc_getConnectedNodes(tc_getItem(C,i));
for (j=0; i < parts.length; ++j)
{
if (tc_getItem(parts,j) != p)
{
tc_setItem( tfs, k, tc_getItem(parts,j)); //save tfs
++k;
}
}
tc_deleteItemsArray(parts);
}
}
names = tc_getUniqueNames(tfs); //get names of proteins
jnames = tc_getUniqueNames(js); //get names of reactions
//main function that generates the full stoichiometry and rates
m = fullBindingKinetics(N,jnames.strings,names.strings);
//output that matrix to screen and item
tc_printTable(m);
tc_setRates(js,m.colnames);
if (m.colnames.strings) free(m.colnames.strings);
m.colnames = tc_createStringsArray(0);
tc_setStoichiometry(js,m);
tc_deleteItemsArray(js);
tc_deleteItemsArray(tfs);
tc_deleteMatrix(m);
tc_deleteStringsArray(names);
tc_deleteStringsArray(jnames);
tc_deleteItemsArray(selected);
return;
}
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\
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\
dat.cols = 1+TCvars;\n\
dat.colnames = tc_createStringsArray(1+TCvars);\n\
for(i=0; i<TCvars; ++i) dat.colnames.strings[1+i] = TCvarnames[i];\n\
}\n\
dat.values = malloc(dat.cols * dat.rows * sizeof(double));\n\
dat.rownames = tc_createStringsArray(0);\n\
dat.colnames.strings[0] = \"%s\";\n",end,start,dt,rateplot,param);
fprintf( out, "\n\
for (i=0; i < dat.rows; ++i)\n\
{\n\
(*model) = TC_initial_model;\n");
if (slider)
{
for (i=0; i < allParams.rows; ++i)
fprintf(out, " model->%s = tc_getMatrixValue(input,%i,0);\n",tc_getRowName(allParams,i),i);
