*/ TCAPIEXPORT
tc_items tc_getConnections(long part)
{
if (_tc_getConnections)
return _tc_getConnections(part);
return tc_createItemsArray(0);
}
*/ TCAPIEXPORT
tc_items tc_getConnectionsWithRole(long part, const char* role)
{
if (_tc_getConnectionsWithRole)
return _tc_getConnectionsWithRole(part,role);
return tc_createItemsArray(0);
}
*/ TCAPIEXPORT
tc_items tc_getConnectedNodes(long connection)
{
if (_tc_getConnectedNodes)
return _tc_getConnectedNodes(connection);
return tc_createItemsArray(0);
}
*/ TCAPIEXPORT
tc_items tc_getConnectedNodesWithRole(long connection, const char* role)
{
if (_tc_getConnectedNodesWithRole)
return _tc_getConnectedNodesWithRole(connection,role);
return tc_createItemsArray(0);
}
*/ TCAPIEXPORT
tc_items tc_allItems()
{
if (_tc_allItems)
return _tc_allItems();
return tc_createItemsArray(0);
}
*/ TCAPIEXPORT
tc_items tc_findItemsUsingRegexp(const char* re)
{
if (_tc_findItemsUsingRegexp)
return _tc_findItemsUsingRegexp(re);
return tc_createItemsArray(0);
}
*/ TCAPIEXPORT
tc_items tc_getChildren(long o)
{
if (_tc_getChildren)
return _tc_getChildren(o);
return tc_createItemsArray(0);
}
*/ TCAPIEXPORT
tc_items tc_findItems(tc_strings names)
{
if (_tc_findItems)
return _tc_findItems(names);
return tc_createItemsArray(0);
}
*/ TCAPIEXPORT
tc_items tc_itemsOfFamilyFrom(const char* family, tc_items itemsToSelectFrom)
{
if (_tc_itemsOfFamilyFrom)
return _tc_itemsOfFamilyFrom(family,itemsToSelectFrom);
return tc_createItemsArray(0);
}
*/ TCAPIEXPORT
tc_items tc_itemsOfFamily(const char* family)
{
if (_tc_itemsOfFamily)
return _tc_itemsOfFamily(family);
return tc_createItemsArray(0);
}
*/ TCAPIEXPORT
tc_items tc_partsIn(long o)
{
if (_tc_partsIn)
return _tc_partsIn(o);
return tc_createItemsArray(0);
}
*/ TCAPIEXPORT
tc_items tc_partsDownstream(long o)
{
if (_tc_partsDownstream)
return _tc_partsDownstream(o);
return tc_createItemsArray(0);
}
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);
}
}
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;
}
