public static void refreshGateAttributes(Gate g, GateLibrary gate_library) {
if (g.Type == GateType.OUTPUT || g.Type == GateType.OUTPUT_OR) {
g.set_params(null);
ArrayList<String> variable_names = new ArrayList<>();
variable_names.add("x");
g.set_variable_names(variable_names);
HashMap<String, Double[]> variable_thresholds = new HashMap<>();
variable_thresholds.put("x", new Double[] {null, null});
g.set_variable_thresholds(variable_thresholds);
String equation = String.valueOf("x");
g.set_equation(equation);
} else if (gate_library.get_GATES_BY_NAME().containsKey(g.Name)) {
g.set_params(gate_library.get_GATES_BY_NAME().get(g.Name).get_params());
if (g.get_variable_names().isEmpty()) {
g.set_variable_names(gate_library.get_GATES_BY_NAME().get(g.Name).get_variable_names());
}
g.set_variable_thresholds(
gate_library.get_GATES_BY_NAME().get(g.Name).get_variable_thresholds());
g.set_equation(gate_library.get_GATES_BY_NAME().get(g.Name).get_equation());
g.System = gate_library.get_GATES_BY_NAME().get(g.Name).System;
g.ColorHex = gate_library.get_GATES_BY_NAME().get(g.Name).ColorHex;
g.Group = gate_library.get_GATES_BY_NAME().get(g.Name).Group;
g.Regulator = gate_library.get_GATES_BY_NAME().get(g.Name).Regulator;
g.Inducer = gate_library.get_GATES_BY_NAME().get(g.Name).Inducer;
// if(Args.histogram) {
if (gate_library.get_GATES_BY_NAME().get(g.Name).get_xfer_hist() != null) {
g.set_xfer_hist(gate_library.get_GATES_BY_NAME().get(g.Name).get_xfer_hist());
}
} else {
g.System = "null";
g.ColorHex = "null";
g.Group = "null";
g.Regulator = "null";
g.Inducer = "";
}
}
/**
* A gate with two transcriptional units (e.g. AND) can have two different wirings. Doesn't matter
* for a gate with one txn unit.
*
* @param g
* @param gate_library
* @param options
*/
public static void setBestVariableMapping(Gate g, GateLibrary gate_library, Args options) {
ArrayList<ArrayList<String>> variable_name_orders =
Permute.getVariableNamePermutation(g.get_variable_names());
Integer best_variable_name_order_index = 0;
Double best_score = 0.0;
int v = 0;
for (ArrayList<String> variable_name_order : variable_name_orders) {
g.get_outreus().clear();
for (int i = 0; i < g.get_logics().size(); ++i) { // rows in truth table
/*if (Args.dontcare_rows.contains(i)) {
g.get_outreus().add(0.0);
continue;
}*/
GateUtil.mapWiresToVariables(g, variable_name_order);
double output_reu =
ResponseFunction.computeOutput(
GateUtil.getVariableValues(g, i, gate_library, options),
g.get_params(),
g.get_equation());
g.get_outreus().add(output_reu);
}
evaluateGate(g, options);
if (g.get_scores().get_score() > best_score) {
best_score = g.get_scores().get_score();
best_variable_name_order_index = v;
}
v++;
}
// this is the critical part, it's ordering the variable names in the list
g.set_variable_names(variable_name_orders.get(best_variable_name_order_index));
}