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));
}
/**
* *********************************************************************
*
* <p>Synopsis [ ]
*
* <p>keep tracing back to child until find one with logics defined assume it has either 1 or 2
* children this method is recursive Note: Recursion is not necessary and does not occur if we
* sort the gates by distance to input, then simulate logic in that order.
*
* <p>For NOT gate, compute output REU based on child1 REU and xfer function For NOR gate, compute
* output REU based on child1 REU + child2 REU and xfer function For OUTPUT gate, output REU =
* child1 REU For OUTPUT_OR gate, output REU = child1 REU + child2 REU
*
* <p>*********************************************************************
*/
public static void simulateREU(Gate g, GateLibrary gate_library, Args options) {
if (g.is_unvisited()) {
g.set_unvisited(false);
ArrayList<Gate> children = g.getChildren();
for (Gate child : children) {
if (child.is_unvisited()) {
simulateREU(child, gate_library, options);
}
}
/**
* Multidimensional response functions are not symmetric, so which wire maps to which variable
* must be determined. Not relevant if there is only a single independent variable in the
* response function (i.e. Hill equation).
*/
if (g.get_variable_names().size() > 1) {
setBestVariableMapping(g, gate_library, options);
}
///////////////////////////////////////////////////////////////////
// now that the best variable mapping was found, resimulate
///////////////////////////////////////////////////////////////////
g.get_outreus().clear();
g.get_inreus().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, g.get_variable_names());
/**
* For example, String = "x". Double = summed REUs for tandem promoters i is the row in the
* truth table.
*/
HashMap<String, Double> variable_values =
GateUtil.getVariableValues(g, i, gate_library, options);
// v = "x"
for (String v : variable_values.keySet()) {
if (!g.get_inreus().containsKey(v)) {
// initialize with empty arraylist
g.get_inreus().put(v, new ArrayList<Double>());
}
g.get_inreus().get(v).add(variable_values.get(v));
}
double output_reu =
ResponseFunction.computeOutput(
// sum contributions of tandem promoters for this row in the truth table
// ...unless there is tandem promoter data, then we look up the value instead of
// adding
variable_values, g.get_params(), g.get_equation());
g.get_outreus().add(output_reu);
}
// evaluateGate(g);
//////////////////////////////////////////////
}
}