/** Same as above, but converts input distr to output distr using a matrix transfer function */
public static void simulateHistogramREU(LogicCircuit lc, GateLibrary gate_library, Args options) {
ArrayList<Gate> logic_and_output_gates = new ArrayList<Gate>();
logic_and_output_gates.addAll(lc.get_logic_gates());
logic_and_output_gates.addAll(lc.get_output_gates());
// input gate REU already set
for (Gate gate : logic_and_output_gates) {
gate.set_unvisited(true);
}
for (Gate gate : logic_and_output_gates) {
simulateHistogramREU(gate, gate_library, options);
}
}
/**
* for all logic and output gates: set flag simulate_reu = true (indicates that REU needs to be
* simulated) then call simulateREU() in Gate.java
*
* <p>Hill function evaluation
*/
public static void simulateREU(LogicCircuit lc, GateLibrary gate_library, Args options) {
ArrayList<Gate> logic_and_output_gates = new ArrayList<Gate>();
logic_and_output_gates.addAll(lc.get_logic_gates());
logic_and_output_gates.addAll(lc.get_output_gates());
// input gate REU already set
// make sure that all gates are re-simulated by setting simulate_reu to TRUE
for (Gate gate : logic_and_output_gates) {
gate.set_unvisited(true);
}
for (Gate gate : logic_and_output_gates) {
simulateREU(gate, gate_library, options);
}
}
/**
* *********************************************************************
*
* <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>logic is computed according to Gate type and input logics
*
* <p>*********************************************************************
*/
public static void simulateLogic(Gate g) {
if (g.is_unvisited()) {
ArrayList<Gate> children = g.getChildren();
for (Gate child : children) {
if (child.is_unvisited()) {
simulateLogic(child); // recursive
}
}
// if all children have been visited, visit the current gate 'g'
g.set_unvisited(false);
g.set_logics(GateUtil.computeGateLogics(g));
}
}
/**
* *********************************************************************
*
* <p>Synopsis [ ]
*
* <p>*********************************************************************
*/
public static void simulateHistogramREU(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()) {
simulateHistogramREU(child, gate_library, options);
}
}
// initialize
g.get_histogram_reus().clear();
for (int i = 0; i < g.get_logics().size(); ++i) { // rows in truth table
g.get_histogram_reus().add(new double[g.get_histogram_bins().get_NBINS()]);
for (int j = 0; j < g.get_histogram_bins().get_NBINS(); ++j) {
g.get_histogram_reus().get(i)[j] = 0.0;
}
}
if (g.Type == GateType.OUTPUT_OR || g.Type == GateType.OUTPUT) {
g.set_histogram_reus(GateUtil.getSumOfGateInputHistograms(g, gate_library, options));
} else if (g.Type == GateType.AND) {
g.set_histogram_reus(GateUtil.getANDOfGateInputHistograms(g));
} else if (g.Type == GateType.NOT || g.Type == GateType.NOR) {
// 2. For each row: for each bin: for each output bin: add normalizeToValue
ArrayList<double[]> input_convreus =
GateUtil.getSumOfGateInputHistograms(g, gate_library, options);
g.set_in_histogram_reus(input_convreus);
for (int i = 0; i < input_convreus.size(); ++i) {
/*if(Args.dontcare_rows.contains(i)) {
for(int bin=0; bin< g.get_histogram_reus().get(i).length; ++bin) {
g.get_histogram_reus().get(i)[bin] = 0.0;
}
continue;
}*/
double[] convhist = input_convreus.get(i);
for (int bin = 0; bin < g.get_histogram_bins().get_NBINS(); ++bin) {
double fractional_counts = convhist[bin];
double[] xslice = g.get_xfer_hist().get_xfer_interp().get(bin);
for (int xslice_bin = 0;
xslice_bin < g.get_histogram_bins().get_NBINS();
++xslice_bin) {
g.get_histogram_reus().get(i)[xslice_bin] += xslice[xslice_bin] * fractional_counts;
}
}
}
}
// evaluateGateHistogramOverlap(g); //to compute gate scores
}
}
/**
* *********************************************************************
*
* <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);
//////////////////////////////////////////////
}
}