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 = "";
}
}
@Override
public ArrayList<Map> getObjects() {
ArrayList<Map> objects = new ArrayList<>();
ArrayList<Double> REU_TITR = new ArrayList<Double>();
REU_TITR.add(0.018806664);
REU_TITR.add(0.028666538);
REU_TITR.add(0.051722065);
REU_TITR.add(0.14837545);
REU_TITR.add(0.261559417);
REU_TITR.add(0.447725869);
REU_TITR.add(0.687508549);
REU_TITR.add(1.131011516);
REU_TITR.add(1.891798237);
REU_TITR.add(3.27479675);
REU_TITR.add(4.549973162);
REU_TITR.add(8.687342616);
HistogramBins hbins = new HistogramBins();
hbins.init();
GateLibrary gate_library = new GateLibrary(0, 0);
ArrayList<String> gate_names = new ArrayList<String>();
gate_names.add("an0_AmeR");
gate_names.add("js2_AmtR");
gate_names.add("js2_BM3R1");
gate_names.add("js2_BetI");
gate_names.add("js2_HlyIIR");
gate_names.add("js2_IcaRA");
gate_names.add("js2_LitR");
gate_names.add("js2_PhlF");
gate_names.add("js2_SrpR");
gate_names.add("js_QacR");
gate_names.add("js2_LitR");
for (String gate_name : gate_names) {
Gate g = new Gate();
g.Name = gate_name;
gate_library.get_GATES_BY_NAME().put(g.Name, g);
}
for (Gate g : gate_library.get_GATES_BY_NAME().values()) {
String gate_name = g.Name;
String rootpath = collection_writer.getRootPath();
String filepath = rootpath + "/resources/data/nor_gates/cytometry_cb1/";
HistogramUtil.getTransferFunctionHistogramTitrations(
gate_name, gate_library, hbins, filepath);
LinkedHashMap obj = new LinkedHashMap();
obj.put("collection", "gate_cytometry"); // tag
obj.put("gate_name", gate_name);
ArrayList<LinkedHashMap> titrations = new ArrayList<LinkedHashMap>();
for (int i = 0; i < REU_TITR.size(); ++i) {
Double inREU = REU_TITR.get(i);
ArrayList<Double> out_reu_bins = new ArrayList<Double>();
ArrayList<Double> out_reu_counts = new ArrayList<Double>();
for (int j = 0; j < hbins.get_NBINS(); ++j) {
double[] normalized = HistogramUtil.normalize(g.get_xfer_hist().get_xfer_binned().get(i));
out_reu_bins.add(Math.pow(10, hbins.get_LOG_BIN_CENTERS()[j]));
out_reu_counts.add(normalized[j]);
}
LinkedHashMap titration = new LinkedHashMap();
titration.put("maps_to_variable", "x");
titration.put("input", inREU);
titration.put("output_bins", out_reu_bins);
titration.put("output_counts", out_reu_counts);
titrations.add(titration);
}
obj.put("cytometry_data", titrations);
objects.add(obj);
// org.cellocad.ucf_writers_tetr.ConstraintFileWriter.JSONPrettyPrint(obj,
// "resources/UCF/Eco1C1G1T1.gate_cytometry.json", true);
}
return objects;
}
