コード例 #1
0
ファイル: Evaluate.java プロジェクト: ucl-cssb/signalMatch
  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 = "";
    }
  }
コード例 #2
0
ファイル: Evaluate.java プロジェクト: ucl-cssb/signalMatch
  /**
   * 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));
  }