public FitnessEstimator(List<int> R0, List<int> Rb, bool increase, int n, IIntFCACalculator<FluxPattern> fca_solver, LinkedList<FluxPattern> witnesses, FluxPattern max, FluxPattern frev, IIntCoupling coupling)
{
this.R0 = R0;
this.Rb = Rb;
this.increase = increase;
this.rand = new Random();
this.n = n;
this.fca_solver = fca_solver;
this.witnesses = witnesses;
this.MAX = max;
this.FREV = frev;
this.coupling = coupling;
}
/// <summary>
/// Does the FCA for the given network and saves the result in a new IntCoupling object.
/// </summary>
/// <param name="n">#reactions in the network.</param>
/// <param name="calculator">An object that calculates the maximal set of reactions in the metabolic network constrained by disabled reactions.</param>
/// <param name="witnesses">A subset of the flux lattice L.</param>
/// <param name="max">The maximum of L / the set of all unblocked reactions in the metabolic network.</param>
/// <param name="frev">The set of all fully reversible reactions in the metabolic network.</param>
/// <param name="R">A set $R \subseteq [n]$ of disabled reactions.</param>
/// <param name="coupling">Flux coupling we already know about.</param>
/// <param name="start">This constructor calculated the flux coupling sets $C_i$ for $i \geq start$.</param>
public IntCoupling(IIntFCACalculator<FluxPattern> calculator, bool show_output, ICollection<FluxPattern> witnesses, out DateTime[] time_reaction, out int[] lps_reaction, out int[] wits_reaction, out int wits_used, FluxPattern max, FluxPattern frev = null, List<int> R = null, IIntCoupling coupling = null, int start = 0)
{
this.max = max;
this.n = max.Length;
this.witnesses = new LinkedList<FluxPattern>();
time_reaction = new DateTime[n];
lps_reaction = new int[n];
wits_reaction = new int[n];
int lps_count = calculator.SolverCalls;
this.maxima = new FluxPattern[n];
coupled = new LinkedList<int>[n];
for (int i = 0; i < n; ++i)
{
coupled[i] = new LinkedList<int>();
coupled[i].AddLast(i);
}
if (R == null)
R = new List<int>();
LinkedList<FluxPattern> new_witnesses = new LinkedList<FluxPattern>(witnesses);
witnesses = new LinkedList<FluxPattern>();
bool allowed;
foreach (FluxPattern w in new_witnesses)
{
allowed = true;
for (int i = 0; allowed && i < R.Count; ++i)
allowed = !w[R[i]];
if (allowed)
witnesses.Add(w);
}
wits_used = witnesses.Count;
if (coupling == null)
coupling = this;
FluxPattern opt, calcs;
R.Add(-1);
ICollection<int> c;
for (int i = start; i < n; ++i)
if (maxima[i] == null)
{
if (max[i])
{
R[R.Count - 1] = i;
opt = calculator.CalculateMax(R, n, witnesses, out new_witnesses, out calcs, max, frev, coupling);
lps_reaction[i] = calculator.SolverCalls - lps_count;
lps_count = calculator.SolverCalls;
c = coupling[i];
foreach (int r in c)
if (r >= i && coupling.Max(r) != null && !coupling.Max(r)[i])
{
maxima[r] = opt;
for (int j = 0; j < n; ++j)
if (max[j] && !maxima[r][j] && r != j)
coupled[r].AddLast(j);
}
if (maxima[i] == null)
{
maxima[i] = opt;
if (maxima[i] == null)
Console.WriteLine("Fehler!");
else
for (int j = 0; j < n; ++j)
if (!maxima[i][j] && max[j] && i != j)
coupled[i].AddLast(j);
}
foreach (FluxPattern a in new_witnesses)
if (a.Count > 0)
{
this.witnesses.AddLast(a);
witnesses.Add(a);
wits_reaction[i]++;
}
time_reaction[i] = DateTime.Now;
if (show_output)
Console.WriteLine("({0})\tCoupling {1} from {2} calculated. ({3} LPs solved, {4} kept.)\n", time_reaction[i], i + 1, n, lps_reaction[i], witnesses.Count);
}
else
maxima[i] = max;
}
R.RemoveAt(R.Count - 1);
}
/// <summary>
/// Simulates all $\choose n 2$ double reaction knock-outs and creates a new EFCACount object for the results.
/// </summary>
/// <param name="calculator">An object that calculates the maximal set of reactions in the metabolic network constrained by disabled reactions.</param>
/// <param name="witnesses">A subset of the flux lattice L.</param>
/// <param name="max">The maximum of L / the set of all unblocked reactions in the metabolic network.</param>
/// <param name="frev">The set of all fully reversible reactions in the metabolic network.</param>
/// <param name="coupling">A flux coupling for the network</param>
public EFCACount(IIntFCACalculator<FluxPattern> calculator, bool keep_witnesses, ICollection<FluxPattern> witnesses, FluxPattern max, FluxPattern frev, out DateTime[] time_reaction, out int[] lps_reaction, out int[] wits_reaction, out int[] wits_usable, IIntCoupling coupling = null, ICollection<int> T = null, bool show_output = true)
{
this.max = max;
this.n = max.Length;
time_reaction = new DateTime[n];
lps_reaction = new int[n];
for (int i = 0; i < n; ++i)
lps_reaction[i] = -1;
wits_reaction = new int[n];
wits_usable = new int[n];
DateTime[] time;
int[] lps, wits;
int temp_counter = calculator.SolverCalls, temp_wits;
if (coupling == null)
{
coupling = new IntCoupling(calculator, false, witnesses, out time, out lps, out wits, out temp_wits, max, frev);
this.witness_counter = coupling.Witnesses.Count;
this.lp_counter = calculator.SolverCalls - temp_counter;
temp_counter = calculator.SolverCalls;
}
if (T == null)
{
this.T = new List<int>(n);
for (int i = 0; i < n; ++i)
this.T.Add(i);
}
else
this.T = new List<int>(T);
LinkedList<FluxPattern> new_witnesses = new LinkedList<FluxPattern>();
witnesses_kept = new LinkedList<FluxPattern>(witnesses);
IIntCoupling row;
max_size = new int[n, n];
targeted_size = new int[n, n];
for (int i = 0; i < n; ++i)
{
max_size[i, i] = -1;
targeted_size[i, i] = -1;
}
List<int> R = new List<int>();
ICollection<int> c;
int wits_used;
R.Add(-1);
for (int i = 0; i < n; ++i)
if (max[i] && max_size[i, i] < 0)
{
R[0] = i;
if (keep_witnesses)
{
foreach (FluxPattern a in new_witnesses)
if (rand.NextDouble() < ((double)a.Count) / witnesses_kept.Count)
witnesses_kept.AddLast(a);
}
row = new IntCoupling(calculator, false, witnesses_kept, out time, out lps, out wits, out wits_used, max, frev, R, coupling, i);
wits_usable[i] = wits_used;
if (show_output)
Console.WriteLine("({0})\tRow {1} from {2} calculated of EFCA. ({3} LPs solved, {4} kept.)\n", System.DateTime.Now, i + 1, n, calculator.SolverCalls - temp_counter, witnesses_kept.Count);
this.lp_counter += calculator.SolverCalls - temp_counter;
temp_counter = calculator.SolverCalls;
new_witnesses = row.Witnesses;
this.witness_counter += row.Witnesses.Count;
c = coupling[i];
foreach (int r in c)
if (r >= i && !coupling.Max(r)[i])
for (int j = r; j < n; ++j)
if (max[j])
{
max_size[r, j] = row.Max(j).Count;
max_size[j, r] = max_size[r, j];
targeted_size[r, j] = row.Max(j).Values.Intersect(this.T).Count();
targeted_size[j, r] = targeted_size[r, j];
}
lps_reaction[i] = lp_counter;
wits_reaction[i] = witness_counter;
time_reaction[i] = DateTime.Now;
}
if (show_output)
Console.WriteLine("({0})\tEFCA uncompressed.\n", System.DateTime.Now);
}
