public static void Analyze(double[,] matrix, bool[] rev, bool[] trans, LinkedList<FluxPattern> forbidden_combinations, double max_value, double tolerance, bool lp, bool fc, bool do_efca, bool keep_witnesses, bool only_internal, bool show_output, out FluxPattern max, out IIntCoupling coupling, out EFCACount efca, out int reactions_unblocked, out int reactions_frev, out int couples, out ICollection<FluxPattern> circuits, out DateTime time_start, out DateTime time_unblocked, out DateTime time_frev, out DateTime time_couples, out DateTime time_efca, out DateTime[] time_reaction, out int lps_unblocked, out int lps_frev, out int lps_couples, out int lps_efca, out int[] lps_reaction, out int wits_unblocked, out int wits_frev, out int wits_couples, out int wits_efca, out int[] wits_reaction, out int[] wits_distribution, out int[] wits_usable, String name = null)
{
//initialisation
time_start = DateTime.Now;
efca = null;
wits_usable = null;
int n = rev.Length;
List<int> irr = new List<int>();
for (int i = 0; i < n; ++i)
if (!rev[i])
irr.Add(i);
LinkedList<FluxPattern> witnesses = new LinkedList<FluxPattern>();
LinkedList<FluxPattern> blocking_witnesses, frev_witnesses;
IIntFCACalculator<FluxPattern> fcacalculator = !lp ? (IIntFCACalculator<FluxPattern>)new MILPIntFCACalculator(matrix, rev, max_value, tolerance) :
!fc ? (IIntFCACalculator<FluxPattern>)new LPIntFCACalculator(matrix, rev, max_value, tolerance) :
forbidden_combinations == null || forbidden_combinations.Count == 0 ? (IIntFCACalculator<FluxPattern>)new FCIntFCACalculator(matrix, rev, trans, max_value, tolerance) :
(IIntFCACalculator<FluxPattern>)new FastFCIntFCACalculator(matrix, rev, forbidden_combinations, max_value, tolerance);
circuits = (fc && forbidden_combinations == null) ? ((FCIntFCACalculator) fcacalculator).Circles : null;
// calculate blocked reactions
FluxPattern calcs;
int wits_used;
bool[] internal_reactions = new bool[n];
for(int i = 0; i<n; ++i)
internal_reactions[i] = !trans[i];
FluxPattern pattern_internal = new FluxPattern(internal_reactions, false);
max = fcacalculator.CalculateMax(new List<int>(), n, new LinkedList<FluxPattern>(), out blocking_witnesses, out calcs, only_internal ? pattern_internal : null, null);
reactions_unblocked = max.Count;
foreach (FluxPattern a in blocking_witnesses)
if (a.Count > 0)
witnesses.AddLast(a);
if (name != null)
SaveStatistics(witnesses, n, name + "_max.stats");
time_unblocked = DateTime.Now;
lps_unblocked = fcacalculator.SolverCalls;
wits_unblocked = witnesses.Count;
if (show_output)
Console.WriteLine("({0})\tBlocked reactions calculated: {1} of {2} blocked.\n", time_unblocked, n-reactions_unblocked, n);
// calculate fully reversible reactions
FluxPattern frev = fcacalculator.CalculateMax(irr, n, blocking_witnesses, out frev_witnesses, out calcs, max, null);
reactions_frev = frev.Count;
foreach (FluxPattern a in frev_witnesses)
if (a.Count > 0)
witnesses.AddLast(a);
if (name != null)
SaveStatistics(witnesses, n, name + "_frev.stats");
time_frev = DateTime.Now;
lps_frev = fcacalculator.SolverCalls - lps_unblocked;
wits_frev = witnesses.Count - wits_unblocked;
if (show_output)
Console.WriteLine("({0})\tFRev calculated.\n", time_frev);
// FCA
Console.WriteLine("Witnesses so far:");
foreach (FluxPattern a in witnesses)
Console.WriteLine("\t{0}", a);
Console.WriteLine("\nStarting FCA.\n");
coupling = new IntCoupling(fcacalculator, show_output, witnesses, out time_reaction, out lps_reaction, out wits_reaction, out wits_used, max, frev);
if (name != null)
SaveStatistics(coupling.Witnesses, n, name + "_fca.stats");
time_couples = DateTime.Now;
wits_couples = coupling.Witnesses.Count - wits_frev - wits_unblocked;
lps_couples = 0; wits_couples = 0;
for (int i = 0; i < n; ++i)
{
lps_couples += lps_reaction[i];
wits_couples += wits_reaction[i];
}
if (show_output)
Console.WriteLine("({0})\tCouples calculated.\n", time_couples);
wits_distribution = new int[n + 1];
foreach (FluxPattern a in coupling.Witnesses)
wits_distribution[a.Count]++;
// EFCA
lps_efca = 0;
wits_efca = 0;
if (do_efca)
{
efca = new EFCACount(fcacalculator, keep_witnesses, coupling.Witnesses, max, frev, out time_reaction, out lps_reaction, out wits_reaction, out wits_usable, coupling, null, show_output);
lps_efca = efca.LPCount;
wits_efca = efca.WitnessCount;
}
time_efca = DateTime.Now;
couples = coupling.ToCoupling().Count;
}
/// <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);
}