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;
}
public static IIntCoupling DoFCA(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, bool save_stats, String name, String model, String method, LinkedList<string> res, LinkedList<string> details, out FluxPattern max, out EFCACount efca, out ICollection<FluxPattern> circuits)
{
LinkedList<FluxPattern> witnesses;
int n_unblocked;
FluxPattern frev = null;
IIntCoupling coupling = null;
DateTime time_start, time_stop;
DateTime[] time_reaction;
int reactions_unblocked, reactions_frev, couples, lps, lps_unblocked, lps_frev, lps_couples, lps_efca, wits, wits_unblocked, wits_frev, wits_couples, wits_efca;
int lps_total, wits_total;
int[] lps_reaction, wits_reaction, wits_distribution, wits_usable;
DateTime time_unblocked, time_frev, time_couples, time_efca;
Analyze(matrix, rev, trans, forbidden_combinations, max_value, tolerance, lp, fc, do_efca, keep_witnesses, only_internal, show_output, out max, out coupling, out efca, out reactions_unblocked, out reactions_frev, out couples, out circuits, out time_start, out time_unblocked, out time_frev, out time_couples, out time_efca, out time_reaction, out lps_unblocked, out lps_frev, out lps_couples, out lps_efca, out lps_reaction, out wits_unblocked, out wits_frev, out wits_couples, out wits_efca, out wits_reaction, out wits_distribution, out wits_usable, save_stats ? name : null);
lps = lps_unblocked + lps_frev + lps_couples + lps_efca;
wits = wits_unblocked + wits_frev + wits_couples + wits_efca;
/*String cellcolor = "\\cellcolor{gray!10}";
res.AddLast("\\midrule\n\\multirowbt{4}{*}{\\Var{" + model.Replace("_", "\\_") + "}}" + String.Format("& {4}Total &{4}{0}&{4}{2}&{4}{3}&{4}{1:0.0}\\\\", rev.Length, (time_efca - time_start).TotalSeconds, lps, wits, ""));
res.AddLast(String.Format("\\cmidrule{4} & {5}$1_L$ &{5}{0}&{5}{2}&{5}{3}&{5}{1:0.0}\\\\", reactions_unblocked, (time_unblocked - time_start).TotalSeconds, lps_unblocked, wits_unblocked, "{2-6}", cellcolor));
res.AddLast(String.Format("\\cmidrule{4} & $\\Frev$ &{0}&{2}&{3}&{1:0.0}\\\\", reactions_frev, (time_frev - time_unblocked).TotalSeconds, lps_frev, wits_frev, "{2-6}"));
res.AddLast(String.Format("\\cmidrule{4} & {5}$\\Coupling$ &{5}{0}&{5}{2}&{5}{3}&{5}{1:0.0}\\\\", couples, (time_couples - time_frev).TotalSeconds, lps_couples, wits_couples, "{2-6}", cellcolor));
if(do_efca)
res.AddLast(String.Format("\\cmidrule{4} & EFCA &{1}&{2}&{3}&{1:0.0}\\\\", efca.Length, (time_efca - time_couples).TotalSeconds, lps_efca, wits_efca, "{2-6}"));
*/
res.AddLast(String.Format("{0} {1} {2} {3} {4} {5} {6} {7:0.000} {8:0.000} {9:0.000} {10:0.000} {11:0.000} {12} {13} {14} {15} {16} {17} {18} {19} {20} {21}", model, method, matrix.Length / rev.Length, rev.Length, reactions_unblocked, reactions_frev, couples, (time_efca - time_start).TotalSeconds, (time_unblocked - time_start).TotalSeconds, (time_frev - time_unblocked).TotalSeconds, (time_couples - time_frev).TotalSeconds, (time_efca - time_couples).TotalSeconds, lps, lps_unblocked, lps_frev, lps_couples, lps_efca, wits, wits_unblocked, wits_frev, wits_couples, wits_efca));
//unblocked
details.AddLast(String.Format("{0} {1} {2} {3} {4} {5} {6} {22:0.000} {23} {24} {25} {26} {27}", model, method, matrix.Length / rev.Length, rev.Length, reactions_unblocked, reactions_frev, couples, (time_efca - time_start).TotalSeconds, (time_unblocked - time_start).TotalSeconds, (time_frev - time_unblocked).TotalSeconds, (time_couples - time_frev).TotalSeconds, (time_efca - time_couples).TotalSeconds, lps, lps_unblocked, lps_frev, lps_couples, lps_efca, wits, wits_unblocked, wits_frev, wits_couples, wits_efca, time_start, -1, lps_unblocked, lps_unblocked, wits_unblocked, wits_unblocked));
//frev
details.AddLast(String.Format("{0} {1} {2} {3} {4} {5} {6} {22:0.000} {23} {24} {25} {26} {27}", model, method, matrix.Length / rev.Length, rev.Length, reactions_unblocked, reactions_frev, couples, (time_efca - time_start).TotalSeconds, (time_unblocked - time_start).TotalSeconds, (time_frev - time_unblocked).TotalSeconds, (time_couples - time_frev).TotalSeconds, (time_efca - time_couples).TotalSeconds, lps, lps_unblocked, lps_frev, lps_couples, lps_efca, wits, wits_unblocked, wits_frev, wits_couples, wits_efca, time_start, 0, lps_frev, lps_unblocked + lps_frev, wits_frev, wits_unblocked + wits_frev));
//couples
lps_total = lps_unblocked + lps_frev;
wits_total = wits_unblocked + wits_frev;
int temp_i = 0;
for (int i = 0; i < rev.Length; ++i)
if (max[i] && lps_reaction[i] > -1)
{
lps_total += lps_reaction[i];
wits_total += wits_reaction[i];
temp_i = i;
details.AddLast(String.Format("{0} {1} {2} {3} {4} {5} {6} {22:0.000} {23} {24} {25} {26} {27} {28} {29}", model, method, matrix.Length / rev.Length, rev.Length, reactions_unblocked, reactions_frev, couples, do_efca ? (time_efca - time_start).TotalSeconds : 0, (time_unblocked - time_start).TotalSeconds, (time_frev - time_unblocked).TotalSeconds, (time_couples - time_frev).TotalSeconds, do_efca ? (time_efca - time_couples).TotalSeconds : 0, lps, lps_unblocked, lps_frev, lps_couples, lps_efca, wits, wits_unblocked, wits_frev, wits_couples, wits_efca, i + 1, (time_reaction[i] - time_start).TotalSeconds, lps_reaction[i], lps_total, wits_reaction[i], wits_total, wits_distribution[i + 1], do_efca ? wits_usable[i] : 0));
}
else
details.AddLast(String.Format("{0} {1} {2} {3} {4} {5} {6} {22:0.000} {23} {24} {25} {26} {27} {28} {29}", model, method, matrix.Length / rev.Length, rev.Length, reactions_unblocked, reactions_frev, couples, do_efca ? (time_efca - time_start).TotalSeconds : 0, (time_unblocked - time_start).TotalSeconds, (time_frev - time_unblocked).TotalSeconds, (time_couples - time_frev).TotalSeconds, do_efca ? (time_efca - time_couples).TotalSeconds : 0, lps, lps_unblocked, lps_frev, lps_couples, lps_efca, wits, wits_unblocked, wits_frev, wits_couples, wits_efca, i + 1, (time_reaction[temp_i] - time_start).TotalSeconds, 0, lps_total, 0, wits_total, wits_distribution[i + 1], do_efca ? wits_usable[i] : 0));
return coupling;
}
