/// <summary> Construct the edge short cycles for the
/// given initial cycles. </summary>
public EdgeShortCycles(InitialCycles initialCycles)
{
int[][] graph = initialCycles.Graph;
int[] sizeOf = new int[initialCycles.GetNumberOfEdges()];
this.paths = new List <int[]>(initialCycles.GetNumberOfCycles());
// cycles are returned ordered by length
foreach (var cycle in initialCycles.GetCycles())
{
int length = cycle.Length;
int[] path = cycle.Path;
bool found = false;
// check if any vertex is the shortest through a vertex in the path
for (int i = 1; i < path.Length; i++)
{
int idx = initialCycles.IndexOfEdge(path[i - 1], path[i]);
if (sizeOf[idx] < 1 || length <= sizeOf[idx])
{
found = true;
sizeOf[idx] = length;
}
}
if (found)
{
foreach (var p in cycle.GetFamily())
{
paths.Add(p);
}
}
}
}
/// <summary> Construct the vertex short cycles for the given initial cycles.</summary>
public VertexShortCycles(InitialCycles initialCycles)
{
int[][] graph = initialCycles.Graph;
int[] sizeOf = new int[graph.Length];
this.paths = new List <int[]>(initialCycles.GetNumberOfCycles());
// cycles are returned ordered by length
foreach (var cycle in initialCycles.GetCycles())
{
int length = cycle.Length;
int[] path = cycle.Path;
bool found = false;
// check if any vertex is the shortest through a vertex in the path
foreach (var v in path)
{
if (sizeOf[v] < 1 || length <= sizeOf[v])
{
found = true;
sizeOf[v] = length;
}
}
if (found)
{
foreach (var p in cycle.GetFamily())
{
paths.Add(p);
}
}
}
}
/// <summary>
/// Generate the relevant cycle basis from a precomputed set of initial
/// cycles.
/// </summary>
/// <param name="initial">set of initial cycles.</param>
/// <exception cref="System.ArgumentNullException">null InitialCycles provided</exception>
internal RelevantCycles(InitialCycles initial)
{
CheckNotNull(initial, nameof(initial), "No InitialCycles provided");
this.basis = new GreedyBasis(initial.GetNumberOfCycles(), initial.GetNumberOfEdges());
// processing by size add cycles which are independent of smaller cycles
foreach (var length in initial.Lengths)
{
basis.AddAll(Independent(initial.GetCyclesOfLength(length)));
}
}
/// <summary>
/// Determine the essential cycles from a precomputed set of initial cycles
/// and relevant cycles.
/// </summary>
/// <param name="relevant"></param>
/// <param name="initial">a molecule graph</param>
internal EssentialCycles(RelevantCycles relevant, InitialCycles initial)
{
CheckNotNull(relevant, nameof(relevant), "No RelevantCycles provided");
this.initial = CheckNotNull(initial, nameof(initial), "No InitialCycles provided");
this.basis = new GreedyBasis(initial.GetNumberOfCycles(), initial.GetNumberOfEdges());
this.essential = new List <Cycle>();
// for each cycle added to the basis, if it can be
// replaced with one of equal size it is non-essential
foreach (var cycles in GroupByLength(relevant))
{
foreach (var c in GetMembersOfBasis(cycles))
{
if (IsEssential(c, cycles))
{
essential.Add(c);
}
}
}
}
/// <summary>
/// Generate the minimum cycle basis from a precomputed set of initial
/// cycles. This constructor allows on to specify that the graph is
/// connected which allows an optimisation to be used.
/// </summary>
/// <param name="initial">set of initial cycles.</param>
/// <param name="connected">the graph is known to be connected</param>
/// <exception cref="System.ArgumentNullException">null InitialCycles provided</exception>
internal MinimumCycleBasis(InitialCycles initial, bool connected)
{
CheckNotNull(initial, nameof(initial), "No InitialCycles provided");
this.graph = initial.Graph;
this.basis = new GreedyBasis(initial.GetNumberOfCycles(), initial.GetNumberOfEdges());
// a undirected unweighted connected graph there are |E| - (|V| + 1)
// cycles in the minimum basis
int lim = connected ? initial.GetNumberOfEdges() - graph.Length + 1 : int.MaxValue;
// processing by size add cycles which are independent of smaller cycles
foreach (var cycle in initial.GetCycles())
{
if (basis.Count < lim && basis.IsIndependent(cycle))
{
basis.Add(cycle);
}
}
}
public virtual void Bioconnected_simpleCycle_limit_6()
{
InitialCycles ic = InitialCycles.OfBiconnectedComponent(Cyclohexane, 6);
Assert.AreEqual(1, ic.GetNumberOfCycles());
}