/// <summary>
/// Compute all simple cycles up to given <paramref name="maxCycleSize"/> in the provided
/// <paramref name="graph"/>. In some graphs the topology makes it impracticable to
/// compute all the simple. To avoid running forever on these molecules the
/// <paramref name="maxDegree"/> provides an escape clause. The value doesn't quantify
/// how many cycles we get.
/// </summary>
/// <remarks>
/// The percentage of molecules in PubChem Compound
/// (Dec '12) which would successfully complete for a given Degree are listed
/// below.
/// <list type="table">
/// <listheader>Table 1. Number of structures processable in PubChem Compound (Dec 2012) as a result of
/// setting the max degree</listheader>
/// <item><term>Percent</term><term>Max Degree</term></item>
/// <item><term>99%</term><term>9</term></item> <item><term>99.95%</term><term>72</term></item>
/// <item><term>99.96%</term><term>84</term></item> <item><term>99.97%</term><term>126</term></item>
/// <item><term>99.98%</term><term>216</term></item> <item><term>99.99%</term><term>684</term></item>
/// </list>
/// </remarks>
/// <param name="graph">adjacency list representation of a graph</param>
/// <param name="maxCycleSize">the maximum cycle size to perceive</param>
/// <param name="maxDegree">escape clause to stop the algorithm running forever</param>
public AllCycles(int[][] graph, int maxCycleSize, int maxDegree)
{
// get the order in which we remove vertices, the rank tells us
// the index in the ordered array of each vertex
int[] rank = GetRank(graph);
int[] vertices = GetVerticesInOrder(rank);
PathGraph pGraph;
if (graph.Length < 64)
{
pGraph = new RegularPathGraph(graph, rank, maxCycleSize);
}
else
{
pGraph = new JumboPathGraph(graph, rank, maxCycleSize);
}
// perceive the cycles by removing the vertices in order
int removed = 0;
foreach (int v in vertices)
{
if (pGraph.Degree(v) > maxDegree)
{
break; // or could throw exception...
}
pGraph.Remove(v, cycles);
removed++;
}
completed = removed == graph.Length;
}
public virtual void K8()
{
int ord = 8;
int[][] k8 = CompleteGraphOfSize(ord);
var pg = new JumboPathGraph(k8, Identity(8), ord);
List <int[]> cycles = new List <int[]>();
for (int v = 0; v < ord; v++)
{
pg.Remove(v, cycles);
}
Assert.AreEqual(8018, cycles.Count);
}
public virtual void K3Degree()
{
int ord = 3;
int[][] k3 = CompleteGraphOfSize(ord);
var pg = new JumboPathGraph(k3, Identity(3), ord);
// note - vertices are only added to either vertex (lowest rank)
Assert.AreEqual(2, pg.Degree(0));
Assert.AreEqual(1, pg.Degree(1));
Assert.AreEqual(0, pg.Degree(2));
pg.Remove(0, new List <int[]>(0));
Assert.AreEqual(0, pg.Degree(0));
Assert.AreEqual(2, pg.Degree(1));
Assert.AreEqual(0, pg.Degree(2));
pg.Remove(1, new List <int[]>(0));
Assert.AreEqual(0, pg.Degree(0));
Assert.AreEqual(0, pg.Degree(1));
Assert.AreEqual(0, pg.Degree(2));
}
public virtual void RepeatRemoval()
{
int ord = 3;
int[][] k3 = CompleteGraphOfSize(ord);
var pg = new JumboPathGraph(k3, Identity(3), ord);
List <int[]> cycles = new List <int[]>();
pg.Remove(0, cycles);
Assert.AreEqual(0, cycles.Count);
pg.Remove(0, cycles);
Assert.AreEqual(0, cycles.Count);
pg.Remove(1, cycles);
Assert.AreEqual(1, cycles.Count);
pg.Remove(1, cycles);
Assert.AreEqual(1, cycles.Count);
pg.Remove(2, cycles);
Assert.AreEqual(1, cycles.Count);
pg.Remove(2, cycles);
Assert.AreEqual(1, cycles.Count);
}