/// <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)));
}
}
public virtual void AddAll()
{
var c1 = new Mock <Cycle>((InitialCycles)null, (ShortestPaths)null, (int[])null);
var c2 = new Mock <Cycle>((InitialCycles)null, (ShortestPaths)null, (int[])null);
c1.SetupGet(c => c.EdgeVector).Returns(new BitArray(0));
c1.SetupGet(c => c.EdgeVector).Returns(new BitArray(0));
c2.SetupGet(c => c.EdgeVector).Returns(new BitArray(0));
var basis = new GreedyBasis(2, 0);
Assert.IsTrue(basis.Members.Count == 0);
basis.AddAll(new[] { c1.Object, c2.Object });
Assert.IsTrue(basis.Members.Contains(c1.Object));
Assert.IsTrue(basis.Members.Contains(c2.Object));
}
public virtual void Size()
{
var basis = new GreedyBasis(3, 12);
Assert.AreEqual(0, basis.Count);
var c1 = new Mock <Cycle>((InitialCycles)null, (ShortestPaths)null, (int[])null);
var c2 = new Mock <Cycle>((InitialCycles)null, (ShortestPaths)null, (int[])null);
var c3 = new Mock <Cycle>((InitialCycles)null, (ShortestPaths)null, (int[])null);
c1.SetupGet(c => c.EdgeVector).Returns(BitArrays.FromString("111000000000"));
c2.SetupGet(c => c.EdgeVector).Returns(BitArrays.FromString("000111000000"));
c3.SetupGet(c => c.EdgeVector).Returns(BitArrays.FromString("111111000000"));
basis.Add(c1.Object);
Assert.AreEqual(1, basis.Count);
basis.Add(c2.Object);
Assert.AreEqual(2, basis.Count);
basis.Add(c3.Object);
Assert.AreEqual(3, basis.Count);
}
public virtual void SubSetOfBasis()
{
var c1 = new Mock <Cycle>((InitialCycles)null, (ShortestPaths)null, (int[])null);
var c2 = new Mock <Cycle>((InitialCycles)null, (ShortestPaths)null, (int[])null);
var c3 = new Mock <Cycle>((InitialCycles)null, (ShortestPaths)null, (int[])null);
c1.SetupGet(c => c.EdgeVector).Returns(BitArrays.FromString("111000000000"));
c2.SetupGet(c => c.EdgeVector).Returns(BitArrays.FromString("000111000000"));
c3.SetupGet(c => c.EdgeVector).Returns(BitArrays.FromString("011110000000"));
c1.SetupGet(c => c.Length).Returns(3);
c2.SetupGet(c => c.Length).Returns(3);
c3.SetupGet(c => c.Length).Returns(4);
var basis = new GreedyBasis(3, 12);
Assert.IsFalse(basis.IsSubsetOfBasis(c3.Object));
basis.Add(c1.Object);
Assert.IsFalse(basis.IsSubsetOfBasis(c3.Object));
basis.Add(c2.Object);
Assert.IsTrue(basis.IsSubsetOfBasis(c3.Object));
}
/// <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);
}
}
}