public void Mark()
{
CompatibilityMatrix m = new CompatibilityMatrix(5, 5);
m.Set1(0, 1);
m.Set1(0, 2);
m.Set1(0, 4);
m.Set1(1, 0);
m.Set1(1, 3);
Assert.IsTrue(m.Get1(0, 1));
Assert.IsTrue(m.Get1(0, 4));
m.Mark(0, 1, -1);
m.Mark(0, 4, -4);
m.Mark(1, 3, -6);
Assert.IsFalse(m.Get1(0, 1));
Assert.IsFalse(m.Get1(0, 4));
Assert.IsFalse(m.Get1(1, 3));
m.ResetRows(0, -1);
Assert.IsTrue(m.Get1(0, 1));
Assert.IsFalse(m.Get1(0, 4));
Assert.IsFalse(m.Get1(1, 3));
m.ResetRows(0, -4);
Assert.IsTrue(m.Get1(0, 1));
Assert.IsTrue(m.Get1(0, 4));
Assert.IsFalse(m.Get1(1, 3));
m.ResetRows(0, -6);
Assert.IsTrue(m.Get1(0, 1));
Assert.IsTrue(m.Get1(0, 4));
Assert.IsTrue(m.Get1(1, 3));
}
/// <summary>
/// Create a state for matching subgraphs using the Ullmann refinement
/// procedure.
/// </summary>
/// <param name="container1">query container</param>
/// <param name="container2">target container</param>
/// <param name="g1">query container adjacency list</param>
/// <param name="g2">target container adjacency list</param>
/// <param name="bonds1">query container bond map</param>
/// <param name="bonds2">target container bond map</param>
/// <param name="atomMatcher">method of matching atom semantics</param>
/// <param name="bondMatcher">method of matching bond semantics</param>
public UllmannState(IAtomContainer container1, IAtomContainer container2, int[][] g1, int[][] g2,
EdgeToBondMap bonds1, EdgeToBondMap bonds2, AtomMatcher atomMatcher, BondMatcher bondMatcher)
{
this.bondMatcher = bondMatcher;
this.g1 = g1;
this.g2 = g2;
this.bond1 = bonds1;
this.bonds2 = bonds2;
this.m1 = new int[g1.Length];
this.m2 = new int[g2.Length];
Arrays.Fill(m1, UNMAPPED);
Arrays.Fill(m2, UNMAPPED);
// build up compatibility matrix
matrix = new CompatibilityMatrix(g1.Length, g2.Length);
for (int i = 0; i < g1.Length; i++)
{
for (int j = 0; j < g2.Length; j++)
{
if (g1[i].Length <= g2[j].Length && atomMatcher.Matches(container1.Atoms[i], container2.Atoms[j]))
{
matrix.Set1(i, j);
}
}
}
}
public void MarkRow()
{
CompatibilityMatrix m = new CompatibilityMatrix(5, 5);
m.Set1(0, 1);
m.Set1(0, 2);
m.Set1(0, 4);
Assert.IsTrue(Compares.AreEqual(new int[] { 0, 1, 1, 0, 1 }, m.Fix()[0]));
m.MarkRow(0, -1);
Assert.IsTrue(Compares.AreEqual(new int[] { 0, -1, -1, 0, -1 }, m.Fix()[0]));
}
public void AccessAndModify()
{
CompatibilityMatrix m = new CompatibilityMatrix(5, 5);
Assert.IsFalse(m.Get1(0, 1));
Assert.IsFalse(m.Get1(0, 4));
Assert.IsFalse(m.Get1(1, 0));
Assert.IsFalse(m.Get1(1, 3));
m.Set1(0, 1);
m.Set1(0, 4);
m.Set1(1, 0);
m.Set1(1, 3);
Assert.IsTrue(m.Get1(0, 1));
Assert.IsTrue(m.Get1(0, 4));
Assert.IsTrue(m.Get1(1, 0));
Assert.IsTrue(m.Get1(1, 3));
}
public void Fix()
{
CompatibilityMatrix m = new CompatibilityMatrix(5, 5);
m.Set1(0, 1);
m.Set1(0, 2);
m.Set1(0, 4);
m.Set1(1, 0);
m.Set1(1, 3);
m.Set1(2, 4);
Assert.IsTrue(Compares.AreDeepEqual(new int[][] {
new[] { 0, 1, 1, 0, 1 },
new[] { 1, 0, 0, 1, 0 },
new[] { 0, 0, 0, 0, 1 },
new[] { 0, 0, 0, 0, 0 },
new[] { 0, 0, 0, 0, 0 },
}, m.Fix()));
}