static void FindSuperFamEdges(FamList &Fams, EdgeList &Edges)
{
const int FamCount = (int) Fams.size();
// Allocate triangular array Related[i][j], value is true
// iff families i and j are related (i.e., there is a local
// alignment between some member of i and some member of j).
const int TriangleSize = (FamCount*(FamCount - 1))/2;
bool *Related = all(bool, TriangleSize);
zero(Related, bool, TriangleSize);
for (PtrFamList p = Fams.begin(); p != Fams.end(); ++p)
{
FamData *Fam = *p;
for (PtrFamData q = Fam->begin(); q != Fam->end(); ++q)
{
FamMemberData &FamMember = *q;
int PileIndex = FamMember.PileIndex;
const PileData &Pile = Piles[PileIndex];
const int FamIndex = Pile.FamIndex;
if (-1 == FamIndex)
continue;
const int ImageCount = Pile.ImageCount;
for (int ImageIndex = 0; ImageIndex < ImageCount; ++ImageIndex)
{
const PileImageData &Image = Pile.Images[ImageIndex];
const int PartnerPileIndex = Image.SIPile;
if (PartnerPileIndex == PileIndex)
continue;
const PileData &PartnerPile = Piles[PartnerPileIndex];
const int PartnerFamIndex = PartnerPile.FamIndex;
if (-1 == PartnerFamIndex || PartnerFamIndex == FamIndex)
continue;
const int Index = TriangleSubscript(FamCount, FamIndex, PartnerFamIndex);
assert(Index >- 0 && Index < TriangleSize);
Related[Index] = true;
}
}
}
Edges.clear();
for (int i = 0; i < FamCount; ++i)
for (int j = i + 1; j < FamCount; ++j)
{
const int Index = TriangleSubscript(FamCount, i, j);
if (Related[Index])
{
// Log("R %d %d\n", i, j);
EdgeData Edge;
Edge.Node1 = i;
Edge.Node2 = j;
Edge.Rev = false;
Edges.push_back(Edge);
}
}
}
static void ListState()
{
Log("Dist matrix\n");
Log(" ");
for (unsigned i = 0; i < g_uLeafCount.get(); ++i)
{
if (uInsane == g_uNodeIndex.get()[i])
continue;
Log(" %5u", g_uNodeIndex.get()[i]);
}
Log("\n");
for (unsigned i = 0; i < g_uLeafCount.get(); ++i)
{
if (uInsane == g_uNodeIndex.get()[i])
continue;
Log("%5u ", g_uNodeIndex.get()[i]);
for (unsigned j = 0; j < g_uLeafCount.get(); ++j)
{
if (uInsane == g_uNodeIndex.get()[j])
continue;
if (i == j)
Log(" ");
else
{
unsigned v = TriangleSubscript(i, j);
Log("%5.2g ", g_Dist.get()[v]);
}
}
Log("\n");
}
Log("\n");
Log(" i Node NrNb Dist\n");
Log("----- ----- ----- --------\n");
for (unsigned i = 0; i < g_uLeafCount.get(); ++i)
{
if (uInsane == g_uNodeIndex.get()[i])
continue;
Log("%5u %5u %5u %8.3f\n",
i,
g_uNodeIndex.get()[i],
g_uNearestNeighbor.get()[i],
g_MinDist.get()[i]);
}
Log("\n");
Log(" Node L R Height LLength RLength\n");
Log("----- ----- ----- ------ ------- -------\n");
for (unsigned i = 0; i <= g_uInternalNodeIndex.get(); ++i)
Log("%5u %5u %5u %6.2g %6.2g %6.2g\n",
i,
g_uLeft.get()[i],
g_uRight.get()[i],
g_Height.get()[i],
g_LeftLength.get()[i],
g_RightLength.get()[i]);
}
void UPGMA2(const DistCalc &DC, Tree &tree, LINKAGE Linkage)
{
g_uLeafCount.get() = DC.GetCount();
g_uTriangleSize.get() = (g_uLeafCount.get()*(g_uLeafCount.get() - 1))/2;
g_uInternalNodeCount.get() = g_uLeafCount.get() - 1;
g_Dist.get() = new dist_t[g_uTriangleSize.get()];
g_uNodeIndex.get() = new unsigned[g_uLeafCount.get()];
g_uNearestNeighbor.get() = new unsigned[g_uLeafCount.get()];
g_MinDist.get() = new dist_t[g_uLeafCount.get()];
unsigned *Ids = new unsigned [g_uLeafCount.get()];
char **Names = new char *[g_uLeafCount.get()];
g_uLeft.get() = new unsigned[g_uInternalNodeCount.get()];
g_uRight.get() = new unsigned[g_uInternalNodeCount.get()];
g_Height.get() = new dist_t[g_uInternalNodeCount.get()];
g_LeftLength.get() = new dist_t[g_uInternalNodeCount.get()];
g_RightLength.get() = new dist_t[g_uInternalNodeCount.get()];
for (unsigned i = 0; i < g_uLeafCount.get(); ++i)
{
g_MinDist.get()[i] = BIG_DIST;
g_uNodeIndex.get()[i] = i;
g_uNearestNeighbor.get()[i] = uInsane;
Ids[i] = DC.GetId(i);
Names[i] = strsave(DC.GetName(i));
}
for (unsigned i = 0; i < g_uInternalNodeCount.get(); ++i)
{
g_uLeft.get()[i] = uInsane;
g_uRight.get()[i] = uInsane;
g_LeftLength.get()[i] = BIG_DIST;
g_RightLength.get()[i] = BIG_DIST;
g_Height.get()[i] = BIG_DIST;
}
// Compute initial NxN triangular distance matrix.
// Store minimum distance for each full (not triangular) row.
// Loop from 1, not 0, because "row" is 0, 1 ... i-1,
// so nothing to do when i=0.
for (unsigned i = 1; i < g_uLeafCount.get(); ++i)
{
dist_t *Row = g_Dist.get() + TriangleSubscript(i, 0);
DC.CalcDistRange(i, Row);
for (unsigned j = 0; j < i; ++j)
{
const dist_t d = Row[j];
if (d < g_MinDist.get()[i])
{
g_MinDist.get()[i] = d;
g_uNearestNeighbor.get()[i] = j;
}
if (d < g_MinDist.get()[j])
{
g_MinDist.get()[j] = d;
g_uNearestNeighbor.get()[j] = i;
}
}
}
#if TRACE
Log("Initial state:\n");
ListState();
#endif
for (g_uInternalNodeIndex.get() = 0; g_uInternalNodeIndex.get() < g_uLeafCount.get() - 1;
++g_uInternalNodeIndex.get())
{
#if TRACE
Log("\n");
Log("Internal node index %5u\n", g_uInternalNodeIndex.get());
Log("-------------------------\n");
#endif
// Find nearest neighbors
unsigned Lmin = uInsane;
unsigned Rmin = uInsane;
dist_t dtMinDist = BIG_DIST;
for (unsigned j = 0; j < g_uLeafCount.get(); ++j)
{
if (uInsane == g_uNodeIndex.get()[j])
continue;
dist_t d = g_MinDist.get()[j];
if (d < dtMinDist)
{
dtMinDist = d;
Lmin = j;
Rmin = g_uNearestNeighbor.get()[j];
assert(uInsane != Rmin);
assert(uInsane != g_uNodeIndex.get()[Rmin]);
}
}
assert(Lmin != uInsane);
assert(Rmin != uInsane);
assert(dtMinDist != BIG_DIST);
#if TRACE
Log("Nearest neighbors Lmin %u[=%u] Rmin %u[=%u] dist %.3g\n",
Lmin,
g_uNodeIndex.get()[Lmin],
Rmin,
g_uNodeIndex.get()[Rmin],
dtMinDist);
#endif
// Compute distances to new node
// New node overwrites row currently assigned to Lmin
dist_t dtNewMinDist = BIG_DIST;
unsigned uNewNearestNeighbor = uInsane;
for (unsigned j = 0; j < g_uLeafCount.get(); ++j)
{
if (j == Lmin || j == Rmin)
continue;
if (uInsane == g_uNodeIndex.get()[j])
continue;
const unsigned vL = TriangleSubscript(Lmin, j);
const unsigned vR = TriangleSubscript(Rmin, j);
const dist_t dL = g_Dist.get()[vL];
const dist_t dR = g_Dist.get()[vR];
dist_t dtNewDist;
switch (Linkage)
{
case LINKAGE_Avg:
dtNewDist = AVG(dL, dR);
break;
case LINKAGE_Min:
dtNewDist = MIN(dL, dR);
break;
case LINKAGE_Max:
dtNewDist = MAX(dL, dR);
break;
case LINKAGE_Biased:
dtNewDist = g_dSUEFF.get()*AVG(dL, dR) + (1 - g_dSUEFF.get())*MIN(dL, dR);
break;
default:
Quit("UPGMA2: Invalid LINKAGE_%u", Linkage);
}
// Nasty special case.
// If nearest neighbor of j is Lmin or Rmin, then make the new
// node (which overwrites the row currently occupied by Lmin)
// the nearest neighbor. This situation can occur when there are
// equal distances in the matrix. If we don't make this fix,
// the nearest neighbor pointer for j would become invalid.
// (We don't need to test for == Lmin, because in that case
// the net change needed is zero due to the change in row
// numbering).
if (g_uNearestNeighbor.get()[j] == Rmin)
g_uNearestNeighbor.get()[j] = Lmin;
#if TRACE
Log("New dist to %u = (%u/%.3g + %u/%.3g)/2 = %.3g\n",
j, Lmin, dL, Rmin, dR, dtNewDist);
#endif
g_Dist.get()[vL] = dtNewDist;
if (dtNewDist < dtNewMinDist)
{
dtNewMinDist = dtNewDist;
uNewNearestNeighbor = j;
}
}
assert(g_uInternalNodeIndex.get() < g_uLeafCount.get() - 1 || BIG_DIST != dtNewMinDist);
assert(g_uInternalNodeIndex.get() < g_uLeafCount.get() - 1 || uInsane != uNewNearestNeighbor);
const unsigned v = TriangleSubscript(Lmin, Rmin);
const dist_t dLR = g_Dist.get()[v];
const dist_t dHeightNew = dLR/2;
const unsigned uLeft = g_uNodeIndex.get()[Lmin];
const unsigned uRight = g_uNodeIndex.get()[Rmin];
const dist_t HeightLeft =
uLeft < g_uLeafCount.get() ? 0 : g_Height.get()[uLeft - g_uLeafCount.get()];
const dist_t HeightRight =
uRight < g_uLeafCount.get() ? 0 : g_Height.get()[uRight - g_uLeafCount.get()];
g_uLeft.get()[g_uInternalNodeIndex.get()] = uLeft;
g_uRight.get()[g_uInternalNodeIndex.get()] = uRight;
g_LeftLength.get()[g_uInternalNodeIndex.get()] = dHeightNew - HeightLeft;
g_RightLength.get()[g_uInternalNodeIndex.get()] = dHeightNew - HeightRight;
g_Height.get()[g_uInternalNodeIndex.get()] = dHeightNew;
// Row for left child overwritten by row for new node
g_uNodeIndex.get()[Lmin] = g_uLeafCount.get() + g_uInternalNodeIndex.get();
g_uNearestNeighbor.get()[Lmin] = uNewNearestNeighbor;
g_MinDist.get()[Lmin] = dtNewMinDist;
// Delete row for right child
g_uNodeIndex.get()[Rmin] = uInsane;
#if TRACE
Log("\nInternalNodeIndex=%u Lmin=%u Rmin=%u\n",
g_uInternalNodeIndex.get(), Lmin, Rmin);
ListState();
#endif
}
unsigned uRoot = g_uLeafCount.get() - 2;
tree.Create(g_uLeafCount.get(), uRoot, g_uLeft.get(), g_uRight.get(), g_LeftLength.get(), g_RightLength.get(),
Ids, Names);
#if TRACE
tree.LogMe();
#endif
delete[] g_Dist.get();
delete[] g_uNodeIndex.get();
delete[] g_uNearestNeighbor.get();
delete[] g_MinDist.get();
delete[] g_Height.get();
delete[] g_uLeft.get();
delete[] g_uRight.get();
delete[] g_LeftLength.get();
delete[] g_RightLength.get();
for (unsigned i = 0; i < g_uLeafCount.get(); ++i)
free(Names[i]);
delete[] Names;
delete[] Ids;
}