void SubFam(const Tree &tree, unsigned uMaxLeafCount, unsigned SubFams[], unsigned *ptruSubFamCount)
{
*ptruSubFamCount = 0;
SubFamRecurse(tree, tree.GetRootNodeIndex(), uMaxLeafCount, SubFams, *ptruSubFamCount);
#if TRACE
{
Log("\n");
Log("Tree:\n");
tree.LogMe();
//void DrawTree(const Tree &tree);
//DrawTree(tree);
Log("\n");
Log("%d subfams:\n", *ptruSubFamCount);
for (unsigned i = 0; i < *ptruSubFamCount; ++i)
Log(" %d=%d", i, SubFams[i]);
Log("\n");
}
#endif
}
void TestBiPart()
{
SetListFileName("c:\\tmp\\lobster.log", false);
Tree tree;
TextFile fileIn("c:\\tmp\\test.phy");
tree.FromFile(fileIn);
tree.LogMe();
const unsigned uNodeCount = tree.GetNodeCount();
unsigned *Leaves1 = new unsigned[uNodeCount];
unsigned *Leaves2 = new unsigned[uNodeCount];
PhyEnumEdgeState ES;
bool bDone = false;
for (;;)
{
unsigned uCount1 = uInsane;
unsigned uCount2 = uInsane;
bool bOk = PhyEnumBiParts(tree, ES, Leaves1, &uCount1, Leaves2, &uCount2);
Log("PEBP=%d ES.Init=%d ES.ni1=%d ES.ni2=%d\n",
bOk,
ES.m_bInit,
ES.m_uNodeIndex1,
ES.m_uNodeIndex2);
if (!bOk)
break;
Log("\n");
Log("Part1: ");
for (unsigned n = 0; n < uCount1; ++n)
Log(" %d(%s)", Leaves1[n], tree.GetLeafName(Leaves1[n]));
Log("\n");
Log("Part2: ");
for (unsigned n = 0; n < uCount2; ++n)
Log(" %d(%s)", Leaves2[n], tree.GetLeafName(Leaves2[n]));
Log("\n");
}
}
void CalcClustalWWeights(const Tree &tree, WEIGHT Weights[])
{
#if TRACE
Log("CalcClustalWWeights\n");
tree.LogMe();
#endif
const unsigned uLeafCount = tree.GetLeafCount();
if (0 == uLeafCount)
return;
else if (1 == uLeafCount)
{
Weights[0] = (WEIGHT) 1.0;
return;
}
else if (2 == uLeafCount)
{
Weights[0] = (WEIGHT) 0.5;
Weights[1] = (WEIGHT) 0.5;
return;
}
if (!tree.IsRooted())
Quit("CalcClustalWWeights requires rooted tree");
const unsigned uNodeCount = tree.GetNodeCount();
unsigned *LeavesUnderNode = new unsigned[uNodeCount];
memset(LeavesUnderNode, 0, uNodeCount*sizeof(unsigned));
const unsigned uRootNodeIndex = tree.GetRootNodeIndex();
unsigned uLeavesUnderRoot = CountLeaves(tree, uRootNodeIndex, LeavesUnderNode);
if (uLeavesUnderRoot != uLeafCount)
Quit("WeightsFromTreee: Internal error, root count %u %u",
uLeavesUnderRoot, uLeafCount);
#if TRACE
Log("Node Leaves Length Strength\n");
Log("---- ------ -------- --------\n");
// 1234 123456 12345678 12345678
#endif
double *Strengths = new double[uNodeCount];
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
{
if (tree.IsRoot(uNodeIndex))
{
Strengths[uNodeIndex] = 0.0;
continue;
}
const unsigned uParent = tree.GetParent(uNodeIndex);
const double dLength = tree.GetEdgeLength(uNodeIndex, uParent);
const unsigned uLeaves = LeavesUnderNode[uNodeIndex];
const double dStrength = dLength / (double) uLeaves;
Strengths[uNodeIndex] = dStrength;
#if TRACE
Log("%4u %6u %8g %8g\n", uNodeIndex, uLeaves, dLength, dStrength);
#endif
}
#if TRACE
Log("\n");
Log(" Seq Path..Weight\n");
Log("-------------------- ------------\n");
#endif
for (unsigned n = 0; n < uLeafCount; ++n)
{
const unsigned uLeafNodeIndex = tree.LeafIndexToNodeIndex(n);
#if TRACE
Log("%20.20s %4u ", tree.GetLeafName(uLeafNodeIndex), uLeafNodeIndex);
#endif
if (!tree.IsLeaf(uLeafNodeIndex))
Quit("CalcClustalWWeights: leaf");
double dWeight = 0;
unsigned uNode = uLeafNodeIndex;
while (!tree.IsRoot(uNode))
{
dWeight += Strengths[uNode];
uNode = tree.GetParent(uNode);
#if TRACE
Log("->%u(%g)", uNode, Strengths[uNode]);
#endif
}
if (dWeight < 0.0001)
{
#if TRACE
Log("zero->one");
#endif
dWeight = 1.0;
}
Weights[n] = (WEIGHT) dWeight;
#if TRACE
Log(" = %g\n", dWeight);
#endif
}
delete[] Strengths;
delete[] LeavesUnderNode;
Normalize(Weights, uLeafCount);
}
void MakeRootMSA(const SeqVect &v, const Tree &GuideTree, ProgNode Nodes[],
MSA &a)
{
#if TRACE
Log("MakeRootMSA Tree=");
GuideTree.LogMe();
#endif
const unsigned uSeqCount = v.GetSeqCount();
unsigned uColCount = uInsane;
unsigned uSeqIndex = 0;
const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
const unsigned uRootNodeIndex = GuideTree.GetRootNodeIndex();
const PWPath &RootPath = Nodes[uRootNodeIndex].m_Path;
const unsigned uRootColCount = RootPath.GetEdgeCount();
const unsigned uEstringSize = uRootColCount + 1;
short *Estring1 = new short[uEstringSize];
short *Estring2 = new short[uEstringSize];
SetProgressDesc("Root alignment");
unsigned uTreeNodeIndex = GetFirstNodeIndex(GuideTree);
do
{
Progress(uSeqIndex, uSeqCount);
unsigned uId = GuideTree.GetLeafId(uTreeNodeIndex);
const Seq &s = *(v[uId]);
Seq sRootE;
short *es = MakeRootSeqE(s, GuideTree, uTreeNodeIndex, Nodes, sRootE,
Estring1, Estring2);
Nodes[uTreeNodeIndex].m_EstringL = EstringNewCopy(es);
#if VALIDATE
Seq sRoot;
MakeRootSeq(s, GuideTree, uTreeNodeIndex, Nodes, sRoot);
if (!sRoot.Eq(sRootE))
{
Log("sRoot=");
sRoot.LogMe();
Log("sRootE=");
sRootE.LogMe();
Quit("Root seqs differ");
}
#if TRACE
Log("MakeRootSeq=\n");
sRoot.LogMe();
#endif
#endif
if (uInsane == uColCount)
{
uColCount = sRootE.Length();
a.SetSize(uSeqCount, uColCount);
}
else
{
assert(uColCount == sRootE.Length());
}
a.SetSeqName(uSeqIndex, s.GetName());
a.SetSeqId(uSeqIndex, uId);
for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)
a.SetChar(uSeqIndex, uColIndex, sRootE[uColIndex]);
++uSeqIndex;
uTreeNodeIndex = GetNextNodeIndex(GuideTree, uTreeNodeIndex);
}
while (NULL_NEIGHBOR != uTreeNodeIndex);
delete[] Estring1;
delete[] Estring2;
ProgressStepsDone();
assert(uSeqIndex == uSeqCount);
}
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;
}
void FindRoot(const Tree &tree, unsigned *ptruNode1, unsigned *ptruNode2,
double *ptrdLength1, double *ptrdLength2,
ROOT RootMethod)
{
#if TRACE
tree.LogMe();
#endif
if (tree.IsRooted())
Quit("FindRoot: tree already rooted");
const unsigned uNodeCount = tree.GetNodeCount();
const unsigned uLeafCount = tree.GetLeafCount();
if (uNodeCount < 2)
Quit("Root: don't support trees with < 2 edges");
EdgeInfo **EIs = new EdgeInfo *[uNodeCount];
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
EIs[uNodeIndex] = new EdgeInfo[3];
EdgeList Edges;
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
if (tree.IsLeaf(uNodeIndex))
{
unsigned uParent = tree.GetNeighbor1(uNodeIndex);
Edges.Add(uParent, uNodeIndex);
}
#if TRACE
Log("Edges: ");
Edges.LogMe();
#endif
// Main loop: iterate until all distances known
double dAllMaxDist = -1e20;
unsigned uMaxFrom = NULL_NEIGHBOR;
unsigned uMaxTo = NULL_NEIGHBOR;
for (;;)
{
EdgeList NextEdges;
#if TRACE
Log("\nTop of main loop\n");
Log("Edges: ");
Edges.LogMe();
Log("MDs:\n");
ListEIs(EIs, uNodeCount);
#endif
// For all edges
const unsigned uEdgeCount = Edges.GetCount();
if (0 == uEdgeCount)
break;
for (unsigned n = 0; n < uEdgeCount; ++n)
{
unsigned uNodeFrom;
unsigned uNodeTo;
Edges.GetEdge(n, &uNodeFrom, &uNodeTo);
CalcInfo(tree, uNodeFrom, uNodeTo, EIs);
#if TRACE
Log("Edge %u -> %u\n", uNodeFrom, uNodeTo);
#endif
const unsigned uNeighborCount = tree.GetNeighborCount(uNodeFrom);
for (unsigned i = 0; i < uNeighborCount; ++i)
{
const unsigned uNeighborIndex = tree.GetNeighbor(uNodeFrom, i);
if (!Known(tree, EIs, uNeighborIndex, uNodeFrom) &&
AllKnownOut(tree, EIs, uNeighborIndex, uNodeFrom))
NextEdges.Add(uNeighborIndex, uNodeFrom);
}
}
Edges.Copy(NextEdges);
}
#if TRACE
ListEIs(EIs, uNodeCount);
#endif
switch (RootMethod)
{
case ROOT_MidLongestSpan:
RootByMidLongestSpan(tree, EIs, ptruNode1, ptruNode2,
ptrdLength1, ptrdLength2);
break;
case ROOT_MinAvgLeafDist:
RootByMinAvgLeafDist(tree, EIs, ptruNode1, ptruNode2,
ptrdLength1, ptrdLength2);
break;
default:
Quit("Invalid RootMethod=%d", RootMethod);
}
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
delete[] EIs[uNodeIndex];
delete[] EIs;
}
void DiffTreesE(const Tree &NewTree, const Tree &OldTree,
unsigned NewNodeIndexToOldNodeIndex[])
{
#if TRACE
Log("DiffTreesE NewTree:\n");
NewTree.LogMe();
Log("\n");
Log("OldTree:\n");
OldTree.LogMe();
#endif
if (!NewTree.IsRooted() || !OldTree.IsRooted())
Quit("DiffTrees: requires rooted trees");
const unsigned uNodeCount = NewTree.GetNodeCount();
const unsigned uOldNodeCount = OldTree.GetNodeCount();
const unsigned uLeafCount = NewTree.GetLeafCount();
const unsigned uOldLeafCount = OldTree.GetLeafCount();
if (uNodeCount != uOldNodeCount || uLeafCount != uOldLeafCount)
Quit("DiffTreesE: different node counts");
{
unsigned *IdToOldNodeIndex = new unsigned[uNodeCount];
for (unsigned uOldNodeIndex = 0; uOldNodeIndex < uNodeCount; ++uOldNodeIndex)
{
if (OldTree.IsLeaf(uOldNodeIndex))
{
unsigned Id = OldTree.GetLeafId(uOldNodeIndex);
IdToOldNodeIndex[Id] = uOldNodeIndex;
}
}
// Initialize NewNodeIndexToOldNodeIndex[]
// All internal nodes are marked as changed, but may be updated later.
for (unsigned uNewNodeIndex = 0; uNewNodeIndex < uNodeCount; ++uNewNodeIndex)
{
if (NewTree.IsLeaf(uNewNodeIndex))
{
unsigned uId = NewTree.GetLeafId(uNewNodeIndex);
assert(uId < uLeafCount);
unsigned uOldNodeIndex = IdToOldNodeIndex[uId];
assert(uOldNodeIndex < uNodeCount);
NewNodeIndexToOldNodeIndex[uNewNodeIndex] = uOldNodeIndex;
}
else
NewNodeIndexToOldNodeIndex[uNewNodeIndex] = NODE_CHANGED;
}
delete[] IdToOldNodeIndex;
}
// Depth-first traversal of tree.
// The order guarantees that a node is visited before
// its parent is visited.
for (unsigned uNewNodeIndex = NewTree.FirstDepthFirstNode();
NULL_NEIGHBOR != uNewNodeIndex;
uNewNodeIndex = NewTree.NextDepthFirstNode(uNewNodeIndex))
{
if (NewTree.IsLeaf(uNewNodeIndex))
continue;
// If either child is changed, flag this node as changed and continue.
unsigned uNewLeft = NewTree.GetLeft(uNewNodeIndex);
unsigned uOldLeft = NewNodeIndexToOldNodeIndex[uNewLeft];
if (NODE_CHANGED == uOldLeft)
{
NewNodeIndexToOldNodeIndex[uNewLeft] = NODE_CHANGED;
continue;
}
unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
unsigned uOldRight = NewNodeIndexToOldNodeIndex[uNewRight];
if (NODE_CHANGED == NewNodeIndexToOldNodeIndex[uNewRight])
{
NewNodeIndexToOldNodeIndex[uNewRight] = NODE_CHANGED;
continue;
}
unsigned uOldParentLeft = OldTree.GetParent(uOldLeft);
unsigned uOldParentRight = OldTree.GetParent(uOldRight);
if (uOldParentLeft == uOldParentRight)
NewNodeIndexToOldNodeIndex[uNewNodeIndex] = uOldParentLeft;
else
NewNodeIndexToOldNodeIndex[uNewNodeIndex] = NODE_CHANGED;
}
#if TRACE
{
Log("NewToOld ");
for (unsigned uNewNodeIndex = 0; uNewNodeIndex < uNodeCount; ++uNewNodeIndex)
{
Log(" [%3u]=", uNewNodeIndex);
if (NODE_CHANGED == NewNodeIndexToOldNodeIndex[uNewNodeIndex])
Log(" X");
else
Log("%3u", NewNodeIndexToOldNodeIndex[uNewNodeIndex]);
if ((uNewNodeIndex+1)%8 == 0)
Log("\n ");
}
Log("\n");
}
#endif
#if DEBUG
{
for (unsigned uNewNodeIndex = 0; uNewNodeIndex < uNodeCount; ++uNewNodeIndex)
{
unsigned uOld = NewNodeIndexToOldNodeIndex[uNewNodeIndex];
if (NewTree.IsLeaf(uNewNodeIndex))
{
if (uOld >= uNodeCount)
{
Log("NewNode=%u uOld=%u > uNodeCount=%u\n",
uNewNodeIndex, uOld, uNodeCount);
Quit("Diff check failed");
}
unsigned uIdNew = NewTree.GetLeafId(uNewNodeIndex);
unsigned uIdOld = OldTree.GetLeafId(uOld);
if (uIdNew != uIdOld)
{
Log("NewNode=%u uOld=%u IdNew=%u IdOld=%u\n",
uNewNodeIndex, uOld, uIdNew, uIdOld);
Quit("Diff check failed");
}
continue;
}
if (NODE_CHANGED == uOld)
continue;
unsigned uNewLeft = NewTree.GetLeft(uNewNodeIndex);
unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
unsigned uOldLeft = OldTree.GetLeft(uOld);
unsigned uOldRight = OldTree.GetRight(uOld);
unsigned uNewLeftPartner = NewNodeIndexToOldNodeIndex[uNewLeft];
unsigned uNewRightPartner = NewNodeIndexToOldNodeIndex[uNewRight];
bool bSameNotRotated = (uNewLeftPartner == uOldLeft && uNewRightPartner == uOldRight);
bool bSameRotated = (uNewLeftPartner == uOldRight && uNewRightPartner == uOldLeft);
if (!bSameNotRotated && !bSameRotated)
{
Log("NewNode=%u NewL=%u NewR=%u\n", uNewNodeIndex, uNewLeft, uNewRight);
Log("OldNode=%u OldL=%u OldR=%u\n", uOld, uOldLeft, uOldRight);
Log("NewLPartner=%u NewRPartner=%u\n", uNewLeftPartner, uNewRightPartner);
Quit("Diff check failed");
}
}
}
#endif
}
void ProgressiveAlign(const SeqVect &v, const Tree &GuideTree, MSA &a)
{
assert(GuideTree.IsRooted());
#if TRACE
Log("GuideTree:\n");
GuideTree.LogMe();
#endif
const unsigned uSeqCount = v.Length();
const unsigned uNodeCount = 2*uSeqCount - 1;
ProgNode *ProgNodes = new ProgNode[uNodeCount];
unsigned uJoin = 0;
unsigned uTreeNodeIndex = GuideTree.FirstDepthFirstNode();
SetProgressDesc("Align node");
do
{
if (GuideTree.IsLeaf(uTreeNodeIndex))
{
if (uTreeNodeIndex >= uNodeCount)
Quit("TreeNodeIndex=%u NodeCount=%u\n", uTreeNodeIndex, uNodeCount);
ProgNode &Node = ProgNodes[uTreeNodeIndex];
unsigned uId = GuideTree.GetLeafId(uTreeNodeIndex);
if (uId >= uSeqCount)
Quit("Seq index out of range");
const Seq &s = *(v[uId]);
Node.m_MSA.FromSeq(s);
Node.m_MSA.SetSeqId(0, uId);
Node.m_uLength = Node.m_MSA.GetColCount();
}
else
{
Progress(uJoin, uSeqCount - 1);
++uJoin;
const unsigned uMergeNodeIndex = uTreeNodeIndex;
ProgNode &Parent = ProgNodes[uMergeNodeIndex];
const unsigned uLeft = GuideTree.GetLeft(uTreeNodeIndex);
const unsigned uRight = GuideTree.GetRight(uTreeNodeIndex);
ProgNode &Node1 = ProgNodes[uLeft];
ProgNode &Node2 = ProgNodes[uRight];
PWPath Path;
AlignTwoMSAs(Node1.m_MSA, Node2.m_MSA, Parent.m_MSA, Path);
Parent.m_uLength = Parent.m_MSA.GetColCount();
Node1.m_MSA.Clear();
Node2.m_MSA.Clear();
}
uTreeNodeIndex = GuideTree.NextDepthFirstNode(uTreeNodeIndex);
}
while (NULL_NEIGHBOR != uTreeNodeIndex);
ProgressStepsDone();
unsigned uRootNodeIndex = GuideTree.GetRootNodeIndex();
const ProgNode &RootProgNode = ProgNodes[uRootNodeIndex];
a.Copy(RootProgNode.m_MSA);
delete[] ProgNodes;
ProgNodes = 0;
}
void DiffTrees(const Tree &Tree1, const Tree &Tree2, Tree &Diffs,
unsigned IdToDiffsLeafNodeIndex[])
{
#if TRACE
Log("Tree1:\n");
Tree1.LogMe();
Log("\n");
Log("Tree2:\n");
Tree2.LogMe();
#endif
if (!Tree1.IsRooted() || !Tree2.IsRooted())
Quit("DiffTrees: requires rooted trees");
const unsigned uNodeCount = Tree1.GetNodeCount();
const unsigned uNodeCount2 = Tree2.GetNodeCount();
const unsigned uLeafCount = Tree1.GetLeafCount();
const unsigned uLeafCount2 = Tree2.GetLeafCount();
assert(uLeafCount == uLeafCount2);
if (uNodeCount != uNodeCount2)
Quit("DiffTrees: different node counts");
// Allocate tables so we can convert tree node index to
// and from the unique id with a O(1) lookup.
unsigned *NodeIndexToId1 = new unsigned[uNodeCount];
unsigned *IdToNodeIndex2 = new unsigned[uNodeCount];
bool *bIsBachelor1 = new bool[uNodeCount];
bool *bIsDiff1 = new bool[uNodeCount];
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
{
NodeIndexToId1[uNodeIndex] = uNodeCount;
bIsBachelor1[uNodeIndex] = false;
bIsDiff1[uNodeIndex] = false;
// Use uNodeCount as value meaning "not set".
IdToNodeIndex2[uNodeIndex] = uNodeCount;
}
// Initialize node index <-> id lookup tables
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
{
if (Tree1.IsLeaf(uNodeIndex))
{
const unsigned uId = Tree1.GetLeafId(uNodeIndex);
if (uId >= uNodeCount)
Quit("Diff trees requires existing leaf ids in range 0 .. (N-1)");
NodeIndexToId1[uNodeIndex] = uId;
}
if (Tree2.IsLeaf(uNodeIndex))
{
const unsigned uId = Tree2.GetLeafId(uNodeIndex);
if (uId >= uNodeCount)
Quit("Diff trees requires existing leaf ids in range 0 .. (N-1)");
IdToNodeIndex2[uId] = uNodeIndex;
}
}
// Validity check. This verifies that the ids
// pre-assigned to the leaves in Tree1 are unique
// (note that the id<N check above does not rule
// out two leaves having duplicate ids).
for (unsigned uId = 0; uId < uLeafCount; ++uId)
{
unsigned uNodeIndex2 = IdToNodeIndex2[uId];
if (uNodeCount == uNodeIndex2)
Quit("DiffTrees, check 2");
}
// Ids assigned to internal nodes are N, N+1 ...
// An internal node id uniquely identifies a set
// of two or more leaves.
unsigned uInternalNodeId = uLeafCount;
// Depth-first traversal of tree.
// The order guarantees that a node is visited before
// its parent is visited.
for (unsigned uNodeIndex1 = Tree1.FirstDepthFirstNode();
NULL_NEIGHBOR != uNodeIndex1;
uNodeIndex1 = Tree1.NextDepthFirstNode(uNodeIndex1))
{
#if TRACE
Log("Main loop: Node1=%u IsLeaf=%d IsBachelor=%d\n",
uNodeIndex1,
Tree1.IsLeaf(uNodeIndex1),
bIsBachelor1[uNodeIndex1]);
#endif
// Leaves are trivial; nothing to do.
if (Tree1.IsLeaf(uNodeIndex1) || bIsBachelor1[uNodeIndex1])
continue;
// If either child is a bachelor, flag
// this node as a bachelor and continue.
unsigned uLeft1 = Tree1.GetLeft(uNodeIndex1);
if (bIsBachelor1[uLeft1])
{
bIsBachelor1[uNodeIndex1] = true;
continue;
}
unsigned uRight1 = Tree1.GetRight(uNodeIndex1);
if (bIsBachelor1[uRight1])
{
bIsBachelor1[uNodeIndex1] = true;
continue;
}
// Both children are married.
// Married nodes are guaranteed to have an id.
unsigned uIdLeft = NodeIndexToId1[uLeft1];
unsigned uIdRight = NodeIndexToId1[uRight1];
if (uIdLeft == uNodeCount || uIdRight == uNodeCount)
Quit("DiffTrees, check 5");
// uLeft2 is the spouse of uLeft1, and similarly for uRight2.
unsigned uLeft2 = IdToNodeIndex2[uIdLeft];
unsigned uRight2 = IdToNodeIndex2[uIdRight];
if (uLeft2 == uNodeCount || uRight2 == uNodeCount)
Quit("DiffTrees, check 6");
// If the spouses of uLeft1 and uRight1 have the same
// parent, then this parent is the spouse of uNodeIndex1.
// Otherwise, uNodeIndex1 is a diff.
unsigned uParentLeft2 = Tree2.GetParent(uLeft2);
unsigned uParentRight2 = Tree2.GetParent(uRight2);
#if TRACE
Log("L1=%u R1=%u L2=%u R2=%u PL2=%u PR2=%u\n",
uLeft1,
uRight1,
uLeft2,
uRight2,
uParentLeft2,
uParentRight2);
#endif
if (uParentLeft2 == uParentRight2)
{
NodeIndexToId1[uNodeIndex1] = uInternalNodeId;
IdToNodeIndex2[uInternalNodeId] = uParentLeft2;
++uInternalNodeId;
}
else
bIsBachelor1[uNodeIndex1] = true;
}
unsigned uDiffCount = 0;
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
{
if (bIsBachelor1[uNodeIndex])
continue;
if (Tree1.IsRoot(uNodeIndex))
{
// Special case: if no bachelors, consider the
// root a diff.
if (!bIsBachelor1[uNodeIndex])
bIsDiff1[uNodeIndex] = true;
continue;
}
const unsigned uParent = Tree1.GetParent(uNodeIndex);
if (bIsBachelor1[uParent])
{
bIsDiff1[uNodeIndex] = true;
++uDiffCount;
}
}
#if TRACE
Log("Tree1:\n");
Log("Node Id Bach Diff Name\n");
Log("---- ---- ---- ---- ----\n");
for (unsigned n = 0; n < uNodeCount; ++n)
{
Log("%4u %4u %d %d",
n,
NodeIndexToId1[n],
bIsBachelor1[n],
bIsDiff1[n]);
if (Tree1.IsLeaf(n))
Log(" %s", Tree1.GetLeafName(n));
Log("\n");
}
Log("\n");
Log("Tree2:\n");
Log("Node Id Name\n");
Log("---- ---- ----\n");
for (unsigned n = 0; n < uNodeCount; ++n)
{
Log("%4u ", n);
if (Tree2.IsLeaf(n))
Log(" %s", Tree2.GetLeafName(n));
Log("\n");
}
#endif
Diffs.CreateRooted();
const unsigned uDiffsRootIndex = Diffs.GetRootNodeIndex();
const unsigned uRootIndex1 = Tree1.GetRootNodeIndex();
for (unsigned n = 0; n < uLeafCount; ++n)
IdToDiffsLeafNodeIndex[n] = uNodeCount;
BuildDiffs(Tree1, uRootIndex1, bIsDiff1, Diffs, uDiffsRootIndex,
IdToDiffsLeafNodeIndex);
#if TRACE
Log("\n");
Log("Diffs:\n");
Diffs.LogMe();
Log("\n");
Log("IdToDiffsLeafNodeIndex:");
for (unsigned n = 0; n < uLeafCount; ++n)
{
if (n%16 == 0)
Log("\n");
else
Log(" ");
Log("%u=%u", n, IdToDiffsLeafNodeIndex[n]);
}
Log("\n");
#endif
for (unsigned n = 0; n < uLeafCount; ++n)
if (IdToDiffsLeafNodeIndex[n] == uNodeCount)
Quit("TreeDiffs check 7");
delete[] NodeIndexToId1;
delete[] IdToNodeIndex2;
delete[] bIsBachelor1;
delete[] bIsDiff1;
}
