// Return false when done
bool PhyEnumEdges(const Tree &tree, PhyEnumEdgeState &ES)
{
unsigned uNode1 = uInsane;
if (!ES.m_bInit)
{
if (tree.GetNodeCount() <= 1)
{
ES.m_uNodeIndex1 = NULL_NEIGHBOR;
ES.m_uNodeIndex2 = NULL_NEIGHBOR;
return false;
}
uNode1 = tree.FirstDepthFirstNode();
ES.m_bInit = true;
}
else
{
uNode1 = tree.NextDepthFirstNode(ES.m_uNodeIndex1);
if (NULL_NEIGHBOR == uNode1)
return false;
if (tree.IsRooted() && tree.IsRoot(uNode1))
{
uNode1 = tree.NextDepthFirstNode(uNode1);
if (NULL_NEIGHBOR == uNode1)
return false;
}
}
unsigned uNode2 = tree.GetParent(uNode1);
ES.m_uNodeIndex1 = uNode1;
ES.m_uNodeIndex2 = uNode2;
return true;
}
static unsigned GetNextNodeIndex(const Tree &tree, unsigned uPrevNodeIndex)
{
if (g_bStable)
{
const unsigned uNodeCount = tree.GetNodeCount();
unsigned uNodeIndex = uPrevNodeIndex;
for (;;)
{
++uNodeIndex;
if (uNodeIndex >= uNodeCount)
return NULL_NEIGHBOR;
if (tree.IsLeaf(uNodeIndex))
return uNodeIndex;
}
}
unsigned uNodeIndex = uPrevNodeIndex;
for (;;)
{
uNodeIndex = tree.NextDepthFirstNode(uNodeIndex);
if (NULL_NEIGHBOR == uNodeIndex || tree.IsLeaf(uNodeIndex))
return uNodeIndex;
}
}
static void ProgressiveAlignSubfams(const Tree &tree, const unsigned Subfams[],
unsigned uSubfamCount, const MSA SubfamMSAs[], MSA &msa)
{
const unsigned uNodeCount = tree.GetNodeCount();
bool *Ready = new bool[uNodeCount];
MSA **MSAs = new MSA *[uNodeCount];
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
{
Ready[uNodeIndex] = false;
MSAs[uNodeIndex] = 0;
}
for (unsigned uSubfamIndex = 0; uSubfamIndex < uSubfamCount; ++uSubfamIndex)
{
unsigned uNodeIndex = Subfams[uSubfamIndex];
Ready[uNodeIndex] = true;
MSA *ptrMSA = new MSA;
// TODO: Wasteful copy, needs re-design
ptrMSA->Copy(SubfamMSAs[uSubfamIndex]);
MSAs[uNodeIndex] = ptrMSA;
}
for (unsigned uNodeIndex = tree.FirstDepthFirstNode();
NULL_NEIGHBOR != uNodeIndex;
uNodeIndex = tree.NextDepthFirstNode(uNodeIndex))
{
if (tree.IsLeaf(uNodeIndex))
continue;
unsigned uRight = tree.GetRight(uNodeIndex);
unsigned uLeft = tree.GetLeft(uNodeIndex);
if (!Ready[uRight] || !Ready[uLeft])
continue;
MSA *ptrLeft = MSAs[uLeft];
MSA *ptrRight = MSAs[uRight];
assert(ptrLeft != 0 && ptrRight != 0);
MSA *ptrParent = new MSA;
PWPath Path;
AlignTwoMSAs(*ptrLeft, *ptrRight, *ptrParent, Path);
MSAs[uNodeIndex] = ptrParent;
Ready[uNodeIndex] = true;
Ready[uLeft] = false;
Ready[uRight] = false;
delete MSAs[uLeft];
delete MSAs[uRight];
MSAs[uLeft] = 0;
MSAs[uRight] = 0;
}
#if DEBUG
{
unsigned uReadyCount = 0;
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
{
if (Ready[uNodeIndex])
{
assert(tree.IsRoot(uNodeIndex));
++uReadyCount;
assert(0 != MSAs[uNodeIndex]);
}
else
assert(0 == MSAs[uNodeIndex]);
}
assert(1 == uReadyCount);
}
#endif
const unsigned uRoot = tree.GetRootNodeIndex();
MSA *ptrRootAlignment = MSAs[uRoot];
msa.Copy(*ptrRootAlignment);
delete ptrRootAlignment;
delete[] Ready;
#if TRACE
Log("After refine subfamilies, root alignment=\n");
msa.LogMe();
#endif
}
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 ProgAlignSubFams()
{
MSA msaOut;
SetOutputFileName(g_pstrOutFileName.get());
SetInputFileName(g_pstrInFileName.get());
SetMaxIters(g_uMaxIters.get());
SetSeqWeightMethod(g_SeqWeight1.get());
TextFile fileIn(g_pstrInFileName.get());
SeqVect v;
v.FromFASTAFile(fileIn);
const unsigned uSeqCount = v.Length();
if (0 == uSeqCount)
Quit("No sequences in input file");
ALPHA Alpha = ALPHA_Undefined;
switch (g_SeqType.get())
{
case SEQTYPE_Auto:
Alpha = v.GuessAlpha();
break;
case SEQTYPE_Protein:
Alpha = ALPHA_Amino;
break;
case SEQTYPE_DNA:
Alpha = ALPHA_DNA;
break;
case SEQTYPE_RNA:
Alpha = ALPHA_RNA;
break;
default:
Quit("Invalid seq type");
}
SetAlpha(Alpha);
v.FixAlpha();
PTR_SCOREMATRIX UserMatrix = 0;
if (0 != g_pstrMatrixFileName.get())
{
const char *FileName = g_pstrMatrixFileName.get();
const char *Path = getenv("MUSCLE_MXPATH");
if (Path != 0)
{
size_t n = strlen(Path) + 1 + strlen(FileName) + 1;
char *NewFileName = new char[n];
sprintf(NewFileName, "%s/%s", Path, FileName);
FileName = NewFileName;
}
TextFile File(FileName);
UserMatrix = ReadMx(File);
g_Alpha = ALPHA_Amino;
g_PPScore = PPSCORE_SP;
}
SetPPScore();
if (0 != UserMatrix)
g_ptrScoreMatrix = UserMatrix;
if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
{
SetPPScore(PPSCORE_SPN);
g_Distance1.get() = DISTANCE_Kmer4_6;
}
unsigned uMaxL = 0;
unsigned uTotL = 0;
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
{
unsigned L = v.GetSeq(uSeqIndex).Length();
uTotL += L;
if (L > uMaxL)
uMaxL = L;
}
SetIter(1);
g_bDiags.get() = g_bDiags1.get();
SetSeqStats(uSeqCount, uMaxL, uTotL/uSeqCount);
SetMuscleSeqVect(v);
MSA::SetIdCount(uSeqCount);
// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
v.SetSeqId(uSeqIndex, uSeqIndex);
if (uSeqCount > 1)
MHackStart(v);
if (0 == uSeqCount)
{
msaOut.Clear();
return;
}
if (1 == uSeqCount && ALPHA_Amino == Alpha)
{
const Seq &s = v.GetSeq(0);
msaOut.FromSeq(s);
return;
}
Tree GuideTree;
TreeFromSeqVect(v, GuideTree, g_Cluster1.get(), g_Distance1.get(), g_Root1.get());
SetMuscleTree(GuideTree);
MSA msa;
if (g_bLow.get())
{
ProgNode *ProgNodes = 0;
ProgNodes = ProgressiveAlignE(v, GuideTree, msa);
delete[] ProgNodes;
}
else
ProgressiveAlign(v, GuideTree, msa);
SetCurrentAlignment(msa);
TreeFromMSA(msa, GuideTree, g_Cluster2.get(), g_Distance2.get(), g_Root2.get());
SetMuscleTree(GuideTree);
unsigned *SubFams = new unsigned[uSeqCount];
unsigned uSubFamCount;
SubFam(GuideTree, g_uMaxSubFamCount.get(), SubFams, &uSubFamCount);
SetProgressDesc("Align node");
const unsigned uNodeCount = 2*uSeqCount - 1;
ProgNode *ProgNodes = new ProgNode[uNodeCount];
bool *NodeIsSubFam = new bool[uNodeCount];
bool *NodeInSubFam = new bool[uNodeCount];
for (unsigned i = 0; i < uNodeCount; ++i)
{
NodeIsSubFam[i] = false;
NodeInSubFam[i] = false;
}
for (unsigned i = 0; i < uSubFamCount; ++i)
{
unsigned uNodeIndex = SubFams[i];
assert(uNodeIndex < uNodeCount);
NodeIsSubFam[uNodeIndex] = true;
SetInFam(GuideTree, uNodeIndex, NodeInSubFam);
}
unsigned uJoin = 0;
unsigned uTreeNodeIndex = GuideTree.FirstDepthFirstNode();
do
{
if (NodeIsSubFam[uTreeNodeIndex])
{
#if TRACE
Log("Node %d: align subfam\n", uTreeNodeIndex);
#endif
ProgNode &Node = ProgNodes[uTreeNodeIndex];
AlignSubFam(v, GuideTree, uTreeNodeIndex, Node.m_MSA);
Node.m_uLength = Node.m_MSA.GetColCount();
}
else if (!NodeInSubFam[uTreeNodeIndex])
{
#if TRACE
Log("Node %d: align two subfams\n", uTreeNodeIndex);
#endif
Progress(uJoin, uSubFamCount - 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();
}
else
{
#if TRACE
Log("Node %d: in subfam\n", uTreeNodeIndex);
#endif
;
}
uTreeNodeIndex = GuideTree.NextDepthFirstNode(uTreeNodeIndex);
}
while (NULL_NEIGHBOR != uTreeNodeIndex);
ProgressStepsDone();
unsigned uRootNodeIndex = GuideTree.GetRootNodeIndex();
ProgNode &RootProgNode = ProgNodes[uRootNodeIndex];
TextFile fOut(g_pstrOutFileName.get(), true);
MHackEnd(RootProgNode.m_MSA);
RootProgNode.m_MSA.ToFile(fOut);
delete[] NodeInSubFam;
delete[] NodeIsSubFam;
delete[] ProgNodes;
delete[] SubFams;
ProgNodes = 0;
NodeInSubFam = 0;
NodeIsSubFam = 0;
SubFams = 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;
}
