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#include "muscle.h"
#include "tree.h"
#define TRACE 0
// 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;
}
bool PhyEnumEdgesR(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.FirstDepthFirstNodeR();
ES.m_bInit = true;
}
else
{
uNode1 = tree.NextDepthFirstNodeR(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 void GetLeavesSubtree(const Tree &tree, unsigned uNodeIndex1,
const unsigned uNodeIndex2, unsigned Leaves[], unsigned *ptruCount)
{
if (tree.IsLeaf(uNodeIndex1))
{
Leaves[*ptruCount] = uNodeIndex1;
++(*ptruCount);
return;
}
const unsigned uLeft = tree.GetFirstNeighbor(uNodeIndex1, uNodeIndex2);
const unsigned uRight = tree.GetSecondNeighbor(uNodeIndex1, uNodeIndex2);
if (NULL_NEIGHBOR != uLeft)
GetLeavesSubtree(tree, uLeft, uNodeIndex1, Leaves, ptruCount);
if (NULL_NEIGHBOR != uRight)
GetLeavesSubtree(tree, uRight, uNodeIndex1, Leaves, ptruCount);
}
static void PhyGetLeaves(const Tree &tree, unsigned uNodeIndex1, unsigned uNodeIndex2,
unsigned Leaves[], unsigned *ptruCount)
{
*ptruCount = 0;
GetLeavesSubtree(tree, uNodeIndex1, uNodeIndex2, Leaves, ptruCount);
}
bool PhyEnumBiParts(const Tree &tree, PhyEnumEdgeState &ES,
unsigned Leaves1[], unsigned *ptruCount1,
unsigned Leaves2[], unsigned *ptruCount2)
{
bool bOk = PhyEnumEdges(tree, ES);
if (!bOk)
{
*ptruCount1 = 0;
*ptruCount2 = 0;
return false;
}
// Special case: in a rooted tree, both edges from the root
// give the same bipartition, so skip one of them.
if (tree.IsRooted() && tree.IsRoot(ES.m_uNodeIndex2)
&& tree.GetRight(ES.m_uNodeIndex2) == ES.m_uNodeIndex1)
{
bOk = PhyEnumEdges(tree, ES);
if (!bOk)
return false;
}
PhyGetLeaves(tree, ES.m_uNodeIndex1, ES.m_uNodeIndex2, Leaves1, ptruCount1);
PhyGetLeaves(tree, ES.m_uNodeIndex2, ES.m_uNodeIndex1, Leaves2, ptruCount2);
if (*ptruCount1 + *ptruCount2 != tree.GetLeafCount())
Quit("PhyEnumBiParts %u + %u != %u",
*ptruCount1, *ptruCount2, tree.GetLeafCount());
#if DEBUG
{
for (unsigned i = 0; i < *ptruCount1; ++i)
{
if (!tree.IsLeaf(Leaves1[i]))
Quit("PhyEnumByParts: not leaf");
for (unsigned j = 0; j < *ptruCount2; ++j)
{
if (!tree.IsLeaf(Leaves2[j]))
Quit("PhyEnumByParts: not leaf");
if (Leaves1[i] == Leaves2[j])
Quit("PhyEnumByParts: dupe");
}
}
}
#endif
return true;
}
#if 0
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");
}
}
#endif
static void GetLeavesSubtreeExcluding(const Tree &tree, unsigned uNodeIndex,
unsigned uExclude, unsigned Leaves[], unsigned *ptruCount)
{
if (uNodeIndex == uExclude)
return;
if (tree.IsLeaf(uNodeIndex))
{
Leaves[*ptruCount] = uNodeIndex;
++(*ptruCount);
return;
}
const unsigned uLeft = tree.GetLeft(uNodeIndex);
const unsigned uRight = tree.GetRight(uNodeIndex);
if (NULL_NEIGHBOR != uLeft)
GetLeavesSubtreeExcluding(tree, uLeft, uExclude, Leaves, ptruCount);
if (NULL_NEIGHBOR != uRight)
GetLeavesSubtreeExcluding(tree, uRight, uExclude, Leaves, ptruCount);
}
void GetLeavesExcluding(const Tree &tree, unsigned uNodeIndex,
unsigned uExclude, unsigned Leaves[], unsigned *ptruCount)
{
*ptruCount = 0;
GetLeavesSubtreeExcluding(tree, uNodeIndex, uExclude, Leaves, ptruCount);
}
void GetInternalNodesInHeightOrder(const Tree &tree, unsigned NodeIndexes[])
{
const unsigned uNodeCount = tree.GetNodeCount();
if (uNodeCount < 3)
Quit("GetInternalNodesInHeightOrder: %u nodes, none are internal",
uNodeCount);
const unsigned uInternalNodeCount = (uNodeCount - 1)/2;
double *Heights = new double[uInternalNodeCount];
unsigned uIndex = 0;
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
{
if (tree.IsLeaf(uNodeIndex))
continue;
NodeIndexes[uIndex] = uNodeIndex;
Heights[uIndex] = tree.GetNodeHeight(uNodeIndex);
++uIndex;
}
if (uIndex != uInternalNodeCount)
Quit("Internal error: GetInternalNodesInHeightOrder");
// Simple but slow bubble sort (probably don't care about speed here)
bool bDone = false;
while (!bDone)
{
bDone = true;
for (unsigned i = 0; i < uInternalNodeCount - 1; ++i)
{
if (Heights[i] > Heights[i+1])
{
double dTmp = Heights[i];
Heights[i] = Heights[i+1];
Heights[i+1] = dTmp;
unsigned uTmp = NodeIndexes[i];
NodeIndexes[i] = NodeIndexes[i+1];
NodeIndexes[i+1] = uTmp;
bDone = false;
}
}
}
#if TRACE
Log("Internal node index Height\n");
Log("------------------- --------\n");
// 1234567890123456789 123456789
for (unsigned n = 0; n < uInternalNodeCount; ++n)
Log("%19u %9.3f\n", NodeIndexes[n], Heights[n]);
#endif
delete[] Heights;
}
void ApplyMinEdgeLength(Tree &tree, double dMinEdgeLength)
{
const unsigned uNodeCount = tree.GetNodeCount();
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
{
const unsigned uNeighborCount = tree.GetNeighborCount(uNodeIndex);
for (unsigned n = 0; n < uNeighborCount; ++n)
{
const unsigned uNeighborNodeIndex = tree.GetNeighbor(uNodeIndex, n);
if (!tree.HasEdgeLength(uNodeIndex, uNeighborNodeIndex))
continue;
if (tree.GetEdgeLength(uNodeIndex, uNeighborNodeIndex) < dMinEdgeLength)
tree.SetEdgeLength(uNodeIndex, uNeighborNodeIndex, dMinEdgeLength);
}
}
}
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