C++ Tree::FirstDepthFirstNode方法代码示例

// 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 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
	}

static unsigned GetFirstNodeIndex(const Tree &tree)
	{
	if (g_bStable)
		return 0;
	return tree.FirstDepthFirstNode();
	}

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         ");
		}
//.........这里部分代码省略.........

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;
	}

//.........这里部分代码省略.........
		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])
//.........这里部分代码省略.........