C++ Tree::GetParent方法代码示例

void Jacobian::ComputeJacobian(const Tree& tree)
{
	Invalidate();
	jacobian_ = MatrixX(3,tree.GetNumJoint()-1); // à cause de son incrémentation débile
	// Traverse this to find all end effectors
	Vector3 temp;
	Joint* n = tree.GetRoot();
	while (n) {	
		if (n->IsEffector())
		{
			int i = n->GetEffectorNum();
			// Find all ancestors (they will usually all be joints)
			// Set the corresponding entries in the Jacobian J
			Joint* m = tree.GetParent(n);
			while (m) {
				int j = m->GetJointNum();
				assert (0 <=i && i<tree.GetNumEffector() && 0<=j && j<tree.GetNumJoint());
				
				temp = m->GetS();			// joint pos.
				temp -= n->GetS();			// -(end effector pos. - joint pos.)
				Vector3 tmp2 = temp.cross(m->GetW());			// cross product with joint rotation axis
				jacobian_.col(j-1) = tmp2;
				m = tree.GetParent(m);
			}
		}
		n = (n->IsEffector() ? 0 : tree.GetSuccessor(n));
	}
}

void ClusterByHeight(const Tree &tree, double dMaxHeight, unsigned Subtrees[],
                     unsigned *ptruSubtreeCount)
{
    if (!tree.IsRooted())
        Quit("ClusterByHeight: requires rooted tree");

#if	TRACE
    Log("ClusterByHeight, max height=%g\n", dMaxHeight);
#endif

    unsigned uSubtreeCount = 0;
    const unsigned uNodeCount = tree.GetNodeCount();
    for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
    {
        if (tree.IsRoot(uNodeIndex))
            continue;
        unsigned uParent = tree.GetParent(uNodeIndex);
        double dHeight = tree.GetNodeHeight(uNodeIndex);
        double dParentHeight = tree.GetNodeHeight(uParent);

#if	TRACE
        Log("Node %3u  Height %5.2f  ParentHeight %5.2f\n",
            uNodeIndex, dHeight, dParentHeight);
#endif
        if (dParentHeight > dMaxHeight && dHeight <= dMaxHeight)
        {
            Subtrees[uSubtreeCount] = uNodeIndex;
#if	TRACE
            Log("Subtree[%u]=%u\n", uSubtreeCount, uNodeIndex);
#endif
            ++uSubtreeCount;
        }
    }
    *ptruSubtreeCount = uSubtreeCount;
}

// 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;
	}

//测试
int main()
{
    cout<<"树的双亲表示法"<<endl;
	Tree<char> newtree;
	int n;
	cout << "输入树节点数目：";
	cin >> n;
	newtree.CreatK(n);
	cout << "当没有对应数据输出，表示没有" << endl;
	cout << "第三个节点的树的值：" << newtree.GetData(3) << endl;
	cout << "第三个节点的最左子树根节点值：" << newtree.GetLeftMostChild(3, n) << endl;
	cout << "第三个节点的最右子树根节点值：" << newtree.GetRightMostChild(3, n) << endl;
	cout << "第三个节点的父亲节点值：" << newtree.GetParent(3) << endl;
	cout << "根节点值：" << newtree.GetRoot() << endl;
	getchar();
	return 0;
}

// test for sgftree function
// [[Rcpp::export]]
void sgftree_test(std::string sgf)
{
  std::vector<unsigned int> c;
  Tree<std::string> t = MakeSgfBranchTree(sgf);
  Rcpp::Rcout << "get_sgftree() has finished!\n";
  Rcpp::Rcout << "SGF = " << sgf << "\n";
  for (unsigned int i = 0; i < t.size(); i++)
  {
    Rcpp::Rcout << i << " : " << t.Get(i) <<
      "\n  parent = " <<  t.GetParent(i) << "\n  children = ";
    c = t.GetChildren(i);
    for (unsigned int j = 0; j < c.size(); j++)
      Rcpp::Rcout << c[j] << " ";
    Rcpp::Rcout << "\n";
  }

  MakeSgfNodeTree(sgf);
}

static void MakeRootSeq(const Seq &s, const Tree &GuideTree, unsigned uLeafNodeIndex,
  const ProgNode Nodes[], Seq &sRoot)
	{
	sRoot.Copy(s);
	unsigned uNodeIndex = uLeafNodeIndex;
	for (;;)
		{
	  	unsigned uParent = GuideTree.GetParent(uNodeIndex);
		if (NULL_NEIGHBOR == uParent)
			break;
		bool bRight = (GuideTree.GetLeft(uParent) == uNodeIndex);
		uNodeIndex = uParent;
		const PWPath &Path = Nodes[uNodeIndex].m_Path;
		Seq sTmp;
		PathSeq(sRoot, Path, bRight, sTmp);
		sRoot.Copy(sTmp);
		}
	}

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);
//.........这里部分代码省略.........

Tree<std::string> MakeSgfBranchTree(const std::string &sgf)
{
  // parse SGF string and returns a tree of SGF nodes
  // As a special case, where there is no branch in the input,
  // returns a tree with a single node
  Tree<std::string> out;
  unsigned int i0;
  unsigned int opencount = 0;

  // This loop finds the beginning of the first branch
  // Usually, a SGF starts at the first letter, but
  // this handles cases where SGF contains few spaces or
  // junk information before the first parenthesis
  for (unsigned i = 0; i < sgf.size(); i++)
  {
    if (sgf[i] == '(') {
      i0 = i + 1;
      opencount = 1;
      break;
    }
  }

  // Return an empty tree if no branch is found
  if (opencount == 0) return out;

  unsigned int myid = 0;
  int parentid = -1;
  int mystart = i0;
  bool intag = false;   // indicates we are now in tag element
  bool inbranch = true; // indicates we are not in a branch, not in-between
  for (unsigned int i = i0; i < sgf.size(); i++)
  {
    // finish if all node is closed
    if (opencount == 0) break;

    if (!intag && sgf[i] == '(') {
      // new branch opens
      // so, add the current node to the tree
      if (inbranch) out.AddNode(sgf.substr(mystart, i - mystart), parentid);

      opencount++;
      parentid = myid;
      myid = out.size();
      mystart = i + 1;
      inbranch = true;
    } else if (!intag && sgf[i] == ')') {
      // current branch closes
      if (inbranch) out.AddNode(sgf.substr(mystart, i - mystart), parentid);

      opencount--;
      if (opencount == 0) break;

      myid = parentid;
      parentid = out.GetParent(myid);
      inbranch = false;
    } else if (!intag && sgf[i] == '[') {
      // new tag starts
      intag = true;
    } else if (intag && sgf[i] == ']' && sgf[i-1] != '\\') {
      intag = false;
    }
  }

  return out;
}

void Tree::PruneTree(const Tree &tree, unsigned Subfams[],
                     unsigned uSubfamCount)
{
    if (!tree.IsRooted())
        Quit("Tree::PruneTree: requires rooted tree");

    Clear();

    m_uNodeCount = 2*uSubfamCount - 1;
    InitCache(m_uNodeCount);

    const unsigned uUnprunedNodeCount = tree.GetNodeCount();

    unsigned *uUnprunedToPrunedIndex = new unsigned[uUnprunedNodeCount];
    unsigned *uPrunedToUnprunedIndex = new unsigned[m_uNodeCount];

    for (unsigned n = 0; n < uUnprunedNodeCount; ++n)
        uUnprunedToPrunedIndex[n] = NULL_NEIGHBOR;

    for (unsigned n = 0; n < m_uNodeCount; ++n)
        uPrunedToUnprunedIndex[n] = NULL_NEIGHBOR;

// Create mapping between unpruned and pruned node indexes
    unsigned uInternalNodeIndex = uSubfamCount;
    for (unsigned uSubfamIndex = 0; uSubfamIndex < uSubfamCount; ++uSubfamIndex)
    {
        unsigned uUnprunedNodeIndex = Subfams[uSubfamIndex];
        uUnprunedToPrunedIndex[uUnprunedNodeIndex] = uSubfamIndex;
        uPrunedToUnprunedIndex[uSubfamIndex] = uUnprunedNodeIndex;
        for (;;)
        {
            uUnprunedNodeIndex = tree.GetParent(uUnprunedNodeIndex);
            if (tree.IsRoot(uUnprunedNodeIndex))
                break;

            // Already visited this node?
            if (NULL_NEIGHBOR != uUnprunedToPrunedIndex[uUnprunedNodeIndex])
                break;

            uUnprunedToPrunedIndex[uUnprunedNodeIndex] = uInternalNodeIndex;
            uPrunedToUnprunedIndex[uInternalNodeIndex] = uUnprunedNodeIndex;

            ++uInternalNodeIndex;
        }
    }

    const unsigned uUnprunedRootIndex = tree.GetRootNodeIndex();
    uUnprunedToPrunedIndex[uUnprunedRootIndex] = uInternalNodeIndex;
    uPrunedToUnprunedIndex[uInternalNodeIndex] = uUnprunedRootIndex;

#if	TRACE
    {
        Log("Pruned to unpruned:\n");
        for (unsigned i = 0; i < m_uNodeCount; ++i)
            Log(" [%u]=%u", i, uPrunedToUnprunedIndex[i]);
        Log("\n");
        Log("Unpruned to pruned:\n");
        for (unsigned i = 0; i < uUnprunedNodeCount; ++i)
        {
            unsigned n = uUnprunedToPrunedIndex[i];
            if (n != NULL_NEIGHBOR)
                Log(" [%u]=%u", i, n);
        }
        Log("\n");
    }
#endif

    if (uInternalNodeIndex != m_uNodeCount - 1)
        Quit("Tree::PruneTree, Internal error");

// Nodes 0, 1 ... are the leaves
    for (unsigned uSubfamIndex = 0; uSubfamIndex < uSubfamCount; ++uSubfamIndex)
    {
        char szName[32];
        sprintf(szName, "Subfam_%u", uSubfamIndex + 1);
        m_ptrName[uSubfamIndex] = strsave(szName);
    }

    for (unsigned uPrunedNodeIndex = uSubfamCount; uPrunedNodeIndex < m_uNodeCount;
            ++uPrunedNodeIndex)
    {
        unsigned uUnprunedNodeIndex = uPrunedToUnprunedIndex[uPrunedNodeIndex];

        const unsigned uUnprunedLeft = tree.GetLeft(uUnprunedNodeIndex);
        const unsigned uUnprunedRight = tree.GetRight(uUnprunedNodeIndex);

        const unsigned uPrunedLeft = uUnprunedToPrunedIndex[uUnprunedLeft];
        const unsigned uPrunedRight = uUnprunedToPrunedIndex[uUnprunedRight];

        const double dLeftLength =
            tree.GetEdgeLength(uUnprunedNodeIndex, uUnprunedLeft);
        const double dRightLength =
            tree.GetEdgeLength(uUnprunedNodeIndex, uUnprunedRight);

        m_uNeighbor2[uPrunedNodeIndex] = uPrunedLeft;
        m_uNeighbor3[uPrunedNodeIndex] = uPrunedRight;

        m_dEdgeLength1[uPrunedLeft] = dLeftLength;
        m_dEdgeLength1[uPrunedRight] = dRightLength;

//.........这里部分代码省略.........

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.........

//.........这里部分代码省略.........
	// 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])