#include <U2Core/disable-warnings.h>
U2_DISABLE_WARNINGS

#include "muscle.h"
#include "tree.h"

#define TRACE	0

/***
Algorithm to compare two trees, X and Y.

A node x in X and node y in Y are defined to be
similar iff the set of leaves in the subtree under
x is identical to the set of leaves under y.

A node is defined to be dissimilar iff it is not
similar to any node in the other tree.

Nodes x and y are defined to be married iff every
node in the subtree under x is similar to a node
in the subtree under y. Married nodes are considered
to be equal. The subtrees under two married nodes can
at most differ by exchanges of left and right branches,
which we do not consider to be significant here.

A node is defined to be a bachelor iff it is not
married. If a node is a bachelor, then it has a
dissimilar node in its subtree, and it follows
immediately from the definition of marriage that its
parent is also a bachelor. Hence all nodes on the path
from a bachelor node to the root are bachelors.

We assume the trees have the same set of leaves, so
every leaf is trivially both similar and married to
the same leaf in the opposite tree. Bachelor nodes
are therefore always internal (i.e., non-leaf) nodes.

A node is defined to be a diff iff (a) it is married
and (b) its parent is a bachelor. The subtree under
a diff is maximally similar to the other tree. (In
other words, you cannot extend the subtree without
adding a bachelor). 

The set of diffs is the subset of the two trees that
we consider to be identical.

Example:

              -----A
        -----k
   ----j      -----B
--i     -----C
   ------D


              -----A
        -----p
   ----n      -----B
--m     -----D
   ------C


The following pairs of internal nodes are similar.

	Nodes	Set of leaves
	-----	-------------
	k,p		A,B
	i,m		A,B,C,D

Bachelors in the first tree are i and j, bachelors
in the second tree are m and n.

Node k and p are married, but i and m are not (because j
and n are bachelors). The diffs are C, D and k.

The set of bachelor nodes can be viewed as the internal
nodes of a tree, the leaves of which are diffs. (To see
that there can't be disjoint subtrees, note that the path
from a diff to a root is all bachelor nodes, so there is
always a path between two diffs that goes through the root).
We call this tree the "diffs tree".

There is a simple O(N) algorithm to build the diffs tree.
To achieve O(N) we avoid traversing a given subtree multiple
times and also avoid comparing lists of leaves. 

We visit nodes in depth-first order (i.e., a node is visited
before its parent).

If either child of a node is a bachelor, we flag it as
a bachelor.

If both children of the node we are visiting are married,
we check whether the spouses of those children have the
same parent in the other tree. If the parents are different,
the current node is a bachelor. If they have the same parent,
then the node we are visiting is the spouse of that parent.
We assign this newly identified married couple a unique integer
id. The id of a node is in one-to-one correspondence with the
set of leaves in its subtree. Two nodes have the same set of
leaves iff they have the same id. Bachelor nodes do not get
an id.
***/

static void BuildDiffs(const Tree &tree, unsigned uTreeNodeIndex,
  const bool bIsDiff[], Tree &Diffs, unsigned uDiffsNodeIndex,
  unsigned IdToDiffsLeafNodeIndex[])
	{
#if	TRACE
	Log("BuildDiffs(TreeNode=%u IsDiff=%d IsLeaf=%d)\n",
	  uTreeNodeIndex, bIsDiff[uTreeNodeIndex], tree.IsLeaf(uTreeNodeIndex));
#endif
	if (bIsDiff[uTreeNodeIndex])
		{
		unsigned uLeafCount = tree.GetLeafCount();
		unsigned *Leaves = new unsigned[uLeafCount];
		GetLeaves(tree, uTreeNodeIndex, Leaves, &uLeafCount);
		for (unsigned n = 0; n < uLeafCount; ++n)
			{
			const unsigned uLeafNodeIndex = Leaves[n];
			const unsigned uId = tree.GetLeafId(uLeafNodeIndex);
			if (uId >= tree.GetLeafCount())
				Quit("BuildDiffs, id out of range");
			IdToDiffsLeafNodeIndex[uId] = uDiffsNodeIndex;
#if	TRACE
			Log("  Leaf id=%u DiffsNode=%u\n", uId, uDiffsNodeIndex);
#endif
			}
		delete[] Leaves;
		return;
		}

	if (tree.IsLeaf(uTreeNodeIndex))
		Quit("BuildDiffs: should never reach leaf");

	const unsigned uTreeLeft = tree.GetLeft(uTreeNodeIndex);
	const unsigned uTreeRight = tree.GetRight(uTreeNodeIndex);

	const unsigned uDiffsLeft = Diffs.AppendBranch(uDiffsNodeIndex);
	const unsigned uDiffsRight = uDiffsLeft + 1;

	BuildDiffs(tree, uTreeLeft, bIsDiff, Diffs, uDiffsLeft, IdToDiffsLeafNodeIndex);
	BuildDiffs(tree, uTreeRight, bIsDiff, Diffs, uDiffsRight, IdToDiffsLeafNodeIndex);
	}

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;
	}
