完整优化的SuffixTree代码

一些朋友提醒，这次一次放出实现了Ukkonen 的paper的三个优化的完整SuffixTree的代码。看了之前博客的只实现SuffixLink优化的代码，再看这个应该就很简单了。

下面是SuffixTree的头文件SuffixTree.h

 

#pragma once

#include <vector>
#include <string>
using namespace std;


class SuffixNode
{
public:
	vector<SuffixNode*> m_pSons;
	SuffixNode* m_pFarther;
	SuffixNode* m_pSuffixLink;
	int m_iPathPos;
	int m_iEdgeStart;
	int m_iEdgeEnd;
};

class SuffixTree
{
public:
	int m_iE;//The virtual end of all leaves.
	SuffixNode* m_pRoot;//The root of the tree.
	string m_czTreeStr;//the string that the tree represent.
};

//Means a sub string of the suffix tree (string[beging],string[end]). 
class TreePath
{
public:
	int m_iBegin;
	int m_iEnd;
};


//Represent the char in a node's incoming edge.
class TreePos
{
public:
	TreePos()
	{
		m_iEdgePos = 0;
		m_pNode = NULL;
	}
	TreePos(int edgePos,SuffixNode* pNode)
	{
		m_iEdgePos = edgePos;
		m_pNode = pNode;
	}
	int m_iEdgePos;//The ith char of the incoming edge.
	SuffixNode* m_pNode;//The node we are going to search.
};


//=====================================Class Declarations============================== 


void SingleCharExtesion(SuffixTree* pTree,TreePos*& pPos ,TreePath extendStrPath,int* firstExtensionFlag,bool * rule3Applied,int* iLeafNum);


/*
  Add s[0....i+1],s[1...i+1].... to the suffix tree
  Input:
  SuffixNode* pNode : When we only use trick 1,pNode is the pointer to the longest leaf,s[0........i].
  phase : Equals i+1 in the paper.
*/
void SinglePhaseExtend(SuffixTree* pTree,TreePos* & pPos,int phase,int* iExtension,int* ruleApplied,bool* lastRule3Applied,int *iLeafNum);



SuffixNode* CreateTreeNode(SuffixNode* pFarther,int iedgeStart,int iedgeEnd,int pathPos);



/*
   FollowSuffixLink :
   Follows the suffix link of the source node according to Ukkonen's rules(jump from s[j-1...i] to s[j....i]). 

   Input : The tree, and node. The node is the last internal node we visited.
   Output: The destination node that represents the longest suffix of node's 
           path. Example: if node represents the path "abcde" then it returns 
           the node that represents "bcde".
*/
void FollowSuffixLink(SuffixTree* pTree,TreePos*& pPos, TreePath strji);



int GetNodeLabelLength(SuffixTree* pTree, SuffixNode* pNode);



int GetNodeLabelEnd(SuffixTree* pTree,SuffixNode* pNode);



/*
  Find the son node which starts with the char,ch.
*/
SuffixNode* Find_Son(SuffixTree* pTree,SuffixNode* pFarNode, char ch);



bool IsTheLastCharInEdge(SuffixTree* pTree, SuffixNode* pNode, int edge_pos);



SuffixNode* ApplyExtensionRule2(SuffixNode* pNode,int edgeLabelBeg,int edgeLabelEnd,int edgePos,int pathPos,bool newLeafFlag);


/*
  Trace the sub string(TreePath str) from the node(SuffixNode* pNode).
  Input:
  int* edgePos : where the last char is found at that edge
  int* charsFound : how many chars of str have been found.
  bool skipFlag : Use skip trick or not.  
*/
SuffixNode* TraceString(SuffixTree* pTree,SuffixNode* pNode,TreePath str,int* edgePos,int* charsFound,bool skipFlag);


/*
  Trace the substring(TreePath strPath) in one single edge out of pNode.
*/
SuffixNode* TraceSingleEdge(SuffixTree* pTree,SuffixNode* pNode,TreePath strPath,int* charsFound,int* edgePos,bool* searchDone,bool skipFlag);


SuffixNode* CreateFirstCharacter(SuffixTree* pTree);//Add the first character to the suffix tree.


SuffixTree* CreateSuffixTree(string tStr);


/*
For Debug:
See if the sub string (from root to pPos) equals pTree->string[subPath.m_iBegin,subPath.m_iEnd]
*/
bool TestPosSubStringEqualPath(SuffixTree* pTree,TreePos *pPos, TreePath subPath);


/*
  For debugging, We want to see if the suffix link from linkFrom to linkTo is right.
*/
bool TestSuffixLinkMatch(SuffixTree *pTree, SuffixNode* linkFrom,SuffixNode *linkTo);


int FindSubString(SuffixTree* pTree,string subStr);
//=====================================================================================

 

下面是SuffixTree的实现文件SuffixTree.cpp

#pragma once

#include "SuffixTree.h"
#include <iostream>
using namespace std;


SuffixNode* pNodeNoSuffixLink=NULL;

//=====================================Class Definitions==============================


/*
  Trace the substring(TreePath strPath) in one single edge going out of pNode.
  Input:
  int* edgeCharsFound : how many characters we find matched in the outgoing edge of pNode.
*/
SuffixNode* TraceSingleEdge(SuffixTree* pTree,SuffixNode* pNode,TreePath strPath,int* edgeCharsFound,int* edgePos,bool* searchDone,bool skipFlag)
{
	//Find outgoing edge of pNode with our first character.
	SuffixNode* nextNode = Find_Son(pTree,pNode,pTree->m_czTreeStr[strPath.m_iBegin]);

	*searchDone = true;

	if(nextNode == NULL)
	{//There is no match in pNode's sons,so we can only return to pNode.
		*edgePos = GetNodeLabelLength(pTree,pNode); 
		*edgeCharsFound = 0;
		return pNode;
	}

	int edgeLen = GetNodeLabelLength(pTree,nextNode);
	int strLen = strPath.m_iEnd - strPath.m_iBegin + 1;

	if(skipFlag == true)//Use the trick1 : skip
	{
		if(edgeLen < strLen)
		{
			*searchDone = false;
			*edgeCharsFound = edgeLen;
			*edgePos = edgeLen - 1;
		}
		else if(edgeLen == strLen)
		{
			*edgeCharsFound = edgeLen;
			*edgePos = edgeLen - 1;
		}
		else
		{
			*edgeCharsFound = strLen;
			*edgePos = strLen - 1;
		}

		return nextNode;
	}


	else//No skip,match each char one after another
	{
		*edgePos = 0;
		*edgeCharsFound = 0;

		//Find out the min length
		if(strLen < edgeLen)
			edgeLen = strLen;

		for(*edgeCharsFound=1,*edgePos=1;(*edgePos)<edgeLen ;(*edgePos)++,(*edgeCharsFound)++)
		{
			if( pTree->m_czTreeStr[ nextNode->m_iEdgeStart + *edgePos ] != pTree->m_czTreeStr[strPath.m_iBegin + *edgePos ])
			{
				(*edgePos)--;
				return nextNode;
			}
		}
	}

	//When it comes here, (*edgePos) is one more;
	(*edgePos)--;

	if(*edgeCharsFound < strLen)
	{
		*searchDone = false;
	}
	return nextNode;
}


/*
  Trace the sub string(TreePath str) from the node(SuffixNode* pNode).
  Input:
  int* edgePos :For output , where the last char is found at that edge
  int* charsFound : How many chars of str have been found.
  bool skipFlag : Use skip trick or not.  
*/
SuffixNode* TraceString(SuffixTree* pTree,SuffixNode* pNode,TreePath str,int* edgePos,int* charsFound,bool skipFlag)
{
	bool searchDone=false;
	*charsFound = 0;
	*edgePos=0 ;
	int edgeCharsFound=0;

	while(searchDone==false)
	{
		edgeCharsFound = 0;
		*edgePos=0;

		pNode = TraceSingleEdge(pTree,pNode,str,&edgeCharsFound,edgePos,&searchDone,skipFlag);

		str.m_iBegin += edgeCharsFound;
		*charsFound += edgeCharsFound;
	}

	//if(*charsFound == 0)
	//	return NULL;

	return pNode;
}



/*
  Input:
   (1) pNode : the node who is going to add a new son or whose edge is going to be split.
   (2) edgeLabelBeg :  when newleafFlag==true,it's the edge begin label of the new leaf. when when newleafFlag==false, it's the edge begin label of the new new leaf( the leaf of s[i+1], not s[i]).
   (3) like above : just the end
   (4 )int edgePos : where split is done to pNode if newLeafFlag==false (the 0th position or 1th position or...)
*/
SuffixNode* ApplyExtensionRule2(SuffixNode* pNode,int edgeLabelBeg,int edgeLabelEnd,int edgePos,int pathPos,bool newLeafFlag)
{
	if(newLeafFlag==true)
	{
		//Add an new leaf
		SuffixNode* newLeaf = CreateTreeNode(pNode,edgeLabelBeg,edgeLabelEnd,pathPos);

		return newLeaf;
	}

	else
	{
		//Add an new internal node and an new leaf

		//First create the new internal node.
		SuffixNode* nInternalNode = CreateTreeNode(pNode->m_pFarther,pNode->m_iEdgeStart,pNode->m_iEdgeStart + edgePos,pNode->m_iPathPos);
		
		//Remove pNode from its farther's sons
		for(vector<SuffixNode*>::iterator pNodeIter=pNode->m_pFarther->m_pSons.begin();
			pNodeIter!=pNode->m_pFarther->m_pSons.end();pNodeIter++)
		{
			if( pNode == *pNodeIter )
			{
				pNode->m_pFarther->m_pSons.erase(pNodeIter);
				break;
			}
		}

		//Adjust pNode's information.
		pNode->m_iEdgeStart += (edgePos + 1);
		pNode->m_pFarther = nInternalNode;
		nInternalNode->m_pSons.push_back(pNode);

		//Create the new leaf for s[i+1]
		SuffixNode* nLeafNode = CreateTreeNode(nInternalNode,edgeLabelBeg,edgeLabelEnd,pathPos);

		return nInternalNode;
	}
}


bool IsTheLastCharInEdge(SuffixTree* pTree, SuffixNode* pNode, int edge_pos)
{
	if( edge_pos == GetNodeLabelLength(pTree,pNode) - 1 )
		return true;
	return false;
}

int GetNodeLabelEnd(SuffixTree* pTree,SuffixNode* pNode)
{
	if(pNode->m_pSons.size() == NULL)
	{
		return pTree->m_iE;
	}
	return pNode->m_iEdgeEnd;
}

int GetNodeLabelLength(SuffixTree* pTree, SuffixNode* pNode)
{
	int length = GetNodeLabelEnd(pTree,pNode) - pNode->m_iEdgeStart + 1;
	return length;
}

SuffixNode* CreateTreeNode(SuffixNode* pFarther,int iedgeStart,int iedgeEnd,int pathPos)
{
	SuffixNode* pNode=new SuffixNode();

	pNode->m_iEdgeStart = iedgeStart;
	pNode->m_iEdgeEnd = iedgeEnd;
	pNode->m_pFarther = pFarther;
	pNode->m_iPathPos = pathPos;
	pNode->m_pSuffixLink = NULL;
	if(pFarther!=NULL)
	pFarther->m_pSons.push_back(pNode);

	return pNode;
}

//Find the son node which starts with the ch
SuffixNode* Find_Son(SuffixTree* pTree,SuffixNode* pFarNode, char ch)
{
	for(vector<SuffixNode*>::iterator nodeIter=pFarNode->m_pSons.begin();
		nodeIter!=pFarNode->m_pSons.end();nodeIter++)
	{
		if(pTree->m_czTreeStr[(*nodeIter) -> m_iEdgeStart] == ch )
		{
			return *nodeIter;
		}
	}
	return NULL;
}


/*
   FollowSuffixLink :
   Follows the suffix link of the source node according to Ukkonen's rules(jump from s[j-1...i] to s[j....i]). 

   Input : The tree, and node. The node is the last internal node we visited.
   Output: The destination node that represents the longest suffix of node's 
           path. Example: if node represents the path "abcde" then it returns 
           the node that represents "bcde".
*/
void FollowSuffixLink(SuffixTree* pTree,TreePos* & pPos,TreePath strji)
{
	/*gama : the string(r in Gusfield's paper) between node and its father.
	If the node doesn't have suffix link , we need to go up to its farther*/
	TreePath gama;

	if(pPos->m_pNode == pTree->m_pRoot)
	{
		pPos->m_iEdgePos = 0;
		return;
	}

	// No suffix link,walk up at most one step(if it is not the root).
	if( pPos->m_pNode->m_pSuffixLink == NULL ) 
	{
		if(pPos->m_pNode->m_pFarther == pTree->m_pRoot)
		{//its farther is the root
			pPos->m_pNode = pTree->m_pRoot;
			pPos->m_iEdgePos = 0;
			return;
		}


		else
		{
			// Find the gamma (the substring between pPos's parent's and pPos's)
			gama.m_iBegin = pPos->m_pNode->m_iEdgeStart;
			gama.m_iEnd = pPos->m_pNode->m_iEdgeStart + pPos->m_iEdgePos;// the end of s[j..i] 

			//Follow farther's suffix link
			pPos->m_pNode = pPos->m_pNode->m_pFarther->m_pSuffixLink;

			//Down-walk gamma (until we found s[i],the character we add last extension)
			int charsFound=0;
			pPos->m_pNode = TraceString(pTree,pPos->m_pNode,gama,&pPos->m_iEdgePos,&charsFound,true);
			////////////////////////////////////////////////
		}
	}
	else
	{
		//A suffix link exists - just follow it.
		pPos->m_pNode = pPos->m_pNode->m_pSuffixLink;
		pPos->m_iEdgePos = GetNodeLabelLength(pTree,pPos->m_pNode) - 1; //The last char of pPos's suffix link represents s[i] (the character we add last extension).
	}
	return;
}


/*
For Debug:
See if the sub string (from root to pPos) equals pTree->string[subPath.m_iBegin,subPath.m_iEnd]
*/
bool TestPosSubStringEqualPath(SuffixTree* pTree,TreePos *pPos, TreePath subPath)
{
	if(pTree->m_pRoot == pPos->m_pNode )
	{
		return true;
	}
	int strRevIndex = subPath.m_iEnd;
	SuffixNode* tmpNode = pPos->m_pNode;
	int edgeRevIndex = tmpNode->m_iEdgeStart + pPos->m_iEdgePos;

	while(tmpNode != pTree->m_pRoot)
	{
		while( edgeRevIndex >= tmpNode->m_iEdgeStart && strRevIndex >= subPath.m_iBegin)
		{
			if( pTree->m_czTreeStr[edgeRevIndex] != pTree->m_czTreeStr[strRevIndex] )
			{
				return false;
			}

			edgeRevIndex--;
			strRevIndex--;
		}

		tmpNode = tmpNode->m_pFarther;
		edgeRevIndex = tmpNode->m_iEdgeEnd;
	}

	if(strRevIndex != subPath.m_iBegin-1)
		return false;

	return true;
}

/*
Input:
(1) SuffixTree* pTree : The suffix tree
(2) TreePos* pPos : The last internal node we visited , then we are going to jump to its suffix link in this extension.
(3) TreePath extendStrPath : The suffix (s[j...i+1]) we are goint to add to the tree.
*/
void SingleCharExtesion(SuffixTree* pTree,TreePos*& pPos ,TreePath extendStrPath,int* ruleApplied,bool* lastRule3Applied,int *iLeafNum)
{
	TreePath sji;
	sji.m_iBegin = extendStrPath.m_iBegin;
	sji.m_iEnd = extendStrPath.m_iEnd - 1;

	int pathPos = extendStrPath.m_iBegin;


	if(*lastRule3Applied == false)
	{
		//Ready to jump from suffix link at or above s[j-1...i] that either has a suffix link to s[j...i] or the root .
		FollowSuffixLink(pTree,pPos,sji);
	}
	else
	{
		*lastRule3Applied = false;
	}


	//////////////////////////////////////////For Debug//////////////////////////////////////////////////
	if(sji.m_iEnd >= sji.m_iBegin)
	{
		if(TestPosSubStringEqualPath(pTree,pPos, sji) == false && pPos->m_pNode != pTree->m_pRoot)
		{
			cout<<"FollowSuffixLink doesn't go to the right s[j..i]:"<<extendStrPath.m_iBegin<<":"<<extendStrPath.m_iEnd-1<<endl;
		}
	}
	///////////////////////////////////////////////////////////////////////////////////////////////////////

	int chars_found=0;

	if(pPos->m_pNode == pTree->m_pRoot && sji.m_iEnd >= sji.m_iBegin)
	{
		pPos->m_pNode = TraceString(pTree,pTree->m_pRoot,sji,&pPos->m_iEdgePos,&chars_found,false);
		if(pPos->m_pNode == NULL)
		{
			pPos->m_iEdgePos = 0;
			pPos->m_pNode =pTree->m_pRoot;

			//////////////////////////////////For Debug//////////////////////////////////////
			if(sji.m_iBegin != sji.m_iEnd)
			{
				cout<<"There is s[j-1..i](not empty) doesn't exist!"<<endl;
				return;
			}
			//////////////////////////////////For Debug//////////////////////////////////////
		}

		//////////////////////////////////For Debug//////////////////////////////////////
		if(sji.m_iEnd != sji.m_iBegin &&  chars_found != sji.m_iEnd - sji.m_iBegin + 1)
		{
			cout<<"s[j...i] doesn't exit from root:["<<sji.m_iBegin<<","<<sji.m_iEnd<<"]"<<endl;
			return;
		}
	}

	//Now we are going to found out which rule to use for extension,rule1?rule2?rule3?
	//First test rule3 and rule1.
	{
		/*
		We only need to extend the last character(s[i+1]) since 
		we use suffix link to jump from s[j-1..i] to s[j..i],
		and extendStrPath.m_iEnd is s[i+1].
		*/
		chars_found = 0;
		/*
		If the last character(s[i]) is the last of its edge,
		try to find s[i+1] in the next edge.
		*/
		if(IsTheLastCharInEdge(pTree,pPos->m_pNode,pPos->m_iEdgePos))
		{
			SuffixNode* pTmp = Find_Son(pTree,pPos->m_pNode,pTree->m_czTreeStr[extendStrPath.m_iEnd]);
			if(pTmp != 0)
			{  //s[i+1] exits already.
				chars_found = 1;

				*ruleApplied = 3; //We found s[i+1] which is already in the tree.
				
				pPos->m_iEdgePos = 0;
				pPos->m_pNode = pTmp;

				if(pNodeNoSuffixLink != NULL)
				{
					pNodeNoSuffixLink->m_pSuffixLink = pPos->m_pNode->m_pFarther;//Let s[j-1..i] jump to s[j...i]
					///////////////////////////For Debug//////////////////////////////////////////////////////////////////
					if(!TestSuffixLinkMatch(pTree,pNodeNoSuffixLink ,pNodeNoSuffixLink->m_pSuffixLink))
					{
						cout<<"Suffix Tree Build Error"<<endl;
					}
					//////////////////////////////////////////////////////////////////
					pNodeNoSuffixLink = NULL;
				}
			}
		}

		//Else see if can find extendStrPath.m_iEnd in the current edge
		else
		{
			if( pTree->m_czTreeStr[ pPos->m_pNode->m_iEdgeStart + pPos->m_iEdgePos + 1]
			    == pTree->m_czTreeStr[extendStrPath.m_iEnd]
				)//Notice that " + 1 " means the next char of s[j...i] : yes, s[i+1]
				{//s[i+1] exits already.
					chars_found = 1;

					if(pPos->m_pNode->m_pSons.size() == 0)//We found s[i+1] in the leaf
					{
						if( pPos->m_iEdgePos + 1 == GetNodeLabelLength(pTree,pPos->m_pNode) - 1) //Rule1 applied, we just add s[i+1] to the leaf.
						{
							*ruleApplied = 1;
						}
						else
						{
							*ruleApplied = 3;
							pPos->m_iEdgePos++;//Go to the s[i+1]
						}
					}
					else//We found s[i+1] in the internal node
					{
						*ruleApplied = 3;
						pPos->m_iEdgePos++;//Go to s[i+1]
						if(pNodeNoSuffixLink != NULL)
						{
							pNodeNoSuffixLink->m_pSuffixLink = pPos->m_pNode;

							///////////////////////////For Debug//////////////////////////////////////////////////////////////////
							if(! TestSuffixLinkMatch(pTree,pNodeNoSuffixLink ,pNodeNoSuffixLink->m_pSuffixLink))
							{
								cout<<"Suffix Tree Build Error"<<endl;
							}
							//////////////////////////////////////////////////////////////////

							pNodeNoSuffixLink = NULL;
						}
					}
				}
		}

	}

	if(chars_found == 1)
	{
		return;
	}



	/*Since rule3 and rule1 doesn't fit ( that s[j...i+1] is not in the tree),
	we are going to see rule2.
	*/ 

	/* If last char s[j...i] found is the last char of an edge - create an new leaf
	,apply rule2(add a new leaf) or rule1 */
	if(IsTheLastCharInEdge(pTree,pPos->m_pNode,pPos->m_iEdgePos) || pPos->m_pNode==pTree->m_pRoot)
	{
		if(pPos->m_pNode->m_pSons.size() != 0)
		{
			//Internal node or root,apply rule2 that add a new leaf
			ApplyExtensionRule2(pPos->m_pNode, extendStrPath.m_iEnd, extendStrPath.m_iEnd, 0, pathPos, true);

			//Suffix Link
			if(pNodeNoSuffixLink != NULL)
			{
				pNodeNoSuffixLink->m_pSuffixLink = pPos->m_pNode;

				///////////////////////////For Debug//////////////////////////////////////////////////////////////////
				if(! TestSuffixLinkMatch(pTree,pNodeNoSuffixLink ,pNodeNoSuffixLink->m_pSuffixLink))
				{
					cout<<"Suffix Tree Build Error"<<endl;
				}
				//////////////////////////////////////////////////////////////////

				pNodeNoSuffixLink = NULL;
			}
			*ruleApplied = 2;
			(*iLeafNum)++;
		}
		//else in a leaf, We do nothing (implicitly add a char to the end of a leaf).
	}

	//Else apply rule2 that adds an new intern node
	else
	{
		SuffixNode* nInternalNode = ApplyExtensionRule2(pPos->m_pNode,extendStrPath.m_iEnd,extendStrPath.m_iEnd,pPos->m_iEdgePos,pathPos,false);

		if(pNodeNoSuffixLink != NULL)
		{
			pNodeNoSuffixLink->m_pSuffixLink = nInternalNode;

			///////////////////////////For Debug//////////////////////////////////////////////////////////////////
			if(! TestSuffixLinkMatch(pTree,pNodeNoSuffixLink ,pNodeNoSuffixLink->m_pSuffixLink))
			{
				cout<<"Suffix Tree Build Error"<<endl;
			}
			//////////////////////////////////////////////////////////////////

			pNodeNoSuffixLink = NULL;
		}
		

		//See the new internal node's suffix link.
		if( GetNodeLabelLength(pTree,nInternalNode)==1 && nInternalNode->m_pFarther == pTree->m_pRoot)
		{
			nInternalNode->m_pSuffixLink = pTree->m_pRoot;
			pNodeNoSuffixLink = NULL;
		}
		else
		{
			pNodeNoSuffixLink = nInternalNode;
		}

		//Adjust the node for the next extension
		pPos->m_pNode = nInternalNode;

		(*iLeafNum)++;

		*ruleApplied = 2;
	}

	return ;
}


/*
  Add s[0....i+1],s[1...i+1].... to the suffix tree
  Input:
  SuffixNode* pNode: When we only use trick 1,pNode is the pointer to the longest leaf,s[0........i].
*/
void SinglePhaseExtend(SuffixTree* pTree,TreePos* & pPos,int phase,int* iExtension,int* ruleApplied,bool *lastRule3Applied,int *iLeafNum)
{
	//pTree->m_iE = phase-1;
	//int ruleApplied=-1;
	while(*iExtension <= phase )
	{
		TreePath extendPath;
		extendPath.m_iBegin = *iExtension;
		extendPath.m_iEnd = phase;

		SingleCharExtesion(pTree,pPos,extendPath,ruleApplied,lastRule3Applied,iLeafNum);

		if(*ruleApplied == 3)//We already found s[j...i+1] which means s[j+1...i+1] and the rest are already in the tree too.
		{
			*lastRule3Applied = true;
			break;
		}

		(*iExtension)++;
	}

	return;
}

SuffixNode* CreateFirstCharacter(SuffixTree* pTree)
{
	pTree->m_iE = 0;
	SuffixNode* firstLeaf = CreateTreeNode(pTree->m_pRoot,0,0,0);
	return firstLeaf;
}

SuffixTree* CreateSuffixTree(string tStr)
{
	SuffixTree* psTree=new SuffixTree();
	psTree->m_czTreeStr = tStr+"$";

	psTree->m_pRoot = CreateTreeNode(NULL,0,0,0);

	//Add the first char into it.
	SuffixNode* firstLeaf = CreateFirstCharacter(psTree);
	TreePos* lastLeafPos = new TreePos(0,firstLeaf);
	int ruleApplied = 2;
	int iExtension = 1;
	int iLeafNum = 1;

	bool lastRule3Applied = false;
	for(int phase = 1 ; phase<psTree->m_czTreeStr.length() ; phase++)
	{
		psTree->m_iE = phase;
		iExtension = iLeafNum;
		//lastLeafPos->m_iEdgePos = lastLeafPos->m_pNode->m_iEdgeEnd - lastLeafPos->m_pNode->m_iEdgeStart; //start from s[j..i]
		SinglePhaseExtend(psTree,lastLeafPos,phase,&iExtension,&ruleApplied,&lastRule3Applied,&iLeafNum);
	}

	return psTree;
}


int FindSubString(SuffixTree* pTree,string subStr)
{
	SuffixNode* node = Find_Son(pTree,pTree->m_pRoot,subStr[0]);
	if(node == NULL)
	{
		return -1;
	}

	int startIndex = node->m_iEdgeStart;

	int strIndex=0;
	int edgeIndex;

	while(node != NULL)
	{
		edgeIndex = node->m_iEdgeStart;
		int edgeLabelEnd = GetNodeLabelEnd(pTree,node);
		while(strIndex < subStr.length() && edgeIndex <= edgeLabelEnd && pTree->m_czTreeStr[edgeIndex] == subStr[strIndex])
		{
			strIndex++;
			edgeIndex++;
		}

		if(strIndex == subStr.length())
		{
			//we found it
			return node->m_iPathPos;
		}
		else if(edgeIndex > node->m_iEdgeEnd)
		{
			node = Find_Son(pTree,node,subStr[strIndex]);
		}
		else
		{
			return -1;
		}
	}

	return -1;
}

/*
  For debugging, We want to see if the suffix link from linkFrom to linkTo is right.
*/
bool TestSuffixLinkMatch(SuffixTree *pTree, SuffixNode* linkFrom,SuffixNode *linkTo)
{
	char ch1,ch2;
	while(linkFrom->m_pFarther->m_pFarther!=pTree->m_pRoot && linkFrom->m_pFarther != pTree->m_pRoot)
	{
		linkFrom = linkFrom->m_pFarther;
	}
	
	if(linkFrom->m_pFarther == pTree->m_pRoot)
	{
		if(linkFrom->m_iEdgeEnd == linkFrom->m_iEdgeStart)
		{
			if(linkTo != pTree->m_pRoot)
			{
				return false;
			}
			else
			{
				return true;
			}
		}
		else
		{
			ch1 = pTree->m_czTreeStr[linkFrom->m_iEdgeStart + 1];
		}
	}
	else
	{
		if(linkFrom->m_pFarther->m_iEdgeStart == linkFrom->m_pFarther->m_iEdgeEnd)
		{
			ch1 = pTree->m_czTreeStr[linkFrom->m_iEdgeStart];
		}
		else
		{
			ch1 = pTree->m_czTreeStr[linkFrom->m_pFarther->m_iEdgeStart + 1];
		}
	}

	while(linkTo->m_pFarther != pTree->m_pRoot)
	{
		linkTo = linkTo->m_pFarther;
	}
	ch2 = pTree->m_czTreeStr[linkTo->m_iEdgeStart];
	
	if(ch1 == ch2)
		return true;
	else
		return false;
}

 

 

最后是调用的主函数，一个简单的判断子串是否在字符串中，如果子串subStr存在于字符创str中，输出它的起点，否则输出不存在。

#include "SuffixTree.h"
#include <string>
#include <iostream>
using namespace std;
int main()
{
 string str="avnaoihvnjovsdvaeveavsfvwevfwa vafjoajv aoja aojfoaj afowajop afoajv afjoajo csvweavefvs  fjwojvwoajv  haovpjvowj ajovwjavo aojvowajv ajvoajv vnaojv vfdvdfvavaewvavaisadnvioenvoehnvPIavnaoihvnjovsdvaeveavsfvwevfwa vafjoajv aoja aojfoaj afowajop afoajv afjoajo csvweavefvs  fjwojvwoajv  haovpjvowj ajovwjavo aojvowajv ajvoajv vnaojv vfdvdfvavaewvavaisadnvioenvoehnvPI";
 string subStr=" vafjoajv aoja aojfoaj afowajop afoajv afjoajo csvweavefvs  fjwojvwoajv  haov";
 SuffixTree* pTree = CreateSuffixTree(str);
 int existFlag = FindSubString(pTree,subStr);
 if(existFlag>=0)
  cout<<"Sub string starts from "<<existFlag<<endl;
 else
  cout<<"sub string doesn't exist"<<endl;
 
 return 0;
}