suffixtree.cpp

   1 /*
   2  *  suffixtree.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 12/15/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  *      This is my half-assed attempt to implement a suffix tree.  This is a cobbled together algorithm using materials that
   9  *      I found at http://marknelson.us/1996/08/01/suffix-trees/ and:
  10  *
  11  *              Ukkonen E. (1995). On-line construction of suffix trees. Algorithmica 14 (3): 249--260
  12  *              Gusfield, Dan (1999). Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology.
  13  *                      USA: Cambridge University Press
  14  *
  15  *      The Ukkonen paper is the seminal paper describing the on-line method of constructing a suffix tree.
  16  *
  17  *      I have chosen to store the nodes of the tree as a vector of pointers to SuffixNode objects.  The root is stored at
  18  *      nodeVector[0].  Each tree also stores the sequence name and the string that corresponds to the actual sequence.
  19  *      Finally, this class provides a way of counting the number of suffixes that are needed in one tree to generate a new
  20  *      sequence (countSuffixes).  This method is used to determine similarity between sequences and was inspired by the
  21  *      article and Perl source code provided at http://www.ddj.com/web-development/184416093.
  22  *
  23  */
  24
  25 #include "sequence.hpp"
  26 #include "suffixnodes.hpp"
  27 #include "suffixtree.hpp"
  28
  29
  30 //********************************************************************************************************************
  31
  32 inline bool compareParents(SuffixNode* left, SuffixNode* right){//      this is necessary to print the tree and to sort the
  33         return (left->getParentNode() < right->getParentNode());        //      nodes in order of their parent
  34 }
  35
  36 //********************************************************************************************************************
  37
  38 SuffixTree::SuffixTree(){}
  39
  40 //********************************************************************************************************************
  41
  42 SuffixTree::~SuffixTree(){
  43         for(int i=0;i<nodeVector.size();i++){   delete nodeVector[i];   }
  44 }
  45
  46 //********************************************************************************************************************
  47
  48 void SuffixTree::loadSequence(Sequence* seq){
  49         nodeCounter = 0;                                                        //      initially there are 0 nodes in the tree
  50         activeStartPosition = 0;
  51         activeEndPosition = -1;
  52         seqName = seq->getName();
  53         sequence = seq->convert2ints();
  54         sequence += '5';                                                        //      this essentially concatenates a '$' to the end of the sequence to
  55         int seqLength = sequence.length();                      //      make it a cononical suffix tree
  56
  57         nodeVector.push_back(new SuffixBranch(-1, 0, -1));      //      enter the root of the suffix tree
  58
  59         activeNode = root = 0;
  60         string hold;
  61         for(int i=0;i<seqLength;i++){
  62                 addPrefix(i);                                                   //      step through the sequence adding each prefix
  63         }
  64 }
  65
  66 //********************************************************************************************************************
  67
  68 string SuffixTree::getSeqName() {
  69         return seqName;
  70 }
  71
  72 //********************************************************************************************************************
  73
  74 void SuffixTree::print(){
  75         vector<SuffixNode*> hold = nodeVector;
  76         sort(hold.begin(), hold.end(), compareParents);
  77         cout << "Address\t\tParent\tNode\tSuffix\tStartC\tEndC\tSuffix" << endl;
  78         for(int i=1;i<=nodeCounter;i++){
  79                 hold[i]->print(sequence, i);
  80         }
  81 }
  82
  83 //********************************************************************************************************************
  84
  85 int SuffixTree::countSuffixes(string compareSequence, int& minValue){   //      here we count the number of suffix parts
  86                                                                                                                         //      we need to rewrite a user supplied sequence.  if the
  87         int numSuffixes = 0;                                                                    //      count exceeds the supplied minValue, bail out.  The
  88         int seqLength = compareSequence.length();                               //      time complexity should be O(L)
  89         int position = 0;
  90
  91         int presentNode = 0;
  92
  93         while(position < seqLength){            //      while the position in the query sequence isn't at the end...
  94
  95                 if(numSuffixes > minValue)      {       return 1000000;         }       //      bail if the count gets too high
  96
  97                 int newNode = nodeVector[presentNode]->getChild(compareSequence[position]);     //      see if the current node has a
  98                                                                                                                                 //      child that matches the next character in the query
  99                 if(newNode == -1){
 100                         if(presentNode == 0){   position++;             }                       //      if not, go back to the root and increase the count
 101                         numSuffixes++;                                                                          //      by one.
 102                         presentNode = 0;
 103                 }
 104                 else{                                                                                                   //      if there is, move to that node and see how far down
 105                         presentNode = newNode;                                                          //      it we can get
 106
 107                         for(int i=nodeVector[newNode]->getStartCharPos(); i<=nodeVector[newNode]->getEndCharPos(); i++){
 108                                 if(compareSequence[position] == sequence[i]){
 109                                         position++;                                                                     //      as long as the query and branch agree, keep going
 110                                 }
 111                                 else{
 112                                         numSuffixes++;                                                          //      if there is a mismatch, increase the number of
 113                                         presentNode = 0;                                                        //      suffixes and go back to the root
 114                                         break;
 115                                 }
 116                         }
 117                 }
 118                 //      if we get all the way through the node we'll go to the top of the while loop and find the child node
 119                 //      that corresponds to what we are interested in
 120         }
 121         numSuffixes--;                                                                                          //      the method puts an extra count on numSuffixes
 122
 123         if(numSuffixes < minValue)      {       minValue = numSuffixes; }       //      if the count is less than the previous minValue,
 124         return numSuffixes;                                                                                     //      change the value and return the number of suffixes
 125
 126 }
 127
 128 //********************************************************************************************************************
 129
 130 void SuffixTree::canonize(){    //      if you have to ask how this works, you don't really want to know and this really
 131                                                                 //      isn't the place to ask.
 132         if ( isExplicit() == 0 ) {      //      if the node has no children...
 133
 134                 int tempNodeIndex = nodeVector[activeNode]->getChild(sequence[activeStartPosition]);
 135                 SuffixNode* tempNode = nodeVector[tempNodeIndex];
 136
 137                 int span = tempNode->getEndCharPos() - tempNode->getStartCharPos();
 138
 139                 while ( span <= ( activeEndPosition - activeStartPosition ) ) {
 140
 141             activeStartPosition = activeStartPosition + span + 1;
 142
 143                         activeNode = tempNodeIndex;
 144
 145             if ( activeStartPosition <= activeEndPosition ) {
 146                                 tempNodeIndex = nodeVector[tempNodeIndex]->getChild(sequence[activeStartPosition]);
 147                                 tempNode = nodeVector[tempNodeIndex];
 148                                 span = tempNode->getEndCharPos() - tempNode->getStartCharPos();
 149             }
 150
 151         }
 152     }
 153 }
 154
 155 //********************************************************************************************************************
 156
 157 int SuffixTree::split(int nodeIndex, int position){     //      leaves stay leaves, etc, to split a leaf we make a new interior
 158                                                                                                         //      node and reconnect everything
 159         SuffixNode* node = nodeVector[nodeIndex];                                       //      get the node that needs to be split
 160         SuffixNode* parentNode = nodeVector[node->getParentNode()];     //      get it's parent node
 161
 162         parentNode->eraseChild(sequence[node->getStartCharPos()]);      //      erase the present node from the registry of its parent
 163
 164         nodeCounter++;
 165         SuffixNode* newNode = new SuffixBranch(node->getParentNode(), node->getStartCharPos(), node->getStartCharPos() + activeEndPosition - activeStartPosition);      //      create a new node that will link the parent with the old child
 166         parentNode->setChildren(sequence[newNode->getStartCharPos()], nodeCounter);//   give the parent the new child
 167         nodeVector.push_back(newNode);
 168
 169         node->setParentNode(nodeCounter);       //      give the original node the new node as its parent
 170         newNode->setChildren(sequence[node->getStartCharPos() + activeEndPosition - activeStartPosition + 1], nodeIndex);
 171         //      put the original node in the registry of the new node's children
 172         newNode->setSuffixNode(activeNode);//link the new node with the old active node
 173
 174         //      recalculate the startCharPosition of the outermost node
 175         node->setStartCharPos(node->getStartCharPos() + activeEndPosition - activeStartPosition + 1 );
 176
 177         return node->getParentNode();
 178 }
 179
 180 //********************************************************************************************************************
 181
 182 void SuffixTree::makeSuffixLink(int& previous, int present){
 183
 184 //      here we link the nodes that are suffixes of one another to rapidly speed through the tree
 185         if ( previous > 0 ) {   nodeVector[previous]->setSuffixNode(present);   }
 186         else                            {       /*      do nothing                                                              */      }
 187
 188     previous = present;
 189 }
 190
 191 //********************************************************************************************************************
 192
 193 void SuffixTree::addPrefix(int prefixPosition){
 194
 195         int lastParentNode = -1;        //      we need to place a new prefix in the suffix tree
 196         int parentNode = 0;
 197
 198         while(1){
 199
 200                 parentNode = activeNode;
 201
 202                 if(isExplicit() == 1){  //      if the node is explicit (has kids), try to follow it down the branch if its there...
 203                         if(nodeVector[activeNode]->getChild(sequence[prefixPosition]) != -1){   //      break out and get next prefix...
 204                                 break;
 205                         }
 206                         else{                           //      ...otherwise continue, we'll need to make a new node later on...
 207                         }
 208                 }
 209                 else{                                   //      if it's not explicit (no kids), read through and see if all of the chars agree...
 210                         int tempNode = nodeVector[activeNode]->getChild(sequence[activeStartPosition]);
 211                         int span = activeEndPosition - activeStartPosition;
 212
 213                         if(sequence[nodeVector[tempNode]->getStartCharPos() + span + 1] == sequence[prefixPosition] ){
 214                                 break;                  //      if the existing suffix agrees with the new one, grab a new prefix...
 215                         }
 216                         else{
 217                                 parentNode = split(tempNode, prefixPosition);   //      ... otherwise we need to split the node
 218                         }
 219
 220                 }
 221
 222                 nodeCounter++;  //      we need to generate a new node here if the kid didn't exist, or we split a node
 223                 SuffixNode* newSuffixLeaf = new SuffixLeaf(parentNode, prefixPosition, sequence.length()-1);
 224                 nodeVector[parentNode]->setChildren(sequence[prefixPosition], nodeCounter);
 225                 nodeVector.push_back(newSuffixLeaf);
 226
 227                 makeSuffixLink( lastParentNode, parentNode );           //      make a suffix link for the parent node
 228
 229                 if(nodeVector[activeNode]->getParentNode() == -1){      //      move along the start position for the tree
 230             activeStartPosition++;
 231         }
 232                 else {
 233             activeNode = nodeVector[activeNode]->getSuffixNode();
 234                 }
 235                 canonize();                                                                                     //      frankly, i'm not entirely clear on what canonize does.
 236         }
 237
 238         makeSuffixLink( lastParentNode, parentNode );
 239         activeEndPosition++;                                                                    //      move along the end position for the tree
 240
 241         canonize();                                                                                             //      frankly, i'm not entirely clear on what canonize does.
 242
 243 }
 244
 245 //********************************************************************************************************************
 246