SuffixTree.cpp

Go to the documentation of this file.

//===- llvm/Support/SuffixTree.cpp - Implement Suffix Tree ------*- C++ -*-===//
//
// Part of the LLVM Project, under the Apache License v2.0 with LLVM Exceptions.
// See https://llvm.org/LICENSE.txt for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
//===----------------------------------------------------------------------===//
//
// This file implements the Suffix Tree class.
//
//===----------------------------------------------------------------------===//
 
#include "llvm/Support/SuffixTree.h"
#include "llvm/Support/Allocator.h"
#include <vector>
 
using namespace llvm;
 
SuffixTree::SuffixTree(const std::vector<unsigned> &Str) : Str(Str) {
  Root = insertInternalNode(nullptr, EmptyIdx, EmptyIdx, 0);
  Active.Node = Root;
 
  // Keep track of the number of suffixes we have to add of the current
  // prefix.
  unsigned SuffixesToAdd = 0;
 
  // Construct the suffix tree iteratively on each prefix of the string.
  // PfxEndIdx is the end index of the current prefix.
  // End is one past the last element in the string.
  for (unsigned PfxEndIdx = 0, End = Str.size(); PfxEndIdx < End; PfxEndIdx++) {
    SuffixesToAdd++;
    LeafEndIdx = PfxEndIdx; // Extend each of the leaves.
    SuffixesToAdd = extend(PfxEndIdx, SuffixesToAdd);
  }
 
  // Set the suffix indices of each leaf.
  assert(Root && "Root node can't be nullptr!");
  setSuffixIndices();
}
 
SuffixTreeNode *SuffixTree::insertLeaf(SuffixTreeNode &Parent,
                                       unsigned StartIdx, unsigned Edge) {
 
  assert(StartIdx <= LeafEndIdx && "String can't start after it ends!");
 
  SuffixTreeNode *N = new (NodeAllocator.Allocate())
      SuffixTreeNode(StartIdx, &LeafEndIdx, nullptr);
  Parent.Children[Edge] = N;
 
  return N;
}
 
SuffixTreeNode *SuffixTree::insertInternalNode(SuffixTreeNode *Parent,
                                               unsigned StartIdx,
                                               unsigned EndIdx, unsigned Edge) {
 
  assert(StartIdx <= EndIdx && "String can't start after it ends!");
  assert(!(!Parent && StartIdx != EmptyIdx) &&
         "Non-root internal nodes must have parents!");
 
  unsigned *E = new (InternalEndIdxAllocator) unsigned(EndIdx);
  SuffixTreeNode *N =
      new (NodeAllocator.Allocate()) SuffixTreeNode(StartIdx, E, Root);
  if (Parent)
    Parent->Children[Edge] = N;
 
  return N;
}
 
void SuffixTree::setSuffixIndices() {
  // List of nodes we need to visit along with the current length of the
  // string.
  std::vector<std::pair<SuffixTreeNode *, unsigned>> ToVisit;
 
  // Current node being visited.
  SuffixTreeNode *CurrNode = Root;
 
  // Sum of the lengths of the nodes down the path to the current one.
  unsigned CurrNodeLen = 0;
  ToVisit.push_back({CurrNode, CurrNodeLen});
  while (!ToVisit.empty()) {
    std::tie(CurrNode, CurrNodeLen) = ToVisit.back();
    ToVisit.pop_back();
    CurrNode->ConcatLen = CurrNodeLen;
    for (auto &ChildPair : CurrNode->Children) {
      assert(ChildPair.second && "Node had a null child!");
      ToVisit.push_back(
          {ChildPair.second, CurrNodeLen + ChildPair.second->size()});
    }
 
    // No children, so we are at the end of the string.
    if (CurrNode->Children.size() == 0 && !CurrNode->isRoot())
      CurrNode->SuffixIdx = Str.size() - CurrNodeLen;
  }
}
 
unsigned SuffixTree::extend(unsigned EndIdx, unsigned SuffixesToAdd) {
  SuffixTreeNode *NeedsLink = nullptr;
 
  while (SuffixesToAdd > 0) {
 
    // Are we waiting to add anything other than just the last character?
    if (Active.Len == 0) {
      // If not, then say the active index is the end index.
      Active.Idx = EndIdx;
    }
 
    assert(Active.Idx <= EndIdx && "Start index can't be after end index!");
 
    // The first character in the current substring we're looking at.
    unsigned FirstChar = Str[Active.Idx];
 
    // Have we inserted anything starting with FirstChar at the current node?
    if (Active.Node->Children.count(FirstChar) == 0) {
      // If not, then we can just insert a leaf and move to the next step.
      insertLeaf(*Active.Node, EndIdx, FirstChar);
 
      // The active node is an internal node, and we visited it, so it must
      // need a link if it doesn't have one.
      if (NeedsLink) {
        NeedsLink->Link = Active.Node;
        NeedsLink = nullptr;
      }
    } else {
      // There's a match with FirstChar, so look for the point in the tree to
      // insert a new node.
      SuffixTreeNode *NextNode = Active.Node->Children[FirstChar];
 
      unsigned SubstringLen = NextNode->size();
 
      // Is the current suffix we're trying to insert longer than the size of
      // the child we want to move to?
      if (Active.Len >= SubstringLen) {
        // If yes, then consume the characters we've seen and move to the next
        // node.
        Active.Idx += SubstringLen;
        Active.Len -= SubstringLen;
        Active.Node = NextNode;
        continue;
      }
 
      // Otherwise, the suffix we're trying to insert must be contained in the
      // next node we want to move to.
      unsigned LastChar = Str[EndIdx];
 
      // Is the string we're trying to insert a substring of the next node?
      if (Str[NextNode->StartIdx + Active.Len] == LastChar) {
        // If yes, then we're done for this step. Remember our insertion point
        // and move to the next end index. At this point, we have an implicit
        // suffix tree.
        if (NeedsLink && !Active.Node->isRoot()) {
          NeedsLink->Link = Active.Node;
          NeedsLink = nullptr;
        }
 
        Active.Len++;
        break;
      }
 
      // The string we're trying to insert isn't a substring of the next node,
      // but matches up to a point. Split the node.
      //
      // For example, say we ended our search at a node n and we're trying to
      // insert ABD. Then we'll create a new node s for AB, reduce n to just
      // representing C, and insert a new leaf node l to represent d. This
      // allows us to ensure that if n was a leaf, it remains a leaf.
      //
      //   | ABC  ---split--->  | AB
      //   n                    s
      //                     C / \ D
      //                      n   l
 
      // The node s from the diagram
      SuffixTreeNode *SplitNode =
          insertInternalNode(Active.Node, NextNode->StartIdx,
                             NextNode->StartIdx + Active.Len - 1, FirstChar);
 
      // Insert the new node representing the new substring into the tree as
      // a child of the split node. This is the node l from the diagram.
      insertLeaf(*SplitNode, EndIdx, LastChar);
 
      // Make the old node a child of the split node and update its start
      // index. This is the node n from the diagram.
      NextNode->StartIdx += Active.Len;
      SplitNode->Children[Str[NextNode->StartIdx]] = NextNode;
 
      // SplitNode is an internal node, update the suffix link.
      if (NeedsLink)
        NeedsLink->Link = SplitNode;
 
      NeedsLink = SplitNode;
    }
 
    // We've added something new to the tree, so there's one less suffix to
    // add.
    SuffixesToAdd--;
 
    if (Active.Node->isRoot()) {
      if (Active.Len > 0) {
        Active.Len--;
        Active.Idx = EndIdx - SuffixesToAdd + 1;
      }
    } else {
      // Start the next phase at the next smallest suffix.
      Active.Node = Active.Node->Link;
    }
  }
 
  return SuffixesToAdd;
}