[Outlining] LLVM Suffix Tree (#5821)

This PR adds LLVM's suffix tree data structure to Binaryen. This suffix tree is implemented using Ukkonen's algorithm for linear-time suffix tree construction, and is intended for fast substring queries.

Note: All of the .h and .cpp files included are from LLVM. These files were copied directly instead of imported into our existing LLVM integration (in third_party/) to avoid bumping the commit hash and avoid the potential for complications with upstream changes.

1 files changed, 305 insertions, 0 deletions

diff --git a/src/support/suffix_tree.cpp b/src/support/suffix_tree.cpp
new file mode 100644
index 000000000..a66bcde38
--- /dev/null
+++ b/src/support/suffix_tree.cpp
@@ -0,0 +1,305 @@
+// This file began as an import from LLVM, and so it has the same license as
+// LLVM, copied below together with the code.
+
+//===- 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 "support/suffix_tree.h"
+#include "support/suffix_tree_node.h"
+#include "llvm/Support/Casting.h"
+
+using namespace llvm;
+
+namespace wasm {
+
+/// \returns the number of elements in the substring associated with \p N.
+static size_t numElementsInSubstring(const SuffixTreeNode* N) {
+  assert(N && "Got a null node?");
+  if (auto* Internal = dyn_cast<SuffixTreeInternalNode>(N)) {
+    if (Internal->isRoot()) {
+      return 0;
+    }
+  }
+  return N->getEndIdx() - N->getStartIdx() + 1;
+}
+
+SuffixTree::SuffixTree(const std::vector<unsigned>& Str) : Str(Str) {
+  Root = insertRoot();
+  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(SuffixTreeInternalNode& Parent,
+                                       unsigned StartIdx,
+                                       unsigned Edge) {
+  assert(StartIdx <= LeafEndIdx && "String can't start after it ends!");
+  auto* N = new (LeafNodeAllocator.Allocate())
+    SuffixTreeLeafNode(StartIdx, &LeafEndIdx);
+  Parent.Children[Edge] = N;
+  return N;
+}
+
+SuffixTreeInternalNode*
+SuffixTree::insertInternalNode(SuffixTreeInternalNode* Parent,
+                               unsigned StartIdx,
+                               unsigned EndIdx,
+                               unsigned Edge) {
+  assert(StartIdx <= EndIdx && "String can't start after it ends!");
+  assert(!(!Parent && StartIdx != SuffixTreeNode::EmptyIdx) &&
+         "Non-root internal nodes must have parents!");
+  auto* N = new (InternalNodeAllocator.Allocate())
+    SuffixTreeInternalNode(StartIdx, EndIdx, Root);
+  if (Parent) {
+    Parent->Children[Edge] = N;
+  }
+  return N;
+}
+
+SuffixTreeInternalNode* SuffixTree::insertRoot() {
+  return insertInternalNode(/*Parent = */ nullptr,
+                            SuffixTreeNode::EmptyIdx,
+                            SuffixTreeNode::EmptyIdx,
+                            /*Edge = */ 0);
+}
+
+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();
+    // Length of the current node from the root down to here.
+    CurrNode->setConcatLen(CurrNodeLen);
+    if (auto* InternalNode = dyn_cast<SuffixTreeInternalNode>(CurrNode)) {
+      for (auto& ChildPair : InternalNode->Children) {
+        assert(ChildPair.second && "Node had a null child!");
+        ToVisit.push_back(
+          {ChildPair.second,
+           CurrNodeLen + numElementsInSubstring(ChildPair.second)});
+      }
+    }
+    // No children, so we are at the end of the string.
+    if (auto* LeafNode = dyn_cast<SuffixTreeLeafNode>(CurrNode)) {
+      LeafNode->setSuffixIdx(Str.size() - CurrNodeLen);
+    }
+  }
+}
+
+unsigned SuffixTree::extend(unsigned EndIdx, unsigned SuffixesToAdd) {
+  SuffixTreeInternalNode* 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->setLink(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 = numElementsInSubstring(NextNode);
+
+      // 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.
+        // TODO: Enable the below assert
+        // assert(isa<SuffixTreeInternalNode>(NextNode) &&
+        //       "Expected an internal node?");
+        Active.Idx += SubstringLen;
+        Active.Len -= SubstringLen;
+        Active.Node = cast<SuffixTreeInternalNode>(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->getStartIdx() + 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->setLink(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
+      SuffixTreeInternalNode* SplitNode =
+        insertInternalNode(Active.Node,
+                           NextNode->getStartIdx(),
+                           NextNode->getStartIdx() + 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->incrementStartIdx(Active.Len);
+      SplitNode->Children[Str[NextNode->getStartIdx()]] = NextNode;
+
+      // SplitNode is an internal node, update the suffix link.
+      if (NeedsLink) {
+        NeedsLink->setLink(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->getLink();
+    }
+  }
+
+  return SuffixesToAdd;
+}
+
+void SuffixTree::RepeatedSubstringIterator::advance() {
+  // Clear the current state. If we're at the end of the range, then this
+  // is the state we want to be in.
+  RS = RepeatedSubstring();
+  N = nullptr;
+
+  // Each leaf node represents a repeat of a string.
+  std::vector<unsigned> RepeatedSubstringStarts;
+
+  // Continue visiting nodes until we find one which repeats more than once.
+  while (!InternalNodesToVisit.empty()) {
+    RepeatedSubstringStarts.clear();
+    auto* Curr = InternalNodesToVisit.back();
+    InternalNodesToVisit.pop_back();
+
+    // Keep track of the length of the string associated with the node. If
+    // it's too short, we'll quit.
+    unsigned Length = Curr->getConcatLen();
+
+    // Iterate over each child, saving internal nodes for visiting, and
+    // leaf nodes in LeafChildren. Internal nodes represent individual
+    // strings, which may repeat.
+    for (auto& ChildPair : Curr->Children) {
+      // Save all of this node's children for processing.
+      if (auto* InternalChild =
+            dyn_cast<SuffixTreeInternalNode>(ChildPair.second)) {
+        InternalNodesToVisit.push_back(InternalChild);
+        continue;
+      }
+
+      if (Length < MinLength) {
+        continue;
+      }
+
+      // Have an occurrence of a potentially repeated string. Save it.
+      auto* Leaf = cast<SuffixTreeLeafNode>(ChildPair.second);
+      RepeatedSubstringStarts.push_back(Leaf->getSuffixIdx());
+    }
+
+    // The root never represents a repeated substring. If we're looking at
+    // that, then skip it.
+    if (Curr->isRoot()) {
+      continue;
+    }
+
+    // Do we have any repeated substrings?
+    if (RepeatedSubstringStarts.size() < 2) {
+      continue;
+    }
+
+    // Yes. Update the state to reflect this, and then bail out.
+    N = Curr;
+    RS.Length = Length;
+    for (unsigned StartIdx : RepeatedSubstringStarts) {
+      RS.StartIndices.push_back(StartIdx);
+    }
+    break;
+  }
+  // At this point, either NewRS is an empty RepeatedSubstring, or it was
+  // set in the above loop. Similarly, N is either nullptr, or the node
+  // associated with NewRS.
+}
+
+} // namespace wasm