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< > BotCompany Repo | #1028130 - Suffix Tree Spike v2 [storing substrings efficiently, seems OK]

JavaX source code (Dynamic Module) [tags: use-pretranspiled] - run with: Stefan's OS

Uses 911K of libraries. Click here for Pure Java version (4028L/21K).

!7

// adapted from https://github.com/eugenp/tutorials/tree/master/algorithms-searching/src/main/java/com/baeldung/algorithms/suffixtree

extend Substring {
  bool endsAtEnd() { ret i+l == s.length(); }
}

cmodule SuffixTreeSpike > DynPrintLog {
  switchable S text = "hello world what is up in the world";
  switchable S pattern = "world";
  transient SuffixTree tree;
  
  sclass Node {
    Substring text;
    new L<Node> children;
    int position;

    *(Substring *text, int *position) {}

    Substring getText() { ret text; }
    void setText(Substring text) {
      print("Setting text: " + quote(this.text) + " => " + quote(text);
      this.text = text;
    }

    int getPosition() { ret position; }
    void setPosition(int position) { this.position = position; }
    L<Node> getChildren() { ret children; }
    void setChildren(L<Node> children) { this.children = children; }

    S printTree(String depthIndicator) {
        S str = "";
        S positionStr = position > -1 ? "[" + position + "]" : "";
        str += depthIndicator + text + positionStr + "\n";

        for (int i = 0; i < children.size(); i++)
          str += children.get(i).printTree(depthIndicator + "\t");
        return str;
    }

    toString { ret printTree(""); }
  }
  
  sclass SuffixTree {
    private static final String WORD_TERMINATION = "$";
    private static final int POSITION_UNDEFINED = -1;
    Node root;
    S fullText;
    S textWithTerminator; // all Substrings are constructed off this

    *(S text) {
      textWithTerminator = text + WORD_TERMINATION;
      root = new Node(Substring(textWithTerminator, 0, 0), POSITION_UNDEFINED);
      for i over text:
        addSuffix(Substring(textWithTerminator, i), i);
      fullText = text;
    }

    public LS searchText(S pattern) {
      //LOGGER.info("Searching for pattern \"{}\"", pattern);
      new LS result;
      L<Node> nodes = getAllNodesInTraversePath(pattern, root, false);

      if (nodes.size() > 0) {
          Node lastNode = nodes.get(nodes.size() - 1);
          if (lastNode != null) {
              L<Int> positions = getPositions(lastNode);
              sortInPlace(positions);
              positions.forEach(m -> result.add((markPatternInText(m, pattern))));
          }
      }
      return result;
    }

    private void addSuffix(Substring suffix, int position) {
        print("Adding new suffix: " + quote(suffix));
        List<Node> nodes = getAllNodesInTraversePath(suffix, root, true);
        if (nodes.size() == 0) {
            addChildNode(root, suffix, position);
            //LOGGER.info("{}", printTree());
        } else {
            Node lastNode = nodes.remove(nodes.size() - 1);
            Substring newText = suffix;
            if (nodes.size() > 0) {
                Substring existingSuffixUptoLastNode = joinSubstringObjects(map(nodes, a -> a.getText()));

                // Remove prefix from newText already included in parent
                newText = newText.substring(existingSuffixUptoLastNode.length());
            }
            extendNode(lastNode, newText, position);
            //LOGGER.info("{}", printTree());
        }
    }

    private List<Integer> getPositions(Node node) {
        List<Integer> positions = new ArrayList<>();
        if (node.getText()
            /*.endsWith(WORD_TERMINATION)*/.endsAtEnd()) {
            positions.add(node.getPosition());
        }
        for (int i = 0; i < node.getChildren()
            .size(); i++) {
            positions.addAll(getPositions(node.getChildren()
                .get(i)));
        }
        return positions;
    }

    private String markPatternInText(Integer startPosition, String pattern) {
        String matchingTextLHS = fullText.substring(0, startPosition);
        String matchingText = fullText.substring(startPosition, startPosition + pattern.length());
        String matchingTextRHS = fullText.substring(startPosition + pattern.length());
        return matchingTextLHS + "[" + matchingText + "]" + matchingTextRHS;
    }

    private void addChildNode(Node parentNode, Substring text, int position) {
        parentNode.getChildren()
            .add(new Node(text, position));
    }

    private void extendNode(Node node, Substring newText, int position) {
        Substring currentText = node.getText();
        Substring commonPrefix = getLongestCommonPrefix(currentText, newText);

        if (neq(commonPrefix, currentText)) {
            Substring parentText = currentText.substring(0, commonPrefix.length());
            Substring childText = currentText.substring(commonPrefix.length());
            splitNodeToParentAndChild(node, parentText, childText);
        }

        Substring remainingText = newText.substring(commonPrefix.length());
        addChildNode(node, remainingText, position);
    }

    private void splitNodeToParentAndChild(Node parentNode, Substring parentNewText, Substring childNewText) {
        Node childNode = new Node(childNewText, parentNode.getPosition());

        if (parentNode.getChildren()
            .size() > 0) {
            while (parentNode.getChildren()
                .size() > 0) {
                childNode.getChildren()
                    .add(parentNode.getChildren()
                        .remove(0));
            }
        }

        parentNode.getChildren().add(childNode);
        parentNode.setText(parentNewText);
        parentNode.setPosition(POSITION_UNDEFINED);
    }

    private Substring getLongestCommonPrefix(Substring str1, Substring str2) {
      int compareLength = Math.min(str1.length(), str2.length());
      for (int i = 0; i < compareLength; i++)
          if (str1.charAt(i) != str2.charAt(i))
              ret str1.substring(0, i);
      ret str1.substring(0, compareLength);
    }

    private List<Node> getAllNodesInTraversePath(CharSequence pattern, Node startNode, boolean isAllowPartialMatch) {
        List<Node> nodes = new ArrayList<>();
        for (int i = 0; i < startNode.getChildren().size(); i++) {
            Node currentNode = startNode.getChildren().get(i);
            CharSequence nodeText = currentNode.getText();
            if (empty(nodeText)) fail("Node text empty: " + currentNode);
            if (pattern.charAt(0) == nodeText.charAt(0)) {
                if (isAllowPartialMatch && pattern.length() <= nodeText.length()) {
                    nodes.add(currentNode);
                    return nodes;
                }

                int compareLength = Math.min(nodeText.length(), pattern.length());
                for (int j = 1; j < compareLength; j++) {
                    if (pattern.charAt(j) != nodeText.charAt(j)) {
                        if (isAllowPartialMatch) {
                            nodes.add(currentNode);
                        }
                        return nodes;
                    }
                }

                nodes.add(currentNode);
                if (pattern.length() > compareLength) {
                    List<Node> nodes2 = getAllNodesInTraversePath(subCharSequence(pattern, compareLength), currentNode, isAllowPartialMatch);
                    if (nodes2.size() > 0) {
                        nodes.addAll(nodes2);
                    } else if (!isAllowPartialMatch) {
                        nodes.add(null);
                    }
                }
                return nodes;
            }
        }
        return nodes;
    }

    S printTree() { ret root.printTree(""); }
  }

  start-thread {
    tree = new SuffixTree(text);
    print(tree.printTree());
    print("Estimated tree size: " + nBytes(guessObjectSize(tree)));
    print(+text);
    print(+pattern);
    pnl(tree.searchText(pattern));
  }
}

Author comment

Began life as a copy of #1028128

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Snippet ID: #1028130
Snippet name: Suffix Tree Spike v2 [storing substrings efficiently, seems OK]
Eternal ID of this version: #1028130/18
Text MD5: e425b97cf88c16bf50bdf77698633d61
Transpilation MD5: 747e21e600e736ce64714cb27e224a25
Author: stefan
Category: javax / text searching
Type: JavaX source code (Dynamic Module)
Public (visible to everyone): Yes
Archived (hidden from active list): No
Created/modified: 2020-05-23 12:35:39
Source code size: 7898 bytes / 210 lines
Pitched / IR pitched: No / No
Views / Downloads: 118 / 1891
Version history: 17 change(s)
Referenced in: [show references]

Formerly at http://tinybrain.de/1028130 & http://1028130.tinybrain.de