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BAEL-3480 Java Fast pattern matching using trie and suffix tree

This commit is contained in:
macroscopic64 2020-02-07 23:08:53 +05:30
parent 4e95cec0c3
commit 026324e5a0
3 changed files with 313 additions and 0 deletions
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57
algorithms-searching/src/main/java/com/baeldung/algorithms/suffixtree/Node.java Normal file
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package com.baeldung.algorithms.suffixtree;
import java.util.ArrayList;
import java.util.List;
public class Node {
private String text;
private List<Node> children;
private int position;
public Node(String word, int position) {
this.text = word;
this.position = position;
this.children = new ArrayList<>();
}
public String getText() {
return text;
}
public void setText(String text) {
this.text = text;
}
public int getPosition() {
return position;
}
public void setPosition(int position) {
this.position = position;
}
public List<Node> getChildren() {
return children;
}
public void setChildren(List<Node> children) {
this.children = children;
}
public String printTree(String depthIndicator) {
String str = "";
String positionStr = position > -1 ? "[" + String.valueOf(position) + "]" : "";
str += depthIndicator + text + positionStr + "\n";
for (int i = 0; i < children.size(); i++) {
str += children.get(i)
.printTree(depthIndicator + "\t");
}
return str;
}
@Override
public String toString() {
return printTree("");
}
}

178
algorithms-searching/src/main/java/com/baeldung/algorithms/suffixtree/SuffixTree.java Normal file
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package com.baeldung.algorithms.suffixtree;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class SuffixTree {
private static final Logger LOGGER = LoggerFactory.getLogger(SuffixTree.class);
private static final String WORD_TERMINATION = "$";
private static final int POSITION_UNDEFINED = -1;
private Node root;
private String fullText;
public SuffixTree() {
root = new Node("", POSITION_UNDEFINED);
fullText = "";
}
public void addText(String text) {
for (int i = 0; i < text.length(); i++) {
addSuffix(text.substring(i) + WORD_TERMINATION, i);
}
fullText += text;
}
public List<String> searchText(String pattern) {
LOGGER.info("Searching for pattern \"{}\"", pattern);
List<String> result = new ArrayList<>();
List<Node> nodes = getAllNodesInTraversePath(pattern, root, false);
if (nodes.size() > 0) {
Node lastNode = nodes.get(nodes.size() - 1);
if (lastNode != null) {
List<Integer> positions = getPositions(lastNode);
positions = positions.stream()
.sorted()
.collect(Collectors.toList());
positions.forEach(m -> result.add((markPatternInText(m, pattern))));
}
}
return result;
}
private void addSuffix(String suffix, int position) {
LOGGER.info(">>>>>>>>>>>> Adding new suffix {}", 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);
String newText = suffix;
if (nodes.size() > 0) {
String existingSuffixUptoLastNode = nodes.stream()
.map(a -> a.getText())
.reduce("", String::concat);
// 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)) {
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, String text, int position) {
parentNode.getChildren()
.add(new Node(text, position));
}
private void extendNode(Node node, String newText, int position) {
String currentText = node.getText();
String commonPrefix = getLongestCommonPrefix(currentText, newText);
if (commonPrefix != currentText) {
String parentText = currentText.substring(0, commonPrefix.length());
String childText = currentText.substring(commonPrefix.length());
splitNodeToParentAndChild(node, parentText, childText);
}
String remainingText = newText.substring(commonPrefix.length());
addChildNode(node, remainingText, position);
}
private void splitNodeToParentAndChild(Node parentNode, String parentNewText, String 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 String getLongestCommonPrefix(String str1, String str2) {
int compareLength = Math.min(str1.length(), str2.length());
for (int i = 0; i < compareLength; i++) {
if (str1.charAt(i) != str2.charAt(i)) {
return str1.substring(0, i);
}
}
return str1.substring(0, compareLength);
}
private List<Node> getAllNodesInTraversePath(String 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);
String nodeText = currentNode.getText();
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(pattern.substring(compareLength), currentNode, isAllowPartialMatch);
if (nodes2.size() == 0 && !isAllowPartialMatch) {
nodes.add(null);
return nodes;
}
nodes.addAll(nodes2);
}
return nodes;
}
}
return nodes;
}
public String printTree() {
return root.printTree("");
}
}

78
algorithms-searching/src/test/java/com/baeldung/algorithms/suffixtree/SuffixTreeUnitTest.java Normal file
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package com.baeldung.algorithms.suffixtree;
import java.util.List;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class SuffixTreeUnitTest {
private static final Logger LOGGER = LoggerFactory.getLogger(SuffixTreeUnitTest.class);
private static SuffixTree suffixTree;
@BeforeClass
public static void setUp() {
suffixTree = new SuffixTree();
suffixTree.addText("bananabanana");
printTree();
}
@Test
public void givenSuffixTree_whenSearchingForA_thenReturn6Matches() {
List<String> matches = suffixTree.searchText("a");
matches.stream()
.forEach(m -> LOGGER.info(m));
Assert.assertArrayEquals(new String[] { "b[a]nanabanana", "ban[a]nabanana", "banan[a]banana", "bananab[a]nana", "bananaban[a]na", "bananabanan[a]" }, matches.toArray());
}
@Test
public void givenSuffixTree_whenSearchingForNab_thenReturn1Match() {
List<String> matches = suffixTree.searchText("nab");
matches.stream()
.forEach(m -> LOGGER.info(m));
Assert.assertArrayEquals(new String[] { "bana[nab]anana" }, matches.toArray());
}
@Test
public void givenSuffixTree_whenSearchingForNag_thenReturnNoMatches() {
List<String> matches = suffixTree.searchText("nag");
matches.stream()
.forEach(m -> LOGGER.info(m));
Assert.assertArrayEquals(new String[] {}, matches.toArray());
}
@Test
public void givenSuffixTree_whenSearchingForBanana_thenReturn2Matches() {
List<String> matches = suffixTree.searchText("banana");
matches.stream()
.forEach(m -> LOGGER.info(m));
Assert.assertArrayEquals(new String[] { "[banana]banana", "banana[banana]" }, matches.toArray());
}
@Test
public void givenSuffixTree_whenSearchingForNa_thenReturn4Matches() {
List<String> matches = suffixTree.searchText("na");
matches.stream()
.forEach(m -> LOGGER.info(m));
Assert.assertArrayEquals(new String[] { "ba[na]nabanana", "bana[na]banana", "bananaba[na]na", "bananabana[na]" }, matches.toArray());
}
@Test
public void givenSuffixTree_whenSearchingForX_thenReturnNoMatches() {
List<String> matches = suffixTree.searchText("x");
matches.stream()
.forEach(m -> LOGGER.info(m));
Assert.assertArrayEquals(new String[] {}, matches.toArray());
}
private static void printTree() {
suffixTree.printTree();
LOGGER.info("\n" + suffixTree.printTree());
LOGGER.info("==============================================");
}
}