├── go.mod ├── edge.go ├── suffixtree_test.go ├── README.md ├── node.go ├── suffixtree.go └── LICENSE /go.mod: -------------------------------------------------------------------------------- 1 | module github.com/ljfuyuan/suffixtree 2 | 3 | go 1.14 4 | -------------------------------------------------------------------------------- /edge.go: -------------------------------------------------------------------------------- 1 | package suffixtree 2 | 3 | type edge struct { 4 | label []rune 5 | *node 6 | } 7 | 8 | func newEdge(label []rune, node *node) *edge { 9 | return &edge{label: label, node: node} 10 | } 11 | -------------------------------------------------------------------------------- /suffixtree_test.go: -------------------------------------------------------------------------------- 1 | package suffixtree 2 | 3 | import ( 4 | "fmt" 5 | "testing" 6 | ) 7 | 8 | func TestSuffixTree(t *testing.T) { 9 | words := []string{"banana", "apple", "中文app"} 10 | tree := NewGeneralizedSuffixTree() 11 | for k, word := range words { 12 | tree.Put(word, k) 13 | } 14 | indexes := tree.Search("a", -1) 15 | 16 | if len(indexes) != 3 { 17 | t.Error("indexes len should be 3,but ", len(indexes)) 18 | } 19 | fmt.Println(indexes) 20 | for _, index := range indexes { 21 | fmt.Println(words[index]) 22 | } 23 | 24 | indexes = tree.Search("文", 0) 25 | 26 | if len(indexes) != 1 && indexes[0] != 2 { 27 | t.Error("indexes len should be 1 and indexes[0] must be 2,but ", len(indexes)) 28 | } 29 | 30 | printnode("\t", tree.root) 31 | } 32 | 33 | func printnode(flag string, n *node) { 34 | for _, e := range n.edges { 35 | fmt.Printf("%s %s %v \n", flag, string(e.label), e.node.data) 36 | printnode(flag+"\t-", e.node) 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Generalized Suffix Tree 2 | A Go implementation of a Generalized Suffix Tree using Ukkonen's algorithm 3 | 4 | The package just translate from Alessandro Bahgat Shehata's java version to golang and do some optimization 5 | For more details, you should look at [abahgat/suffixtree](https://github.com/abahgat/suffixtree/) 6 | 7 | ## Usage 8 | 9 | ```go 10 | package main 11 | 12 | import ( 13 | "fmt" 14 | 15 | "github.com/ljfuyuan/suffixtree" 16 | ) 17 | 18 | func main() { 19 | words := []string{"banana", "apple", "中文app"} 20 | tree := suffixtree.NewGeneralizedSuffixTree() 21 | for k, word := range words { 22 | tree.Put(word, k) 23 | } 24 | indexes := tree.Search("a", -1) 25 | 26 | fmt.Println(indexes) 27 | //[0 2 1] 28 | for _, index := range indexes { 29 | fmt.Println(words[index]) 30 | } 31 | //banana 32 | //中文app 33 | //apple 34 | } 35 | ``` 36 | 37 | ## License 38 | 39 | This Generalized Suffix Tree is released under the Apache License 2.0 40 | 41 | Licensed under the Apache License, Version 2.0 (the "License"); 42 | you may not use this file except in compliance with the License. 43 | You may obtain a copy of the License at 44 | 45 | http://www.apache.org/licenses/LICENSE-2.0 46 | 47 | Unless required by applicable law or agreed to in writing, software 48 | distributed under the License is distributed on an "AS IS" BASIS, 49 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 50 | See the License for the specific language governing permissions and 51 | limitations under the License. 52 | -------------------------------------------------------------------------------- /node.go: -------------------------------------------------------------------------------- 1 | package suffixtree 2 | 3 | import ( 4 | "sort" 5 | ) 6 | 7 | type node struct { 8 | /* 9 | * The payload array used to store the data (indexes) associated with this node. 10 | * In this case, it is used to store all property indexes. 11 | */ 12 | data []int 13 | /** 14 | * The set of edges starting from this node 15 | */ 16 | edges []*edge 17 | /** 18 | * The suffix link as described in Ukkonen's paper. 19 | * if str is the string denoted by the path from the root to this, this.suffix 20 | * is the node denoted by the path that corresponds to str without the first rune. 21 | */ 22 | suffix *node 23 | } 24 | 25 | /* 26 | * getData returns the first numElements elements from the ones associated to this node. 27 | * 28 | * Gets data from the payload of both this node and its children, the string representation 29 | * of the path to this node is a substring of the one of the children nodes. 30 | * 31 | * @param numElements the number of results to return. Use <=0 to get all 32 | * @return the first numElements associated to this node and children 33 | */ 34 | func (n *node) getData(numElements int) (ret []int) { 35 | 36 | if numElements > 0 { 37 | if numElements > len(n.data) { 38 | numElements -= len(n.data) 39 | ret = n.data 40 | } else { 41 | ret = n.data[:numElements] 42 | return 43 | } 44 | } else { 45 | ret = n.data 46 | } 47 | 48 | // need to get more matches from child nodes. This is what may waste time 49 | for _, edge := range n.edges { 50 | data := edge.node.getData(numElements) 51 | NEXTIDX: 52 | for _, idx := range data { 53 | for _, v := range ret { 54 | if v == idx { 55 | continue NEXTIDX 56 | } 57 | } 58 | 59 | if numElements > 0 { 60 | numElements-- 61 | } 62 | ret = append(ret, idx) 63 | } 64 | 65 | if numElements == 0 { 66 | break 67 | } 68 | } 69 | 70 | return 71 | } 72 | 73 | // addRef adds the given index to the set of indexes associated with this 74 | func (n *node) addRef(index int) { 75 | if n.contains(index) { 76 | return 77 | } 78 | n.addIndex(index) 79 | // add this reference to all the suffixes as well 80 | iter := n.suffix 81 | for iter != nil { 82 | if iter.contains(index) { 83 | break 84 | } 85 | iter.addRef(index) 86 | iter = iter.suffix 87 | } 88 | } 89 | 90 | func (n *node) contains(index int) bool { 91 | i := sort.SearchInts(n.data, index) 92 | return i < len(n.data) && n.data[i] == index 93 | } 94 | 95 | func (n *node) addEdge(r rune, e *edge) { 96 | if idx := n.search(r); idx == -1 { 97 | n.edges = append(n.edges, e) 98 | sort.Slice(n.edges, func(i, j int) bool { return n.edges[i].label[0] < n.edges[j].label[0] }) 99 | } else { 100 | n.edges[idx] = e 101 | } 102 | 103 | } 104 | 105 | func (n *node) getEdge(r rune) *edge { 106 | idx := n.search(r) 107 | if idx < 0 { 108 | return nil 109 | } 110 | return n.edges[idx] 111 | } 112 | 113 | func (n *node) search(r rune) int { 114 | idx := sort.Search(len(n.edges), func(i int) bool { return n.edges[i].label[0] >= r }) 115 | if idx < len(n.edges) && n.edges[idx].label[0] == r { 116 | return idx 117 | } 118 | 119 | return -1 120 | } 121 | 122 | func (n *node) addIndex(idx int) { 123 | n.data = append(n.data, idx) 124 | } 125 | 126 | func newNode() *node { 127 | return &node{} 128 | } 129 | -------------------------------------------------------------------------------- /suffixtree.go: -------------------------------------------------------------------------------- 1 | // Package suffixtree implements A Generalized Suffix Tree, based on the Ukkonen's paper "On-line construction of suffix trees" 2 | package suffixtree 3 | 4 | import ( 5 | "strings" 6 | "unicode/utf8" 7 | ) 8 | 9 | type generalizedSuffixTree struct { 10 | root *node //The root of the suffix tree 11 | activeLeaf *node //The last leaf that was added during the update operation 12 | } 13 | 14 | // Search search for the given word within the GST and returns at most the given number of matches. 15 | // numElments <= 0 get all matches 16 | func (t *generalizedSuffixTree) Search(word string, numElements int) []int { 17 | node := t.searchNode(word) 18 | if node == nil { 19 | return nil 20 | } 21 | return node.getData(numElements) 22 | } 23 | 24 | // searchNode returns the tree node (if present) that corresponds to the given string. 25 | func (t *generalizedSuffixTree) searchNode(word string) *node { 26 | /* 27 | * Verifies if exists a path from the root to a node such that the concatenation 28 | * of all the labels on the path is a superstring of the given word. 29 | * If such a path is found, the last node on it is returned. 30 | */ 31 | var currentNode *node = t.root 32 | var currentEdge *edge 33 | var i int 34 | 35 | for i < len(word) { 36 | rune, _ := utf8.DecodeRuneInString(word[i:]) 37 | currentEdge = currentNode.getEdge(rune) 38 | if currentEdge == nil { 39 | // there is no edge starting with this rune 40 | return nil 41 | } else { 42 | label := string(currentEdge.label) 43 | lenToMatch := len(word) - i 44 | if lenToMatch > len(label) { 45 | lenToMatch = len(label) 46 | } 47 | if word[i:i+lenToMatch] != label[:lenToMatch] { 48 | // the label on the edge does not correspond to the one in the string to search 49 | return nil 50 | } 51 | 52 | if len(label) >= len(word)-i { 53 | return currentEdge.node 54 | } else { 55 | // advance to next node 56 | currentNode = currentEdge.node 57 | i += lenToMatch 58 | } 59 | } 60 | } 61 | 62 | return nil 63 | } 64 | 65 | // Put adds the specified index to the GST under the given key. 66 | func (t *generalizedSuffixTree) Put(key string, index int) { 67 | // reset activeLeaf 68 | t.activeLeaf = t.root 69 | s := t.root 70 | runes := []rune(key) 71 | 72 | // proceed with tree construction (closely related to procedure in 73 | // Ukkonen's paper) 74 | var text []rune 75 | // iterate over the string, one rune at a time 76 | for k, r := range runes { 77 | // line 6 78 | text = append(text, r) 79 | // line 7: update the tree with the new transitions due to this new rune 80 | s, text = t.update(s, text, runes[k:], index) 81 | // line 8: make sure the active pair is canonical 82 | s, text = t.canonize(s, text) 83 | } 84 | 85 | // add leaf suffix link, is necessary 86 | if t.activeLeaf.suffix == nil && t.activeLeaf != t.root && t.activeLeaf != s { 87 | t.activeLeaf.suffix = s 88 | } 89 | } 90 | 91 | /* 92 | * update updates the tree starting from inputNode and by adding stringPart. 93 | * 94 | * Returns a reference (*node,[]rune) pair for the string that has been added so far. 95 | * This means: 96 | * - the Node will be the Node that can be reached by the longest path string (S1) 97 | * that can be obtained by concatenating consecutive edges in the tree and 98 | * that is a substring of the string added so far to the tree. 99 | * - the String will be the remainder that must be added to S1 to get the string 100 | * added so far. 101 | * 102 | * @param inputNode the node to start from 103 | * @param stringPart the string to add to the tree 104 | * @param rest the rest of the string 105 | * @param value the value to add to the index 106 | */ 107 | func (t *generalizedSuffixTree) update(inputNode *node, stringPart []rune, rest []rune, value int) (s *node, runes []rune) { 108 | s = inputNode 109 | runes = stringPart 110 | newRune := stringPart[len(stringPart)-1] 111 | 112 | // line 1 113 | oldroot := t.root 114 | 115 | // line 1b 116 | endpoint, r := t.testAndSplit(s, stringPart[:len(stringPart)-1], newRune, rest, value) 117 | 118 | var leaf *node 119 | // line 2 120 | for !endpoint { 121 | // line 3 122 | tempEdge := r.getEdge(newRune) 123 | if tempEdge != nil { 124 | // such a node is already present. This is one of the main differences from Ukkonen's case: 125 | // the tree can contain deeper nodes at this stage because different strings were added by previous iterations. 126 | leaf = tempEdge.node 127 | } else { 128 | // must build a new leaf 129 | leaf = newNode() 130 | leaf.addRef(value) 131 | newedge := newEdge(rest, leaf) 132 | r.addEdge(newRune, newedge) 133 | } 134 | 135 | // update suffix link for newly created leaf 136 | if t.activeLeaf != t.root { 137 | t.activeLeaf.suffix = leaf 138 | } 139 | t.activeLeaf = leaf 140 | 141 | // line 4 142 | if oldroot != t.root { 143 | oldroot.suffix = r 144 | } 145 | 146 | // line 5 147 | oldroot = r 148 | 149 | // line 6 150 | if s.suffix == nil { // root node 151 | // this is a special case to handle what is referred to as node _|_ on the paper 152 | runes = runes[1:] 153 | } else { 154 | n, b := t.canonize(s.suffix, safeCutLastChar(runes)) 155 | s = n 156 | // use intern to ensure that runes is a reference from the string pool 157 | runes = append(b, runes[len(runes)-1]) 158 | } 159 | 160 | // line 7 161 | endpoint, r = t.testAndSplit(s, safeCutLastChar(runes), newRune, rest, value) 162 | } 163 | 164 | // line 8 165 | if oldroot != t.root { 166 | oldroot.suffix = r 167 | } 168 | 169 | return 170 | } 171 | 172 | /* 173 | * canonize return a (*node, []rune) (n, remainder) pair such that n is a farthest descendant of 174 | * s (the input node) that can be reached by following a path of edges denoting 175 | * a prefix of inputstr and remainder will be string that must be 176 | * appended to the concatenation of labels from s to n to get inpustr. 177 | */ 178 | func (t *generalizedSuffixTree) canonize(s *node, runes []rune) (*node, []rune) { 179 | 180 | currentNode := s 181 | if len(runes) > 0 { 182 | g := s.getEdge(runes[0]) 183 | // descend the tree as long as a proper label is found 184 | for g != nil && strings.Index(string(runes), string(g.label)) == 0 { 185 | runes = runes[len(g.label):] 186 | currentNode = g.node 187 | if len(runes) > 0 { 188 | g = currentNode.getEdge(runes[0]) 189 | } 190 | } 191 | } 192 | return currentNode, runes 193 | } 194 | 195 | /* 196 | * testAndSplit tests whether the string stringPart + r is contained in the subtree that has inputs as root. 197 | * If that's not the case, and there exists a path of edges e1, e2, ... such that 198 | * e1.label + e2.label + ... + $end = stringPart 199 | * and there is an edge g such that 200 | * g.label = stringPart + rest 201 | * 202 | * Then g will be split in two different edges, one having $end as label, and the other one 203 | * having rest as label. 204 | * 205 | * @param inputs the starting node 206 | * @param stringPart the string to search 207 | * @param r the following character 208 | * @param remainder the remainder of the string to add to the index 209 | * @param value the value to add to the index 210 | * @return a pair containing 211 | * true/false depending on whether (stringPart + t) is contained in the subtree starting in inputs 212 | * the last node that can be reached by following the path denoted by stringPart starting from inputs 213 | * 214 | */ 215 | func (t *generalizedSuffixTree) testAndSplit(inputs *node, stringPart []rune, r rune, remainder []rune, value int) (bool, *node) { 216 | // descend the tree as far as possible 217 | s, str := t.canonize(inputs, stringPart) 218 | 219 | if len(str) > 0 { 220 | g := s.getEdge(str[0]) 221 | 222 | // must see whether "str" is substring of the label of an edge 223 | if len(g.label) > len(str) && g.label[len(str)] == r { 224 | return true, s 225 | } else { 226 | // need to split the edge 227 | newlabel := g.label[len(str):] 228 | 229 | // build a new node 230 | w := newNode() 231 | // build a new edge 232 | newedge := newEdge(str, w) 233 | s.addEdge(str[0], newedge) 234 | 235 | // link s -> r 236 | g.label = newlabel 237 | w.addEdge(newlabel[0], g) 238 | 239 | return false, w 240 | } 241 | } else { 242 | e := s.getEdge(r) 243 | if e == nil { 244 | // if there is no t-transtion from s 245 | return false, s 246 | } else { 247 | if string(remainder) == string(e.label) { 248 | // update payload of destination node 249 | e.node.addRef(value) 250 | return true, s 251 | } else if strings.Index(string(remainder), string(e.label)) == 0 { 252 | return true, s 253 | } else if strings.Index(string(e.label), string(remainder)) == 0 { 254 | // need to split as above 255 | newNode := newNode() 256 | newNode.addRef(value) 257 | newEdge := newEdge(remainder, newNode) 258 | s.addEdge(r, newEdge) 259 | 260 | e.label = e.label[len(remainder):] 261 | newNode.addEdge(e.label[0], e) 262 | return false, s 263 | } else { 264 | // they are different words. No prefix. but they may still share some common substr 265 | return true, s 266 | } 267 | } 268 | } 269 | 270 | } 271 | 272 | func safeCutLastChar(runes []rune) []rune { 273 | if len(runes) == 0 { 274 | return nil 275 | } 276 | return runes[:len(runes)-1] 277 | } 278 | 279 | func NewGeneralizedSuffixTree() *generalizedSuffixTree { 280 | t := &generalizedSuffixTree{} 281 | t.root = newNode() 282 | t.activeLeaf = t.root 283 | return t 284 | } 285 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Apache License 2 | Version 2.0, January 2004 3 | http://www.apache.org/licenses/ 4 | 5 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 6 | 7 | 1. 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