public class GeneralizedSuffixTree
extends java.lang.Object
Allows for fast storage and fast(er) retrieval by creating a tree-based index out of a set of strings. Unlike common suffix trees, which are generally used to build an index out of one (very) long string, a Generalized Suffix Tree can be used to build an index over many strings.
Its main operations are put and search: Put adds the given key to the index, allowing for later retrieval of the given value. Search can be used to retrieve the set of all the values that were put in the index with keys that contain a given input.
In particular, after put(K, V), search(H) will return a set containing V for any string H that is substring of K.
The overall complexity of the retrieval operation (search) is O(m) where m is the length of the string to search within the index.
Although the implementation is based on the original design by Ukkonen, there are a few aspects where it differs significantly.
The tree is composed of a set of nodes and labeled edges. The labels on the edges can have any length as long as it's greater than 0. The only constraint is that no two edges going out from the same node will start with the same character.
Because of this, a given (startNode, stringSuffix) pair can denote a unique path within the tree, and it is the path (if any) that can be composed by sequentially traversing all the edges (e1, e2, ...) starting from startNode such that (e1.label + e2.label + ...) is equal to the stringSuffix. See the search method for details.
The union of all the edge labels from the root to a given leaf node denotes the set of the strings explicitly contained within the GST. In addition to those Strings, there are a set of different strings that are implicitly contained within the GST, and it is composed of the strings built by concatenating e1.label + e2.label + ... + $end, where e1, e2, ... is a proper path and $end is prefix of any of the labels of the edges starting from the last node of the path.
This kind of "implicit path" is important in the testAndSplit method.
Edited by mezz: - improve performance of search by passing a set around instead of creating new ones and using addAll - only allow full searches - add nullable/nonnull annotations - formatting
Constructor and Description |
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GeneralizedSuffixTree() |
Modifier and Type | Method and Description |
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int |
computeCount() |
void |
put(java.lang.String key,
int index)
Adds the specified index to the GST under the given key.
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gnu.trove.set.TIntSet |
search(java.lang.String word)
Searches for the given word within the GST.
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public gnu.trove.set.TIntSet search(java.lang.String word)
Returns all the indexes for which the key contains the word that was supplied as input.
word
- the key to search forpublic void put(java.lang.String key, int index) throws java.lang.IllegalStateException
Entries must be inserted so that their indexes are in non-decreasing order, otherwise an IllegalStateException will be raised.
key
- the string key that will be added to the indexindex
- the value that will be added to the indexjava.lang.IllegalStateException
- if an invalid index is passed as inputpublic int computeCount()