suffixtree-0.2.2.1: Efficient, lazy suffix tree implementation

Portability portable experimental bos@serpentine.com

Data.SuffixTree

Description

A lazy, efficient suffix tree implementation.

Since many function names (but not the type name) clash with Prelude names, this module is usually imported `qualified`, e.g.

```  import Data.SuffixTree (STree)
import qualified Data.SuffixTree as T
```

The implementation is based on the first of those described in the following paper:

This implementation constructs the suffix tree lazily, so subtrees are not created until they are traversed. Two construction functions are provided, `constructWith` for sequences composed of small alphabets, and `construct` for larger alphabets.

Estimates are given for performance. The value k is a constant; n is the length of a query string; and t is the number of elements (nodes and leaves) in a suffix tree.

Synopsis

# Types

type Alphabet a = [a]Source

The list of symbols that `constructWith` can possibly see in its input.

type Edge a = (Prefix a, STree a)Source

An edge in the suffix tree.

data Prefix a Source

The prefix string associated with an `Edge`. Use `mkPrefix` to create a value of this type, and `prefix` to deconstruct one.

Instances

 Functor Prefix Eq a => Eq (Prefix a) Ord a => Ord (Prefix a) Show a => Show (Prefix a)

data STree a Source

The suffix tree type. The implementation is exposed to ease the development of custom traversal functions. Note that ```(Prefix a, STree a)``` pairs are not stored in any order.

Constructors

 Node [Edge a] Leaf

Instances

 Functor STree Show a => Show (STree a)

# Construction

constructWith :: Eq a => Alphabet a -> [a] -> STree aSource

O(k n log n). Constructs a suffix tree using the given alphabet. The performance of this function is linear in the size k of the alphabet. That makes this function suitable for small alphabets, such as DNA nucleotides. For an alphabet containing more than a few symbols, `construct` is usually several orders of magnitude faster.

construct :: Ord a => [a] -> STree aSource

O(n log n). Constructs a suffix tree.

# Querying

elem :: Eq a => [a] -> STree a -> BoolSource

O(n). Indicates whether the suffix tree contains the given sublist. Performance is linear in the length n of the sublist.

findEdge :: Eq a => [a] -> STree a -> Maybe (Edge a, Int)Source

O(n). Finds the given subsequence in the suffix tree. On failure, returns `Nothing`. On success, returns the `Edge` in the suffix tree at which the subsequence ends, along with the number of elements to drop from the prefix of the `Edge` to get the "real" remaining prefix.

Here is an example:

```> find "ssip" (construct "mississippi")
Just ((mkPrefix "ppi",Leaf),1)
```

This indicates that the edge `(mkPrefix "ppi",Leaf)` matches, and that we must strip 1 character from the string `"ppi"` to get the remaining prefix string `"pi"`.

Performance is linear in the length n of the query list.

findTree :: Eq a => [a] -> STree a -> Maybe (STree a)Source

O(n). Finds the subtree rooted at the end of the given query sequence. On failure, returns `Nothing`.

Performance is linear in the length n of the query list.

findPath :: Eq a => [a] -> STree a -> [Edge a]Source

O(n). Returns the path from the `Edge` in the suffix tree at which the given subsequence ends, up to the root of the tree. If the subsequence is not found, returns the empty list.

Performance is linear in the length of the query list.

O(t). Count the number of leaves in a tree.

Performance is linear in the number t of elements in the tree.

countRepeats :: Eq a => [a] -> STree a -> IntSource

O(n + r). Count the number of times a sequence is repeated in the input sequence that was used to construct the suffix tree.

Performance is linear in the length n of the input sequence, plus the number of times r the sequence is repeated.

# Traversal

foldr :: (Prefix a -> b -> b) -> b -> STree a -> bSource

O(t). Folds the edges in a tree, using post-order traversal. Suitable for lazy use.

Arguments

 :: (a -> Prefix b -> a) step function (evaluated strictly) -> a initial state -> STree b -> a

O(t). Folds the edges in a tree, using pre-order traversal. The step function is evaluated strictly.

Arguments

 :: (a -> a) downwards state transformer -> (a -> a) upwards state transformer -> (Prefix b -> a -> a -> a) edge state transformer -> (a -> a) leaf state transformer -> a initial state -> STree b tree -> a

O(t). Generic fold over a tree.

A few simple examples.

```countLeaves == fold id id (const const) (1+) 0
```
```countEdges = fold id id (\_ a _ -> a+1) id 0
```

This more complicated example generates a tree of the same shape, but new type, with annotated leaves.

```data GenTree a b = GenNode [(`Prefix` a, GenTree a b)]
| GenLeaf b
deriving (`Show`)
```
```gentree :: `STree` a -> GenTree a Int
gentree = `fold` reset id fprefix reset leaf
where leaf = GenLeaf 1
reset = `const` leaf
fprefix p t (GenLeaf _) = GenNode [(p, t)]
fprefix p t (GenNode es) = GenNode ((p, t):es)
```

# Other useful functions

mkPrefix :: [a] -> Prefix aSource

O(1). Construct a `Prefix` value.

prefix :: Prefix a -> [a]Source

O(n). Obtain the list stored in a `Prefix`.

suffixes :: [a] -> [[a]]Source

O(n). Returns all non-empty suffixes of the argument, longest first. Behaves as follows:

```suffixes xs == init (tails xs)
```