SuffixTree (biojava-legacy 1.9.5 API)

java.lang.Object
- org.biojava.bio.symbol.SuffixTree

All Implemented Interfaces:

Serializable
```
public class SuffixTree
extends Object
implements Serializable
```
Suffix tree implementation. The interface is a bit strange, as it needed to be as space-efficient as possible. More work could be done on the space issue.
A suffix tree is an efficient method for encoding the frequencies of motifs in a sequence. They are sometimes used to quickly screen for similar sequences. For instance, all motifs of length up to 2 in the sequence AAGT could be encoded as:
```
 root(4)
 |
 A(2)--------G(1)-----T(1)
 |           |
 A(1)--G(1)  T(1)
 
```
A possible method of comparing SuffixTrees is provided as a kernel function as org.biojava.stats.svm.tools.SuffixTreeKernel.
Author:

Matthew Pocock, Thomas Down (documentation and other updates)

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class SuffixTree.SuffixNode
A node in the suffix tree.

Nested Classes
Modifier and Type	Class	Description
`static class`	`SuffixTree.SuffixNode`	A node in the suffix tree.

Constructor Summary

Constructors
Constructor Description

SuffixTree(FiniteAlphabet alphabet)
Construct a new SuffixTree to contain motifs over the specified alphabet.

Constructors
Constructor	Description
`SuffixTree(FiniteAlphabet alphabet)`	Construct a new SuffixTree to contain motifs over the specified alphabet.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addSymbols(SymbolList sList, int window)`	Add a count for all motifs with length of up to `window` to this tree.
`int`	`frequency(int length)`	Return the number of motifs of a given length encoded in this SuffixTree.
`FiniteAlphabet`	`getAlphabet()`	Return the Alphabet containing all Symbols which might be found in this SuffixTree.
`SuffixTree.SuffixNode`	`getChild(SuffixTree.SuffixNode node, int i)`	Get the n'th child of a node.
`SuffixTree.SuffixNode`	`getChild(SuffixTree.SuffixNode node, Symbol s)`	Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.
`SuffixTree.SuffixNode`	`getRoot()`	Return the node object which is the root of this suffix tree.
`protected void`	`incCounts(int i, int c)`
`int`	`maxLength()`	Return the length of the longest motif represented in this SuffixTree

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - SuffixTree
```
public SuffixTree(FiniteAlphabet alphabet)
```
    Construct a new SuffixTree to contain motifs over the specified alphabet.
    
    Parameters:
    
    alphabet - The alphabet of this SuffixTree (must be finite).
- Method Detail
  - getAlphabet
```
public FiniteAlphabet getAlphabet()
```
    Return the Alphabet containing all Symbols which might be found in this SuffixTree.
  - getRoot
```
public SuffixTree.SuffixNode getRoot()
```
    Return the node object which is the root of this suffix tree. This represents the set of all motifs found in this tree.
  - getChild
```
public SuffixTree.SuffixNode getChild(SuffixTree.SuffixNode node,
                                      Symbol s)
                               throws IllegalSymbolException
```
    Get a child of a SuffixTree.SuffixNode, constructing a new one if need be. This method is here due to memory optimisations.
    
    Throws:
    
    IllegalSymbolException
  - getChild
```
public SuffixTree.SuffixNode getChild(SuffixTree.SuffixNode node,
                                      int i)
```
    Get the n'th child of a node.
  - addSymbols
```
public void addSymbols(SymbolList sList,
                       int window)
                throws IllegalSymbolException
```
    Add a count for all motifs with length of up to window to this tree.
    
    Parameters:
    
    sList - a SymbolList whose motifs should be added to the tree.
    
    window - The maximum motif length to count.
    
    Throws:
    
    IllegalSymbolException
  - incCounts
```
protected void incCounts(int i,
                         int c)
```
  - maxLength
```
public int maxLength()
```
    Return the length of the longest motif represented in this SuffixTree
  - frequency
```
public int frequency(int length)
```
    Return the number of motifs of a given length encoded in this SuffixTree.

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SuffixTree

Method Detail

getAlphabet

getRoot

getChild

getChild

addSymbols

incCounts

maxLength

frequency