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## org.biojava.bio.symbol
Class SuffixTree

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

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

Method Summary
`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.

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