KnuthMorrisPrattSearch (biojava-legacy 1.9.5 API)

java.lang.Object
- org.biojava.bio.search.KnuthMorrisPrattSearch

```
public final class KnuthMorrisPrattSearch
extends Object
```
An object to find exact subsequences within a sequence.
Reference: KNUTH D.E., MORRIS (Jr) J.H., PRATT V.R., 1977, Fast pattern matching in strings, SIAM Journal on Computing 6(1):323-350. USAGE:
When the object is constructed the findMatches() method would be called. This will return an int[] giving the offsets (ie the location of the first symbol of each match in the text). The getKMPNextTable() returns the table of border lengths used in the algorithm. This method is protected as it is unlikely it will be needed except for debugging.

The algorithm finds exact matches therefore ambiguity symbols will match only themselves. The class cannot perform regular expressions. The class operates on all alphabets thus if searching for a DNA pattern you should compile both the pattern and its reverse complement.

WARNING the behaviour of a pattern containing gaps is undefined. It's not recommended that you try it.

Copyright: Copyright (c) 2002

Company: AgResearch

Version:

1.0

Author:

Mark Schreiber

Constructor Summary

Constructors
Constructor	Description
`KnuthMorrisPrattSearch(SymbolList pattern)`	Constructs a KMP matcher to find exact occurances of `pattern` in `text` using the Knuth-Morris-Pratt algorithm.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int[]`	`findMatches(SymbolList text)`	This will return an int[] giving the offsets of the matches in `text` (ie the location of the first symbol of each match in the `text`).
`protected int[]`	`getKmpNextTable()`	Returns the table of border lengths
`SymbolList`	`getPattern()`
`static void`	`main(String[] args)`	Demo and Test method

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

- Constructor Detail
  - KnuthMorrisPrattSearch
```
public KnuthMorrisPrattSearch(SymbolList pattern)
```
    Constructs a KMP matcher to find exact occurances of pattern in text using the Knuth-Morris-Pratt algorithm.
    A new class should be constructed for each occurance of pattern.
    
    Parameters:
    
    pattern - the pattern to search for
- Method Detail
  - findMatches
```
public int[] findMatches(SymbolList text)
```
    This will return an int[] giving the offsets of the matches in text (ie the location of the first symbol of each match in the text).
    
    Parameters:
    
    text - the text or sequence to search for the pattern
    
    Returns:
    
    an int[] giving the offsets to the matches or a zero length array if there are no matches.
  - getKmpNextTable
```
protected int[] getKmpNextTable()
```
    Returns the table of border lengths
    
    Returns:
    
    an int[] of border lenghts
  - getPattern
```
public SymbolList getPattern()
```
    Returns:
    
    the pattern being searched for
  - main
```
public static void main(String[] args)
                 throws Exception
```
    Demo and Test method
    
    Parameters:
    
    args - no arguments required
    
    Throws:
    
    Exception - if the test fails