MaxMismatchPattern (biojava-legacy 1.9.5 API)

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

All Implemented Interfaces:

BioPattern
```
public class MaxMismatchPattern
extends Object
implements BioPattern
```
This class permits searching a SymbolList with another SymbolList while permitting a specified number of mismatches. The search pattern can include ambiguity Symbols.

Author:

Matthew Pocock (wrote original MaxMissmatchPattern class), David Huen (debugging and extension to permit ambiguity symbols)

Constructor Summary

Constructors
Constructor Description

MaxMismatchPattern()

MaxMismatchPattern(SymbolList pattern, int mismatches)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`getMismatches()`
`SymbolList`	`getPattern()`
`BioMatcher`	`matcher(SymbolList symList)`	Get a matcher that will use these parameters to search a SymbolList.
`void`	`setMismatches(int mismatches)`
`void`	`setPattern(SymbolList pattern)`

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

- Constructor Detail
  - MaxMismatchPattern
```
public MaxMismatchPattern()
```
  - MaxMismatchPattern
```
public MaxMismatchPattern(SymbolList pattern,
                          int mismatches)
```
- Method Detail
  - getMismatches
```
public int getMismatches()
```
  - setMismatches
```
public void setMismatches(int mismatches)
```
  - getPattern
```
public SymbolList getPattern()
```
  - setPattern
```
public void setPattern(SymbolList pattern)
```
  - matcher
```
public BioMatcher matcher(SymbolList symList)
                   throws IllegalAlphabetException
```
    Description copied from interface: BioPattern
    
    Get a matcher that will use these parameters to search a SymbolList.
    The resulting BioMatcher is independant of this BioPattern. In particular, calling any mutator methods on this pattern will not affect the matcher.
    
    Specified by:
    
    matcher in interface BioPattern
    
    Parameters:
    
    symList - the SymbolList to match against
    
    Returns:
    
    a BioMatcher that will perform the search
    
    Throws:
    
    IllegalAlphabetException - if symList is not over the right alphabet