MaxMismatchMatcher (biojava-legacy 1.9.5 API)

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

All Implemented Interfaces:

BioMatcher
```
public class MaxMismatchMatcher
extends Object
implements BioMatcher
```
A BioMatcher class returned by MaxMismatchPattern.matcher() that implements searching of a SymbolList.
This class is public only to allow access to the mismatchCount() method.

Author:

Matthew Pocock (wrote original MaxMissmatchMatcher class), David Huen (debugging and extension of functionality)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`end()`	Get the last symbol index that matches the pattern.
`boolean`	`find()`	Attempt to find the next match.
`SymbolList`	`group()`	Get the matching region as a SymbolList.
`int`	`mismatchCount()`	Returns number of mismatches
`int`	`start()`	Get the first symbol index that matches the pattern.

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

- Method Detail
  - find
```
public boolean find()
```
    Description copied from interface: BioMatcher
    
    Attempt to find the next match.
    If the pattern can be found, then this will return true. If it could not, then it will return false. This is convenient within for or while loops.
    
    Each time this is called, the next match will be found. The start() and end() values will increase each time, regardless of wether you called any other methods.
    
    Specified by:
    
    find in interface BioMatcher
    
    Returns:
    
    true if there is another match
  - start
```
public int start()
```
    Description copied from interface: BioMatcher
    
    Get the first symbol index that matches the pattern.
    
    Specified by:
    
    start in interface BioMatcher
    
    Returns:
    
    the start of the current match
  - end
```
public int end()
```
    Description copied from interface: BioMatcher
    
    Get the last symbol index that matches the pattern.
    
    Specified by:
    
    end in interface BioMatcher
    
    Returns:
    
    the end of the current match
  - group
```
public SymbolList group()
```
    Description copied from interface: BioMatcher
    
    Get the matching region as a SymbolList.
    
    Specified by:
    
    group in interface BioMatcher
    
    Returns:
    
    the matching symbols
  - mismatchCount
```
public int mismatchCount()
```
    Returns number of mismatches