org.biojava.bio.search
Class MaxMismatchPattern

java.lang.Object
  extended by 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
MaxMismatchPattern()
           
MaxMismatchPattern(SymbolList pattern, int mismatches)
           
 
Method Summary
 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