org.biojava.bio.search
Class MaxMismatchPattern
java.lang.Object
org.biojava.bio.search.MaxMismatchPattern
- All Implemented Interfaces:
- BioPattern
public class MaxMismatchPattern
- extends java.lang.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)
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
MaxMismatchPattern
public MaxMismatchPattern()
MaxMismatchPattern
public MaxMismatchPattern(SymbolList pattern,
int mismatches)
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