Package org.biojava.bio.search
Class MaxMismatchPattern
java.lang.Object
org.biojava.bio.search.MaxMismatchPattern
- All Implemented Interfaces:
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)
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionint
matcher
(SymbolList symList) Get a matcher that will use these parameters to search a SymbolList.void
setMismatches
(int mismatches) void
setPattern
(SymbolList pattern)
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Constructor Details
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MaxMismatchPattern
public MaxMismatchPattern() -
MaxMismatchPattern
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Method Details
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getMismatches
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setMismatches
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getPattern
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setPattern
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matcher
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 interfaceBioPattern
- 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
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