org.biojava.bio.search

Interface BioPattern

All Known Implementing Classes:

MaxMismatchPattern, SeqContentPattern

public interface BioPattern

Author:

Matthew Pocock

Method Summary

Modifier and Type	Method and Description
BioMatcher	matcher(SymbolList symList) Get a matcher that will use these parameters to search a SymbolList.

Method Detail

matcher

BioMatcher matcher(SymbolList symList)
            throws IllegalAlphabetException

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.

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