org.biojava.bio.search

Interface BioMatcher

All Known Implementing Classes:

MaxMismatchMatcher

public interface BioMatcher

Interface for things that perform matches.

These will almost always be produced by a factory method on a BioPattern object.

Author:

Matthew Pocock

Method Summary

Methods

Modifier and Type	Method and 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	start() Get the first symbol index that matches the pattern.

Method Detail

find

boolean find()

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.

Returns:

true if there is another match

start

int start()

Get the first symbol index that matches the pattern.

Returns:

the start of the current match

Throws:

IllegalStateException - if there is no current match

end

int end()

Get the last symbol index that matches the pattern.

Returns:

the end of the current match

Throws:

IllegalStateException - if there is no current match

group

SymbolList group()

Get the matching region as a SymbolList.

Returns:

the matching symbols

Throws:

IllegalStateException - if there is no current match