Package org.biojava.utils.regex

Class Search

java.lang.Object

org.biojava.utils.regex.Search

public class Search
extends Object

A utility class to make searching a Sequence with many regex patterns easier.

Since:

1.4

Author:

David Huen

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	Search.Listener	Interface for a class that will recieve match information from this class.

Constructor Summary

Constructors

Constructor	Description
Search(FiniteAlphabet alfa)

Method Summary

Modifier and Type	Method	Description
void	addPattern(String patternString, boolean overlap)	add a search pattern to the searches to be conducted by this object.
void	addPattern(String label, String patternString, boolean overlap)	add a search pattern to the searches to be conducted by this object.
char	charValue(Symbol sym)
void	clearPatterns()	remove all patterns from the pattern cache.
void	search(SymbolList seq)	search the Sequence with the patterns already registered with this object.
void	search(SymbolList seq, int loLimit, int hiLimit)	search part of the SymbolList with the patterns already registered with this object.
void	setListener(Search.Listener listener)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Search

public Search(FiniteAlphabet alfa)

Method Detail

setListener

public void setListener(Search.Listener listener)

addPattern

public void addPattern(String patternString,
                       boolean overlap)
                throws RegexException,
                       IllegalAlphabetException

add a search pattern to the searches to be conducted by this object.

Parameters:

patternString - String representation of the pattern.

overlap - if true, the search continues at the base following the start to the previous hit. If false, it continues at the base after the existing hit.

Throws:

RegexException - if the requested pattern is not valid

IllegalAlphabetException - if the requested pattern is not valid

addPattern

public void addPattern(String label,
                       String patternString,
                       boolean overlap)
                throws RegexException,
                       IllegalAlphabetException

add a search pattern to the searches to be conducted by this object.

Parameters:

patternString - String representation of the pattern.

overlap - if true, the search continues at the base following the start to the previous hit. If false, it continues at the base after the existing hit.

Throws:

RegexException - if the requested pattern is not valid

IllegalAlphabetException - if the requested pattern is not valid

clearPatterns

public void clearPatterns()

remove all patterns from the pattern cache.

charValue

public char charValue(Symbol sym)
               throws IllegalSymbolException

Throws:

IllegalSymbolException

search

public void search(SymbolList seq)

search the Sequence with the patterns already registered with this object.

search

public void search(SymbolList seq,
                   int loLimit,
                   int hiLimit)

search part of the SymbolList with the patterns already registered with this object.

Parameters:

loLimit - low limit of search range.

hiLimit - high limit of search range.