Package org.biojava.utils.regex

Class PatternFactory

java.lang.Object

org.biojava.utils.regex.PatternFactory

public class PatternFactory
extends Object

A class that creates Patterns for regex matching on SymbolLists of a specific Alphabet.

Since:

1.4

Author:

David Huen

Method Summary

Modifier and Type	Method	Description
char	charValue(Symbol sym)	Returns the character that represents the specified Symbol in the Alphabet that this PatternFactory was defined for.
Pattern	compile(String pattern)	Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
Pattern	compile(String pattern, String label)	Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
static PatternFactory	makeFactory(FiniteAlphabet alfa)	Returns a factory for Patterns in the specified Alphabet.

Methods inherited from class java.lang.Object

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

Method Detail

compile

public Pattern compile(String pattern)
                throws RegexException,
                       IllegalAlphabetException

Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against. The String returned by getName() is set to pattern.

Throws:

RegexException

IllegalAlphabetException

compile

public Pattern compile(String pattern,
                       String label)
                throws RegexException,
                       IllegalAlphabetException

Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.

Parameters:

pattern - regex pattern expressed as a String.

label - A String label assigned to the Pattern object. Can be retrieved later with getName().

Throws:

RegexException

IllegalAlphabetException

charValue

public char charValue(Symbol sym)
               throws IllegalSymbolException

Returns the character that represents the specified Symbol in the Alphabet that this PatternFactory was defined for.

The character will be ASCII in Alphabets that define a Character tokenization. In Alphabets that don't a Unicode character in the private range is returned instead and this can be used to assemble the String that is the argument for the compile method.

Throws:

IllegalSymbolException

makeFactory

public static PatternFactory makeFactory(FiniteAlphabet alfa)

Returns a factory for Patterns in the specified Alphabet.