org.biojava.bio.symbol

Class PackedSymbolListFactory

java.lang.Object

org.biojava.bio.symbol.PackedSymbolListFactory

All Implemented Interfaces:

SymbolListFactory

public class PackedSymbolListFactory
extends Object
implements SymbolListFactory

This class makes PackedSymbolLists. It could be refactored into the PackedSymbolList class eventually.

Author:

David Huen

Constructor Summary

Constructors

Constructor and Description
PackedSymbolListFactory() Create a factory for PackedSymbolLists.
PackedSymbolListFactory(boolean ambiguity) Deprecated. the argumentless constructor creates a SymbolListFactory that will autoselect the packing appropriately.

Method Summary

Modifier and Type	Method and Description
SymbolList	makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) Makes a packed SymbolList out of a list of Symbols.

Methods inherited from class java.lang.Object

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

Constructor Detail

PackedSymbolListFactory

public PackedSymbolListFactory()

Create a factory for PackedSymbolLists. The use of ambiguity packing is determined automatically as required.

PackedSymbolListFactory

public PackedSymbolListFactory(boolean ambiguity)

Deprecated. the argumentless constructor creates a SymbolListFactory that will autoselect the packing appropriately.

Create a factory for PackedSymbolLists with specified packing type.

Parameters:

ambiguity - is ambiguity to be supported by the encoding?

Method Detail

makeSymbolList

public SymbolList makeSymbolList(Symbol[] symbolArray,
                                 int size,
                                 Alphabet alfa)
                          throws IllegalAlphabetException

Makes a packed SymbolList out of a list of Symbols.

Specified by:

makeSymbolList in interface SymbolListFactory

Parameters:

symbolArray - the symbols to be make in a packed SymbolList

size - the length of the symbolArray array.

alfa - the Alphabet over which the SymbolList shoudl be

Returns:

a packed SymbolList with the Symbols in symbolArray and the Alphabet in alfa

Throws:

IllegalAlphabetException - if alfa and the Symbols in symbolArray disagree.