org.biojava.bio.symbol
Class PackedSymbolListFactory

java.lang.Object
  |
  +--org.biojava.bio.symbol.PackedSymbolListFactory

All Implemented Interfaces:

SymbolListFactory

public class PackedSymbolListFactory

extends java.lang.Object

implements SymbolListFactory

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

Author:

David Huen

Constructor Summary

PackedSymbolListFactory()
Create a factory for PackedSymbolLists.

PackedSymbolListFactory(boolean ambiguity)
Deprecated. the argumentless constructor creates a SymbolListFactory that will autoselect the packing appropriately.

Method Summary

SymbolList

makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) makes a SymbolList containing size Symbols from a Symbol array.

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.

Method Detail

makeSymbolList

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

Description copied from interface: SymbolListFactory

makes a SymbolList containing size Symbols from a Symbol array. primarily used to create chunks for a chunked symbol list.

Specified by:

makeSymbolList in interface SymbolListFactory

IllegalAlphabetException