org.biojava.bio.symbol
Class PackedSymbolListFactory

java.lang.Object
  extended byorg.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
Throws:
IllegalAlphabetException