org.biojava.bio.symbol
Class PackedSymbolListFactory

java.lang.Object
  extended by 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 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.