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 Details

    • 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 Details

    • 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.