Package org.biojava.bio.symbol
Class PackedSymbolListFactory
java.lang.Object
org.biojava.bio.symbol.PackedSymbolListFactory
- All Implemented Interfaces:
SymbolListFactory
This class makes PackedSymbolLists.
It could be refactored into the PackedSymbolList class eventually.
- Author:
- David Huen
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Constructor Summary
ConstructorsConstructorDescriptionCreate a factory for PackedSymbolLists.PackedSymbolListFactory
(boolean ambiguity) Deprecated.the argumentless constructor creates a SymbolListFactory that will autoselect the packing appropriately. -
Method Summary
Modifier and TypeMethodDescriptionmakeSymbolList
(Symbol[] symbolArray, int size, Alphabet alfa) Makes a packed SymbolList out of a list of Symbols.
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Constructor Details
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PackedSymbolListFactory
public PackedSymbolListFactory()Create a factory for PackedSymbolLists. The use of ambiguity packing is determined automatically as required. -
PackedSymbolListFactory
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?
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Method Details
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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 interfaceSymbolListFactory
- Parameters:
symbolArray
- the symbols to be make in a packed SymbolListsize
- 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.
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