Package org.biojava.bio.symbol
Class DNANoAmbPack
java.lang.Object
org.biojava.bio.symbol.DNANoAmbPack
- All Implemented Interfaces:
Serializable
,Packing
A
Packing
implementation which handles the DNA alphabet, without any
support for ambiguity symbols. In normal use, the only returns values between
0 and 3, and so requires only two bits of storage per symbol.- Since:
- 1.3
- Author:
- Matthew Pocock, Thomas Down
- See Also:
-
Constructor Summary
ConstructorsConstructorDescriptionDNANoAmbPack
(byte placeHolder) Construct a new packing which returns the specified byte value for unknown Symbols (such as ambiguity symbols).DNANoAmbPack
(Symbol placeHolderSymbol) Construct a new packing which translates unknown symbols into the specified symbol. -
Method Summary
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Constructor Details
-
DNANoAmbPack
Construct a new packing which returns the specified byte value for unknown Symbols (such as ambiguity symbols). This might be outside the normal range of return values (0-3), allowing callers to detect ambiguity symbols and ignore them. -
DNANoAmbPack
Construct a new packing which translates unknown symbols into the specified symbol.
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Method Details
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getAlphabet
Description copied from interface:Packing
The FiniteAlphabet this packing is for.- Specified by:
getAlphabet
in interfacePacking
- Returns:
- the FiniteAlphabet that we can pack
-
pack
Description copied from interface:Packing
Return a byte representing the packing of a symbol. The bits will be from 1 >> 0 through to 1 >> (wordSize - 1).
-
unpack
Description copied from interface:Packing
Return the symbol for a packing.
- Specified by:
unpack
in interfacePacking
- Parameters:
b
- the byte pattern for a Symbol- Returns:
- the Symbol that was packed
- Throws:
IllegalSymbolException
- if the packing doesn't represent a valid Symbol
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wordSize
Description copied from interface:Packing
The number of bits required to pack a symbol.
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handlesAmbiguity
Description copied from interface:Packing
Flag to state if ambiguities are stored.
Packings are free to either store ambiguity information or to discard it (presumably converting all ambiguities to a standard AtomicSymbol and then packing that). You can check wether ambiguities are handled by calling this method.
- Specified by:
handlesAmbiguity
in interfacePacking
- Returns:
- true if ambiguities are stored, false otherwise
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