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java.lang.Objectorg.biojava.bio.symbol.DNANoAmbPack
public class DNANoAmbPack
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.
Constructor Summary | |
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DNANoAmbPack(byte placeHolder)
Construct a new packing which returns the specified byte value for unknown Symbols (such as ambiguity symbols). |
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DNANoAmbPack(Symbol placeHolderSymbol)
Construct a new packing which translates unknown symbols into the specified symbol. |
Method Summary | |
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FiniteAlphabet |
getAlphabet()
The FiniteAlphabet this packing is for. |
boolean |
handlesAmbiguity()
Flag to state if ambiguities are stored. |
byte |
pack(Symbol sym)
Return a byte representing the packing of a symbol. |
Symbol |
unpack(byte b)
Return the symbol for a packing. |
byte |
wordSize()
The number of bits required to pack a symbol. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public DNANoAmbPack(byte placeHolder)
public DNANoAmbPack(Symbol placeHolderSymbol)
Method Detail |
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public FiniteAlphabet getAlphabet()
Packing
getAlphabet
in interface Packing
public byte pack(Symbol sym)
Packing
Return a byte representing the packing of a symbol. The bits will be from 1 >> 0 through to 1 >> (wordSize - 1).
pack
in interface Packing
sym
- the Symbol to pack
public Symbol unpack(byte b) throws IllegalSymbolException
Packing
Return the symbol for a packing.
unpack
in interface Packing
b
- the byte pattern for a Symbol
IllegalSymbolException
- if the packing doesn't represent a valid
Symbolpublic byte wordSize()
Packing
The number of bits required to pack a symbol.
wordSize
in interface Packing
public boolean handlesAmbiguity()
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.
handlesAmbiguity
in interface Packing
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