Uses of Interface
org.biojava.bio.symbol.Packing

Packages that use Packing

Package	Description
org.biojava.bio.program.ssaha	SSAHA sequence searching API.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.

Uses of Packing in org.biojava.bio.program.ssaha

Methods in org.biojava.bio.program.ssaha with parameters of type Packing

Modifier and Type	Method and Description
DataStore	NIODataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
DataStore	DataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) Build a new DataStore.
DataStore	MappedDataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
DataStore	CompactedDataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
DataStore	CompactedDataStoreFactory.buildDataStore(File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, int threshold)

Uses of Packing in org.biojava.bio.symbol

Classes in org.biojava.bio.symbol that implement Packing

Modifier and Type	Class and Description
class	DNAAmbPack Packing utility class for DNA.
class	DNANoAmbPack A Packing implementation which handles the DNA alphabet, without any support for ambiguity symbols.

Methods in org.biojava.bio.symbol that return Packing

Modifier and Type	Method and Description
static Packing	PackingFactory.getPacking(FiniteAlphabet alpha, boolean ambiguity) Get the default packing for an alphabet.

Methods in org.biojava.bio.symbol with parameters of type Packing

Modifier and Type	Method and Description
static int	PackingFactory.nextWord(SymbolList symList, int word, int offset, int wordLength, Packing packing)
static int	PackingFactory.primeWord(SymbolList symList, int wordLength, Packing packing)

Constructors in org.biojava.bio.symbol with parameters of type Packing

Constructor and Description
PackedSymbolList(Packing packing, long[] syms, int length) Create a new PackedSymbolList directly from a bit pattern.
PackedSymbolList(Packing packing, Symbol[] symbols, int length, Alphabet alfa) Create a new PackedSymbolList from an array of Symbols.
PackedSymbolList(Packing packing, SymbolList symList) Create a new PackedSymbolList as a packed copy of another symbol list.