Uses of Interface org.biojava.bio.symbol.Packing (BioJava-1.5-beta API)

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

Packages that use Packing
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
`DataStore` | `CompactedDataStoreFactory.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` | `NIODataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)`
`DataStore` | `MappedDataStoreFactory.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
`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
`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
`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
`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.

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