Uses of Interface
org.biojava.bio.symbol.Packing
Packages that use Packing
Package
Description
SSAHA sequence searching API.
Representation of the Symbols that make up a sequence, and locations within
them.
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Uses of Packing in org.biojava.bio.program.ssaha
Methods in org.biojava.bio.program.ssaha with parameters of type PackingModifier and TypeMethodDescriptionCompactedDataStoreFactory.buildDataStore
(File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, int threshold) CompactedDataStoreFactory.buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) DataStoreFactory.buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) Build a new DataStore.MappedDataStoreFactory.buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) NIODataStoreFactory.buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) -
Uses of Packing in org.biojava.bio.symbol
Classes in org.biojava.bio.symbol that implement PackingModifier and TypeClassDescriptionclass
Packing utility class for DNA.class
APacking
implementation which handles the DNA alphabet, without any support for ambiguity symbols.Methods in org.biojava.bio.symbol that return PackingModifier and TypeMethodDescriptionstatic Packing
PackingFactory.getPacking
(FiniteAlphabet alpha, boolean ambiguity) Get the default packing for an alphabet.Methods in org.biojava.bio.symbol with parameters of type PackingModifier and TypeMethodDescriptionstatic 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 PackingModifierConstructorDescriptionPackedSymbolList
(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.