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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(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
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DataStore |
CompactedDataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceStreamer streamer,
Packing packing,
int wordLength,
int stepSize,
int threshold)
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DataStore |
DataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
Build a new DataStore. |
DataStore |
NIODataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
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DataStore |
MappedDataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
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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.primeWord(SymbolList symList,
int wordLength,
Packing packing)
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static int |
PackingFactory.nextWord(SymbolList symList,
int word,
int offset,
int wordLength,
Packing packing)
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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. |
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PackedSymbolList(Packing packing,
SymbolList symList)
Create a new PackedSymbolList as a packed copy of another symbol list. |
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PackedSymbolList(Packing packing,
Symbol[] symbols,
int length,
Alphabet alfa)
Create a new PackedSymbolList from an array of Symbols. |
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