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