org.biojava3.core.sequence.storage
Class FourBitSequenceReader<C extends Compound>
java.lang.Object
org.biojava3.core.sequence.storage.BitSequenceReader<C>
org.biojava3.core.sequence.storage.FourBitSequenceReader<C>
- All Implemented Interfaces:
- Iterable<C>, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>
public class FourBitSequenceReader<C extends Compound>
- extends BitSequenceReader<C>
Four bit encoding of the bit formats. This can support up to 16 compounds
from a compound set. To allow us to support the redundant set of Nucleotide
compounds this class will use case-insensitive encoding. The values assigned
to these compounds is also done at runtime; if you want a predictable
ordering then override and use your own encodings. However all
encodings are calculated using lexographical ordering of the compounds
so if a CompoundSet does not change then this encoding should not cauuse
a problem.
- Author:
- ayates
Methods inherited from class org.biojava3.core.sequence.storage.BitSequenceReader |
countCompounds, equals, getAccession, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequence, getSubSequence, hashCode, iterator, setCompoundSet, setContents |
FourBitSequenceReader
public FourBitSequenceReader(Sequence<C> sequence)
FourBitSequenceReader
public FourBitSequenceReader(String sequence,
CompoundSet<C> compoundSet)
FourBitSequenceReader
public FourBitSequenceReader(String sequence,
CompoundSet<C> compoundSet,
AccessionID accession)
FourBitSequenceReader
public FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C> worker)
FourBitSequenceReader
public FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C> worker,
AccessionID accession)