org.biojava3.core.sequence.storage
Class TwoBitSequenceReader<C extends NucleotideCompound>
java.lang.Object
org.biojava3.core.sequence.storage.BitSequenceReader<C>
org.biojava3.core.sequence.storage.TwoBitSequenceReader<C>
- All Implemented Interfaces:
- Iterable<C>, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>
public class TwoBitSequenceReader<C extends NucleotideCompound>
- extends BitSequenceReader<C>
Implementation of the 2bit encoding. This will default to the following
encodings:
We also do not support case sensitive encodings therefore if you pass a
lowercased a this will be treated as if it is an uppercase A and we will
erase that information.
- 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 |
TwoBitSequenceReader
public TwoBitSequenceReader(Sequence<C> sequence)
TwoBitSequenceReader
public TwoBitSequenceReader(String sequence,
CompoundSet<C> compoundSet)
TwoBitSequenceReader
public TwoBitSequenceReader(String sequence,
CompoundSet<C> compoundSet,
AccessionID accession)
TwoBitSequenceReader
public TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker)
TwoBitSequenceReader
public TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker,
AccessionID accession)