org.biojava3.core.sequence.storage
Class TwoBitSequenceReader<C extends NucleotideCompound>

java.lang.Object
  extended by org.biojava3.core.sequence.storage.BitSequenceReader<C>
      extended by 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

Nested Class Summary
static class TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound>
          Extension of the BitArrayWorker which provides the 2bit implementation code.
 
Nested classes/interfaces inherited from class org.biojava3.core.sequence.storage.BitSequenceReader
BitSequenceReader.BitArrayWorker<C extends Compound>
 
Constructor Summary
TwoBitSequenceReader(Sequence<C> sequence)
           
TwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet)
           
TwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet, AccessionID accession)
           
TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker)
           
TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C> worker, AccessionID accession)
           
 
Method Summary
 
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
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

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)