Uses of Class
org.biojava.nbio.core.sequence.compound.NucleotideCompound

Packages that use NucleotideCompound

Package	Description
org.biojava.nbio.core.alignment.matrices
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.compound
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.storage
org.biojava.nbio.core.sequence.template
org.biojava.nbio.core.sequence.transcription
org.biojava.nbio.core.sequence.views
org.biojava.nbio.genome.io.fastq	FASTQ and variants sequence format I/O.

Uses of NucleotideCompound in org.biojava.nbio.core.alignment.matrices

Methods in org.biojava.nbio.core.alignment.matrices that return types with arguments of type NucleotideCompound

Modifier and Type	Method and Description
static SubstitutionMatrix<NucleotideCompound>	SubstitutionMatrixHelper.getNuc4_2() Returns Nuc 4.2 matrix by Lowe Only the first nucleotide sequence to align can contain ambiguous nucleotides
static SubstitutionMatrix<NucleotideCompound>	SubstitutionMatrixHelper.getNuc4_4() Returns Nuc 4.4 matrix by Lowe Both of the nucleotide sequences to align can contain ambiguous nucleotides

Uses of NucleotideCompound in org.biojava.nbio.core.sequence

Methods in org.biojava.nbio.core.sequence that return types with arguments of type NucleotideCompound

Modifier and Type	Method and Description
SequenceView<NucleotideCompound>	RNASequence.getComplement() Get the complement view of the RNA sequence
SequenceView<NucleotideCompound>	DNASequence.getComplement() Returns a Sequence which will complement every base
SequenceView<NucleotideCompound>	RNASequence.getInverse() Get the inverse view of the sequence.
SequenceView<NucleotideCompound>	DNASequence.getReverse() Returns a Sequence which runs in the current reverse order
SequenceView<NucleotideCompound>	RNASequence.getReverseComplement() Get reverse complement view of the sequence
SequenceView<NucleotideCompound>	DNASequence.getReverseComplement() Delegates to AbstractSequence.getInverse() for the reverse complement

Method parameters in org.biojava.nbio.core.sequence with type arguments of type NucleotideCompound

Modifier and Type	Method and Description
void	ProteinSequence.setParentDNASequence(AbstractSequence<NucleotideCompound> parentDNASequence, Integer begin, Integer end) A Protein sequence can be stand alone or loaded from a transcript sequence.

Constructor parameters in org.biojava.nbio.core.sequence with type arguments of type NucleotideCompound

Constructor and Description
ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader) Fairly important constructor given the size of a ChromsomeSequence where the ProxySequenceReader could load from disk via RandomAccessFile so that the sequence doesn't need to be kept in memory.
ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet) Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet
ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet) Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet
ChromosomeSequence(String seqString, CompoundSet<NucleotideCompound> compoundSet) Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet
DNASequence(SequenceReader<NucleotideCompound> proxyLoader) Create a sequence where the actual storage of the sequence data is somewhere else
DNASequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet) Create a sequence from a ProxySequencereader and user defined compound set
DNASequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet) Create a sequence from a ProxySequencereader and user defined compound set
DNASequence(String seqString, CompoundSet<NucleotideCompound> compoundSet) Create a sequence from a string with user defined compound set
RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader) Create a RNA aequence from a proxy reader
RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet) Create a RNA sequence from a proxy reader and user defined RNA compound set
RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet) Create a RNA sequence from a proxy reader and user defined RNA compound set
RNASequence(String seqString, CompoundSet<NucleotideCompound> compoundSet) Create a RNA sequence from a string with a user defined RNA compound set

Uses of NucleotideCompound in org.biojava.nbio.core.sequence.compound

Methods in org.biojava.nbio.core.sequence.compound that return NucleotideCompound

Modifier and Type	Method and Description
NucleotideCompound	CodonCompound.getOne()
NucleotideCompound	CodonCompound.getThree()
NucleotideCompound	CodonCompound.getTwo()
NucleotideCompound	RNACompoundSet.newNucleotideCompound(String base, String complement, String... equivalents)
NucleotideCompound	ABITracerCompoundSet.newNucleotideCompound(String base, String complement, String... equivalents)
NucleotideCompound	DNACompoundSet.newNucleotideCompound(String base, String complement, String... equivalents)

Methods in org.biojava.nbio.core.sequence.compound that return types with arguments of type NucleotideCompound

Modifier and Type	Method and Description
Set<NucleotideCompound>	NucleotideCompound.getConstituents()

Constructors in org.biojava.nbio.core.sequence.compound with parameters of type NucleotideCompound

Constructor and Description
CodonCompound(NucleotideCompound one, NucleotideCompound two, NucleotideCompound three, boolean start)
NucleotideCompound(String base, CompoundSet<NucleotideCompound> compoundSet, String complementStr, NucleotideCompound[] constituents)

Constructor parameters in org.biojava.nbio.core.sequence.compound with type arguments of type NucleotideCompound

Constructor and Description
NucleotideCompound(String base, CompoundSet<NucleotideCompound> compoundSet, String complementStr)
NucleotideCompound(String base, CompoundSet<NucleotideCompound> compoundSet, String complementStr, NucleotideCompound[] constituents)

Uses of NucleotideCompound in org.biojava.nbio.core.sequence.io

Methods in org.biojava.nbio.core.sequence.io that return types with arguments of type NucleotideCompound

Modifier and Type	Method and Description
AbstractSequence<NucleotideCompound>	ABITrace.getSequence() Returns the original programmatically determined (unedited) sequence as a AbstractSequence.
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	FileProxyDNASequenceCreator.getSequence(List<NucleotideCompound> list) Not sure of use case and currently not supported
AbstractSequence<NucleotideCompound>	FileProxyRNASequenceCreator.getSequence(List<NucleotideCompound> list) Not sure of use case and currently not supported
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	FileProxyDNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index) Should be able to extend the same concept to a remote URL call or database connection.
AbstractSequence<NucleotideCompound>	FileProxyRNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index) Should be able to extend the same concept to a remote URL call or database connection.
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	FileProxyDNASequenceCreator.getSequence(String sequence, long index) Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
AbstractSequence<NucleotideCompound>	FileProxyRNASequenceCreator.getSequence(String sequence, long index) Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.

Method parameters in org.biojava.nbio.core.sequence.io with type arguments of type NucleotideCompound

Modifier and Type	Method and Description
CompoundSet<Table.Codon>	IUPACParser.IUPACTable.getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds) Returns the compound set of codons
List<Table.Codon>	IUPACParser.IUPACTable.getCodons(CompoundSet<NucleotideCompound> nucelotides, CompoundSet<AminoAcidCompound> aminoAcids) Returns a list of codons where the source and target compounds are the same as those given by the parameters.
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	FileProxyDNASequenceCreator.getSequence(List<NucleotideCompound> list) Not sure of use case and currently not supported
AbstractSequence<NucleotideCompound>	FileProxyRNASequenceCreator.getSequence(List<NucleotideCompound> list) Not sure of use case and currently not supported
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	FileProxyDNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index) Should be able to extend the same concept to a remote URL call or database connection.
AbstractSequence<NucleotideCompound>	FileProxyRNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index) Should be able to extend the same concept to a remote URL call or database connection.

Constructor parameters in org.biojava.nbio.core.sequence.io with type arguments of type NucleotideCompound

Constructor and Description
DNASequenceCreator(CompoundSet<NucleotideCompound> compoundSet)
FastaGeneWriter(OutputStream os, Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase)
FastaGeneWriter(OutputStream os, Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase, int lineLength)
FileProxyDNASequenceCreator(File file, CompoundSet<NucleotideCompound> compoundSet, SequenceParserInterface sequenceParser) Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
FileProxyRNASequenceCreator(File file, CompoundSet<NucleotideCompound> compoundSet, SequenceParserInterface sequenceParser) Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
RNASequenceCreator(CompoundSet<NucleotideCompound> compoundSet)

Uses of NucleotideCompound in org.biojava.nbio.core.sequence.storage

Classes in org.biojava.nbio.core.sequence.storage with type parameters of type NucleotideCompound

Modifier and Type	Class and Description
class	TwoBitSequenceReader<C extends NucleotideCompound> Implementation of the 2bit encoding.
static class	TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound> Extension of the BitArrayWorker which provides the 2bit implementation code.

Uses of NucleotideCompound in org.biojava.nbio.core.sequence.template

Classes in org.biojava.nbio.core.sequence.template with type parameters of type NucleotideCompound

Modifier and Type	Class and Description
class	AbstractNucleotideCompoundSet<C extends NucleotideCompound>

Methods in org.biojava.nbio.core.sequence.template that return NucleotideCompound

Modifier and Type	Method and Description
NucleotideCompound	AbstractNucleotideCompoundSet.getAmbiguity(NucleotideCompound... compounds) Calculates the best symbol for a collection of compounds.

Methods in org.biojava.nbio.core.sequence.template with parameters of type NucleotideCompound

Modifier and Type	Method and Description
NucleotideCompound	AbstractNucleotideCompoundSet.getAmbiguity(NucleotideCompound... compounds) Calculates the best symbol for a collection of compounds.

Method parameters in org.biojava.nbio.core.sequence.template with type arguments of type NucleotideCompound

Modifier and Type	Method and Description
static int	SequenceMixin.countAT(Sequence<NucleotideCompound> sequence) Returns the count of AT in the given sequence
static int	SequenceMixin.countGC(Sequence<NucleotideCompound> sequence) Returns the count of GC in the given sequence

Uses of NucleotideCompound in org.biojava.nbio.core.sequence.transcription

Methods in org.biojava.nbio.core.sequence.transcription with type parameters of type NucleotideCompound

Modifier and Type	Method and Description
<C extends NucleotideCompound> Sequence<C>	Frame.wrap(Sequence<C> incoming) Optionally wraps a Sequence in a reverse complementing view (if the frame is on the reverse strand) and creates a sub sequence view if it is required.

Methods in org.biojava.nbio.core.sequence.transcription that return NucleotideCompound

Modifier and Type	Method and Description
NucleotideCompound	Table.Codon.getOne()
NucleotideCompound	Table.CaseInsensitiveTriplet.getOne()
NucleotideCompound	Table.Codon.getThree()
NucleotideCompound	Table.CaseInsensitiveTriplet.getThree()
NucleotideCompound	Table.Codon.getTwo()
NucleotideCompound	Table.CaseInsensitiveTriplet.getTwo()
NucleotideCompound	CaseInsensitiveCompound.getUnderlyingCompound()

Methods in org.biojava.nbio.core.sequence.transcription that return types with arguments of type NucleotideCompound

Modifier and Type	Method and Description
Sequence<NucleotideCompound>	DNAToRNATranslator.createSequence(Sequence<NucleotideCompound> originalSequence)
Sequence<NucleotideCompound>	DNAToRNATranslator.createSequence(Sequence<NucleotideCompound> originalSequence, Frame frame)
List<Sequence<NucleotideCompound>>	DNAToRNATranslator.createSequences(Sequence<NucleotideCompound> originalSequence) Overloaded local version which delegates to an optional translator when told to (specified during construction).
CompoundSet<NucleotideCompound>	TranscriptionEngine.getDnaCompounds()
CompoundSet<NucleotideCompound>	TranscriptionEngine.getRnaCompounds()
SequenceCreatorInterface<NucleotideCompound>	TranscriptionEngine.getRnaSequenceCreator()

Methods in org.biojava.nbio.core.sequence.transcription with parameters of type NucleotideCompound

Modifier and Type	Method and Description
int	Table.CaseInsensitiveTriplet.compoundToInt(NucleotideCompound c)

Method parameters in org.biojava.nbio.core.sequence.transcription with type arguments of type NucleotideCompound

Modifier and Type	Method and Description
Sequence<NucleotideCompound>	DNAToRNATranslator.createSequence(Sequence<NucleotideCompound> originalSequence)
Sequence<NucleotideCompound>	DNAToRNATranslator.createSequence(Sequence<NucleotideCompound> originalSequence, Frame frame)
List<Sequence<NucleotideCompound>>	DNAToRNATranslator.createSequences(Sequence<NucleotideCompound> originalSequence) Overloaded local version which delegates to an optional translator when told to (specified during construction).
List<Sequence<AminoAcidCompound>>	RNAToAminoAcidTranslator.createSequences(Sequence<NucleotideCompound> originalSequence) Performs the core conversion of RNA to Peptide.
TranscriptionEngine.Builder	TranscriptionEngine.Builder.dnaCompounds(CompoundSet<NucleotideCompound> compounds)
CompoundSet<Table.Codon>	Table.getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds)
List<Table.Codon>	Table.getCodons(CompoundSet<NucleotideCompound> nucelotides, CompoundSet<AminoAcidCompound> aminoAcids)
Map<Frame,Sequence<AminoAcidCompound>>	TranscriptionEngine.multipleFrameTranslation(Sequence<NucleotideCompound> dna, Frame... frames) A way of translating DNA in a number of frames
protected void	DNAToRNATranslator.postProcessCompoundLists(List<List<NucleotideCompound>> compoundLists)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.rnaCompounds(CompoundSet<NucleotideCompound> compounds)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.rnaCreator(SequenceCreatorInterface<NucleotideCompound> creator)
Sequence<AminoAcidCompound>	TranscriptionEngine.translate(Sequence<NucleotideCompound> dna) Quick method to let you go from a CDS to a Peptide quickly.
protected RNASequence	DNAToRNATranslator.wrapToRna(Sequence<NucleotideCompound> dna) Takes in the given DNA Sequence and returns an instance of RNASequence which is using RnaSequenceView as a ProxySequenceReader.

Constructors in org.biojava.nbio.core.sequence.transcription with parameters of type NucleotideCompound

Constructor and Description
CaseInsensitiveCompound(NucleotideCompound compound)
CaseInsensitiveTriplet(NucleotideCompound one, NucleotideCompound two, NucleotideCompound three)

Constructor parameters in org.biojava.nbio.core.sequence.transcription with type arguments of type NucleotideCompound

Constructor and Description
DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound> rnaCreator, CompoundSet<NucleotideCompound> dna, CompoundSet<NucleotideCompound> rna, boolean shortCutTranslation)
DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound> rnaCreator, CompoundSet<NucleotideCompound> dna, CompoundSet<NucleotideCompound> rna, boolean shortCutTranslation)
DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound> rnaCreator, CompoundSet<NucleotideCompound> dna, CompoundSet<NucleotideCompound> rna, boolean shortCutTranslation)
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons, boolean stopAtStopCodons, boolean waitForStartCodon)

Uses of NucleotideCompound in org.biojava.nbio.core.sequence.views

Methods in org.biojava.nbio.core.sequence.views that return NucleotideCompound

Modifier and Type	Method and Description
NucleotideCompound	RnaSequenceView.getCompoundAt(int position)

Methods in org.biojava.nbio.core.sequence.views that return types with arguments of type NucleotideCompound

Modifier and Type	Method and Description
Map<NucleotideCompound,NucleotideCompound>	RnaSequenceView.getDnaToRna()
Map<NucleotideCompound,NucleotideCompound>	RnaSequenceView.getDnaToRna()
Map<NucleotideCompound,NucleotideCompound>	RnaSequenceView.getRnaToDna()
Map<NucleotideCompound,NucleotideCompound>	RnaSequenceView.getRnaToDna()

Methods in org.biojava.nbio.core.sequence.views with parameters of type NucleotideCompound

Modifier and Type	Method and Description
int	RnaSequenceView.getIndexOf(NucleotideCompound compound)
int	RnaSequenceView.getLastIndexOf(NucleotideCompound compound)

Method parameters in org.biojava.nbio.core.sequence.views with type arguments of type NucleotideCompound

Modifier and Type	Method and Description
void	RnaSequenceView.setCompoundSet(CompoundSet<NucleotideCompound> compoundSet)

Constructor parameters in org.biojava.nbio.core.sequence.views with type arguments of type NucleotideCompound

Constructor and Description
RnaSequenceView(Sequence<NucleotideCompound> sourceDna)
RnaSequenceView(Sequence<NucleotideCompound> sourceDna, CompoundSet<NucleotideCompound> rnaCompounds)
RnaSequenceView(Sequence<NucleotideCompound> sourceDna, CompoundSet<NucleotideCompound> rnaCompounds)

Uses of NucleotideCompound in org.biojava.nbio.genome.io.fastq

Methods in org.biojava.nbio.genome.io.fastq that return types with arguments of type NucleotideCompound

Modifier and Type	Method and Description
static QuantityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>	FastqTools.createErrorProbabilities(Fastq fastq) Create and return a new QuantityFeature from the error probabilities of the specified FASTQ formatted sequence.
static QuantityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>	FastqTools.createErrorProbabilities(Fastq fastq) Create and return a new QuantityFeature from the error probabilities of the specified FASTQ formatted sequence.
static QualityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>	FastqTools.createQualityScores(Fastq fastq) Create and return a new QualityFeature from the quality scores of the specified FASTQ formatted sequence.
static QualityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>	FastqTools.createQualityScores(Fastq fastq) Create and return a new QualityFeature from the quality scores of the specified FASTQ formatted sequence.