Uses of Class
org.biojava3.core.sequence.compound.NucleotideCompound

Packages that use NucleotideCompound

org.biojava3.core.sequence
org.biojava3.core.sequence.compound
org.biojava3.core.sequence.io
org.biojava3.core.sequence.storage
org.biojava3.core.sequence.template
org.biojava3.core.sequence.transcription
org.biojava3.core.sequence.views

Uses of NucleotideCompound in org.biojava3.core.sequence

Methods in org.biojava3.core.sequence that return types with arguments of type NucleotideCompound

SequenceView<NucleotideCompound>	DNASequence.getComplement() Returns a Sequence which will complement every base
SequenceView<NucleotideCompound>	RNASequence.getComplement() Get the complement view of the RNA sequence
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>	DNASequence.getReverseComplement() Delegates to AbstractSequence.getInverse() for the reverse complement
SequenceView<NucleotideCompound>	RNASequence.getReverseComplement() Get reverse complement view of the sequence

Constructor parameters in org.biojava3.core.sequence with type arguments of type NucleotideCompound

ChromosomeSequence(ProxySequenceReader<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(ProxySequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet)
Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet

ChromosomeSequence(ProxySequenceReader<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(ProxySequenceReader<NucleotideCompound> proxyLoader)
Create a sequence where the actual storage of the sequence data is somewhere else

DNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet)
Create a sequence from a ProxySequencereader and user defined compound set

DNASequence(ProxySequenceReader<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.biojava3.core.sequence.compound

Methods in org.biojava3.core.sequence.compound that return NucleotideCompound

NucleotideCompound	CodonCompound.getOne()
NucleotideCompound	CodonCompound.getThree()
NucleotideCompound	CodonCompound.getTwo()
NucleotideCompound	RNACompoundSet.newNucleotideCompound(String base, String complement, String... equivalents)
NucleotideCompound	DNACompoundSet.newNucleotideCompound(String base, String complement, String... equivalents)

Methods in org.biojava3.core.sequence.compound that return types with arguments of type NucleotideCompound

Set<NucleotideCompound>

NucleotideCompound.getConsituents()

Constructors in org.biojava3.core.sequence.compound with parameters of type NucleotideCompound

CodonCompound(NucleotideCompound one, NucleotideCompound two, NucleotideCompound three, boolean start)

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

Constructor parameters in org.biojava3.core.sequence.compound with type arguments of type NucleotideCompound

NucleotideCompound(String base, CompoundSet<NucleotideCompound> compoundSet, String complementStr)

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

Uses of NucleotideCompound in org.biojava3.core.sequence.io

Methods in org.biojava3.core.sequence.io that return types with arguments of type NucleotideCompound

AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(String sequence, long index)

Method parameters in org.biojava3.core.sequence.io with type arguments of type NucleotideCompound

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>	RNASequenceCreator.getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)

Constructor parameters in org.biojava3.core.sequence.io with type arguments of type NucleotideCompound

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)

RNASequenceCreator(CompoundSet<NucleotideCompound> compoundSet)

Uses of NucleotideCompound in org.biojava3.core.sequence.storage

Classes in org.biojava3.core.sequence.storage with type parameters of type NucleotideCompound

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.biojava3.core.sequence.template

Classes in org.biojava3.core.sequence.template with type parameters of type NucleotideCompound

class

AbstractNucleotideCompoundSet<C extends NucleotideCompound>

Methods in org.biojava3.core.sequence.template that return NucleotideCompound

NucleotideCompound

AbstractNucleotideCompoundSet.getAmbiguity(NucleotideCompound... compounds) Calculates the best symbol for a collection of compounds.

Methods in org.biojava3.core.sequence.template with parameters of type NucleotideCompound

NucleotideCompound

AbstractNucleotideCompoundSet.getAmbiguity(NucleotideCompound... compounds) Calculates the best symbol for a collection of compounds.

Method parameters in org.biojava3.core.sequence.template with type arguments of type NucleotideCompound

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.biojava3.core.sequence.transcription

Methods in org.biojava3.core.sequence.transcription with type parameters of type NucleotideCompound

<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.biojava3.core.sequence.transcription that return NucleotideCompound

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.biojava3.core.sequence.transcription that return types with arguments of type NucleotideCompound

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.biojava3.core.sequence.transcription with parameters of type NucleotideCompound

int	Table.CaseInsensitiveTriplet.compoundToInt(NucleotideCompound c)

Method parameters in org.biojava3.core.sequence.transcription with type arguments of type NucleotideCompound

Sequence<NucleotideCompound>	DNAToRNATranslator.createSequence(Sequence<NucleotideCompound> originalSequence)
Sequence<NucleotideCompound>	DNAToRNATranslator.createSequence(Sequence<NucleotideCompound> originalSequence, Frame frame)
List<Sequence<AminoAcidCompound>>	RNAToAminoAcidTranslator.createSequences(Sequence<NucleotideCompound> originalSequence) Performs the core conversion of RNA to Peptide.
List<Sequence<NucleotideCompound>>	DNAToRNATranslator.createSequences(Sequence<NucleotideCompound> originalSequence) Overloaded local version which delegates to an optional translator when told to (specified during construction).
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.biojava3.core.sequence.transcription with parameters of type NucleotideCompound

CaseInsensitiveCompound(NucleotideCompound compound)

Table.CaseInsensitiveTriplet(NucleotideCompound one, NucleotideCompound two, NucleotideCompound three)

Constructor parameters in org.biojava3.core.sequence.transcription with type arguments of type NucleotideCompound

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)

Uses of NucleotideCompound in org.biojava3.core.sequence.views

Methods in org.biojava3.core.sequence.views that return NucleotideCompound

NucleotideCompound

RnaSequenceView.getCompoundAt(int position)

Methods in org.biojava3.core.sequence.views that return types with arguments of type NucleotideCompound

Map<NucleotideCompound,NucleotideCompound>	RnaSequenceView.getDnaToRna()
Map<NucleotideCompound,NucleotideCompound>	RnaSequenceView.getDnaToRna()
Map<NucleotideCompound,NucleotideCompound>	RnaSequenceView.getRnaToDna()
Map<NucleotideCompound,NucleotideCompound>	RnaSequenceView.getRnaToDna()

Methods in org.biojava3.core.sequence.views with parameters of type NucleotideCompound

int	RnaSequenceView.getIndexOf(NucleotideCompound compound)
int	RnaSequenceView.getLastIndexOf(NucleotideCompound compound)

Method parameters in org.biojava3.core.sequence.views with type arguments of type NucleotideCompound

void	RnaSequenceView.setCompoundSet(CompoundSet<NucleotideCompound> compoundSet)

Constructor parameters in org.biojava3.core.sequence.views with type arguments of type NucleotideCompound

RnaSequenceView(Sequence<NucleotideCompound> sourceDna)

RnaSequenceView(Sequence<NucleotideCompound> sourceDna, CompoundSet<NucleotideCompound> rnaCompounds)

RnaSequenceView(Sequence<NucleotideCompound> sourceDna, CompoundSet<NucleotideCompound> rnaCompounds)