Uses of Interface
org.biojava3.core.sequence.template.CompoundSet

Packages that use CompoundSet

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

Uses of CompoundSet in org.biojava3.core.sequence

Methods in org.biojava3.core.sequence that return CompoundSet

CompoundSet<C>

MultipleSequenceAlignment.getCompoundSet() Get the Compounds defined in the first sequence

Constructors in org.biojava3.core.sequence with parameters of type CompoundSet

BasicSequence(String sequence, CompoundSet<C> 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, 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

ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, CompoundSet<AminoAcidCompound> compoundSet)
A protein sequence where the storage of the sequence is somewhere else with user defined set of amino acids.

ProteinSequence(String seqString, CompoundSet<AminoAcidCompound> compoundSet)
Create a protein from a string with a user defined set of amino acids

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 CompoundSet in org.biojava3.core.sequence.compound

Classes in org.biojava3.core.sequence.compound that implement CompoundSet

class	AmbiguityDNACompoundSet
class	AmbiguityRNACompoundSet
class	AminoAcidCompoundSet Set of proteinogenic amino acids.
class	DNACompoundSet
class	RNACompoundSet

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

CompoundSet<AminoAcidCompound>

AminoAcidCompound.getCompoundSet()

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

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

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

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

Methods in org.biojava3.core.sequence.io that return CompoundSet

CompoundSet<Table.Codon>

IUPACParser.IUPACTable.getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds) Returns the compound set of codons

Methods in org.biojava3.core.sequence.io with parameters of type CompoundSet

CompoundSet<Table.Codon>	IUPACParser.IUPACTable.getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds) Returns the compound set of codons
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.
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.

Constructors in org.biojava3.core.sequence.io with parameters of type CompoundSet

DNASequenceCreator(CompoundSet<NucleotideCompound> compoundSet)

FileProxyProteinSequenceCreator(File fastaFile, CompoundSet<AminoAcidCompound> compoundSet)
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read

ProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)

RNASequenceCreator(CompoundSet<NucleotideCompound> compoundSet)

Uses of CompoundSet in org.biojava3.core.sequence.io.util

Methods in org.biojava3.core.sequence.io.util with parameters of type CompoundSet

static <C extends Compound> String

IOUtils.getGCGType(CompoundSet<C> cs) Determines GCG type

Uses of CompoundSet in org.biojava3.core.sequence.loader

Methods in org.biojava3.core.sequence.loader that return CompoundSet

CompoundSet<C>	SequenceFileProxyLoader.getCompoundSet()
CompoundSet<C>	StringProxySequenceReader.getCompoundSet()
CompoundSet<C>	UniprotProxySequenceReader.getCompoundSet()

Methods in org.biojava3.core.sequence.loader with parameters of type CompoundSet

void	SequenceFileProxyLoader.setCompoundSet(CompoundSet<C> compoundSet)
void	StringProxySequenceReader.setCompoundSet(CompoundSet<C> compoundSet)
void	UniprotProxySequenceReader.setCompoundSet(CompoundSet<C> compoundSet)

Constructors in org.biojava3.core.sequence.loader with parameters of type CompoundSet

SequenceFileProxyLoader(File file, SequenceParserInterface sequenceParser, long sequenceStartIndex, int sequenceLength, CompoundSet<C> compoundSet)

StringProxySequenceReader(String sequence, CompoundSet<C> compoundSet)

UniprotProxySequenceReader(String accession, CompoundSet<C> compoundSet)
The uniprot id is used to retrieve the uniprot XML which is then parsed as a DOM object so we know everything about the protein.

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

Methods in org.biojava3.core.sequence.storage that return CompoundSet

CompoundSet<C>	SingleCompoundSequenceReader.getCompoundSet() Returns the compound set given at construction
CompoundSet<C>	BitSequenceReader.getCompoundSet() Returns the compound set backing this store
CompoundSet<C>	BitSequenceReader.BitArrayWorker.getCompoundSet() Returns the compound set backing this store
CompoundSet<C>	ArrayListSequenceReader.getCompoundSet()
CompoundSet<C>	JoiningSequenceReader.getCompoundSet()

Methods in org.biojava3.core.sequence.storage with parameters of type CompoundSet

String	SequenceAsStringHelper.getSequenceAsString(List<C> parsedCompounds, CompoundSet<C> compoundSet, Integer bioBegin, Integer bioEnd, Strand strand)
void	SingleCompoundSequenceReader.setCompoundSet(CompoundSet<C> compoundSet) Unsupported
void	BitSequenceReader.setCompoundSet(CompoundSet<C> compoundSet) Class is immutable & so this is unsupported
void	ArrayListSequenceReader.setCompoundSet(CompoundSet<C> compoundSet)
void	JoiningSequenceReader.setCompoundSet(CompoundSet<C> compoundSet)

Constructors in org.biojava3.core.sequence.storage with parameters of type CompoundSet

ArrayListSequenceReader(List<C> compounds, CompoundSet<C> compoundSet)

ArrayListSequenceReader(String sequence, CompoundSet<C> compoundSet)

BitSequenceReader.BitArrayWorker(CompoundSet<C> compoundSet, int length)

BitSequenceReader.BitArrayWorker(CompoundSet<C> compoundSet, int[] sequence)

BitSequenceReader.BitArrayWorker(String sequence, CompoundSet<C> compoundSet)

FourBitSequenceReader.FourBitArrayWorker(CompoundSet<C> compoundSet, int length)

FourBitSequenceReader.FourBitArrayWorker(CompoundSet<C> compoundSet, int[] sequence)

FourBitSequenceReader.FourBitArrayWorker(String sequence, CompoundSet<C> compoundSet)

FourBitSequenceReader(String sequence, CompoundSet<C> compoundSet)

FourBitSequenceReader(String sequence, CompoundSet<C> compoundSet, AccessionID accession)

JoiningSequenceReader(CompoundSet<C> compoundSet, List<Sequence<C>> sequences)

JoiningSequenceReader(CompoundSet<C> compoundSet, Sequence<C>... sequences)

SingleCompoundSequenceReader(C compound, CompoundSet<C> compoundSet, int length)
Build the object with a compound rather than a String

SingleCompoundSequenceReader(String compound, CompoundSet<C> compoundSet, int length)
Public constructor to be used with String based constructor

TwoBitSequenceReader.TwoBitArrayWorker(CompoundSet<C> compoundSet, int length)

TwoBitSequenceReader.TwoBitArrayWorker(CompoundSet<C> compoundSet, int[] sequence)

TwoBitSequenceReader.TwoBitArrayWorker(String sequence, CompoundSet<C> compoundSet)

TwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet)

TwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet, AccessionID accession)

Uses of CompoundSet in org.biojava3.core.sequence.template

Classes in org.biojava3.core.sequence.template that implement CompoundSet

class	AbstractCompoundSet<C extends Compound>
class	AbstractNucleotideCompoundSet<C extends NucleotideCompound>

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

CompoundSet<C>	LightweightProfile.getCompoundSet() Returns CompoundSet of all Sequences
CompoundSet<C>	AbstractSequence.getCompoundSet()
CompoundSet<C>	SequenceProxyView.getCompoundSet()
CompoundSet<C>	Sequence.getCompoundSet() Gets the compound set used to back this Sequence
CompoundSet<F>	AbstractCompoundTranslator.getFromCompoundSet()
CompoundSet<T>	AbstractCompoundTranslator.getToCompoundSet()

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

void	AbstractSequence.setCompoundSet(CompoundSet<C> compoundSet)
void	SequenceReader.setCompoundSet(CompoundSet<C> compoundSet)

Constructors in org.biojava3.core.sequence.template with parameters of type CompoundSet

AbstractCompoundTranslator(SequenceCreatorInterface<T> creator, CompoundSet<F> fromCompoundSet, CompoundSet<T> toCompoundSet)

AbstractCompoundTranslator(SequenceCreatorInterface<T> creator, CompoundSet<F> fromCompoundSet, CompoundSet<T> toCompoundSet)

AbstractSequence(ProxySequenceReader<C> proxyLoader, CompoundSet<C> compoundSet)
A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location of the sequence data.

AbstractSequence(String seqString, CompoundSet<C> compoundSet)
Create a Sequence from a simple string where the values should be found in compoundSet

Uses of CompoundSet in org.biojava3.core.sequence.transcription

Methods in org.biojava3.core.sequence.transcription that return CompoundSet

CompoundSet<AminoAcidCompound>	TranscriptionEngine.getAminoAcidCompounds()
CompoundSet<Table.Codon>	Table.getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds)
CompoundSet<NucleotideCompound>	TranscriptionEngine.getDnaCompounds()
CompoundSet<NucleotideCompound>	TranscriptionEngine.getRnaCompounds()

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

TranscriptionEngine.Builder	TranscriptionEngine.Builder.aminoAcidsCompounds(CompoundSet<AminoAcidCompound> compounds)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.dnaCompounds(CompoundSet<NucleotideCompound> compounds)
CompoundSet<Table.Codon>	Table.getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds)
CompoundSet<Table.Codon>	Table.getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds)
List<Table.Codon>	Table.getCodons(CompoundSet<NucleotideCompound> nucelotides, CompoundSet<AminoAcidCompound> aminoAcids)
List<Table.Codon>	Table.getCodons(CompoundSet<NucleotideCompound> nucelotides, CompoundSet<AminoAcidCompound> aminoAcids)
TranscriptionEngine.Builder	TranscriptionEngine.Builder.rnaCompounds(CompoundSet<NucleotideCompound> compounds)

Constructors in org.biojava3.core.sequence.transcription with parameters of type CompoundSet

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)

RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons)

RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons)

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

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

void	RnaSequenceView.setCompoundSet(CompoundSet<NucleotideCompound> compoundSet)

Constructors in org.biojava3.core.sequence.views with parameters of type CompoundSet

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