Uses of Interface
org.biojava.nbio.core.sequence.template.CompoundSet

Packages that use CompoundSet

Package	Description
org.biojava.nbio.aaproperties.xml	Set of classes that handles the reading and writing of xml files.
org.biojava.nbio.alignment.template
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.matrices
org.biojava.nbio.core.alignment.template
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.compound
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.io.util
org.biojava.nbio.core.sequence.loader
org.biojava.nbio.core.sequence.storage
org.biojava.nbio.core.sequence.template
org.biojava.nbio.core.sequence.transcription
org.biojava.nbio.core.sequence.views

Uses of CompoundSet in org.biojava.nbio.aaproperties.xml

Classes in org.biojava.nbio.aaproperties.xml that implement CompoundSet

Modifier and Type	Class and Description
class	CaseFreeAminoAcidCompoundSet Set of proteinogenic amino acids.
class	ModifiedAminoAcidCompoundSet

Uses of CompoundSet in org.biojava.nbio.alignment.template

Methods in org.biojava.nbio.alignment.template that return CompoundSet

Modifier and Type	Method and Description
protected abstract CompoundSet<C>	AbstractMatrixAligner.getCompoundSet()
protected CompoundSet<C>	AbstractPairwiseSequenceAligner.getCompoundSet()
protected CompoundSet<C>	AbstractProfileProfileAligner.getCompoundSet()

Uses of CompoundSet in org.biojava.nbio.core.alignment

Methods in org.biojava.nbio.core.alignment that return CompoundSet

Modifier and Type	Method and Description
CompoundSet<C>	SimpleAlignedSequence.getCompoundSet()
CompoundSet<C>	SimpleProfile.getCompoundSet()

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

Methods in org.biojava.nbio.core.alignment.matrices that return CompoundSet

Modifier and Type	Method and Description
CompoundSet<AminoAcidCompound>	ScaledSubstitutionMatrix.getCompoundSet()
CompoundSet<C>	SimpleSubstitutionMatrix.getCompoundSet()

Constructors in org.biojava.nbio.core.alignment.matrices with parameters of type CompoundSet

Constructor and Description
SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, File fileInput) Creates a substitution matrix by reading in a file.
SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, Reader input, String name) Creates a substitution matrix by parsing some input.
SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, short match, short replace) Creates an identity substitution matrix from match and replace values.
SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, String matrixInput, String name) Creates a substitution matrix by parsing a String.

Uses of CompoundSet in org.biojava.nbio.core.alignment.template

Methods in org.biojava.nbio.core.alignment.template that return CompoundSet

Modifier and Type	Method and Description
CompoundSet<C>	SubstitutionMatrix.getCompoundSet() Returns the CompoundSet on which the matrix is defined.
CompoundSet<C>	Profile.getCompoundSet() Returns CompoundSet of all AlignedSequences

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

Methods in org.biojava.nbio.core.sequence that return CompoundSet

Modifier and Type	Method and Description
CompoundSet<C>	MultipleSequenceAlignment.getCompoundSet() Get the Compounds defined in the first sequence

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

Constructor and Description
BasicSequence(String sequence, CompoundSet<C> 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, 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.biojava.nbio.core.sequence.compound

Classes in org.biojava.nbio.core.sequence.compound that implement CompoundSet

Modifier and Type	Class and Description
class	AmbiguityDNACompoundSet
class	AmbiguityDNARNAHybridCompoundSet Ambiguity set for hybrid DNA/RNA sequences.
class	AmbiguityRNACompoundSet
class	AminoAcidCompoundSet Set of proteinogenic amino acids.
class	DNACompoundSet
class	RNACompoundSet

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

Modifier and Type	Method and Description
CompoundSet<AminoAcidCompound>	AminoAcidCompound.getCompoundSet()

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

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

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

Methods in org.biojava.nbio.core.sequence.io that return CompoundSet

Modifier and Type	Method and Description
CompoundSet<Table.Codon>	IUPACParser.IUPACTable.getCodonCompoundSet(CompoundSet<NucleotideCompound> rnaCompounds, CompoundSet<AminoAcidCompound> aminoAcidCompounds) Returns the compound set of codons
CompoundSet<?>	GenbankSequenceParser.getCompoundType()

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

Modifier and Type	Method and Description
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.biojava.nbio.core.sequence.io with parameters of type CompoundSet

Constructor and Description
CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)
DNASequenceCreator(CompoundSet<NucleotideCompound> compoundSet)
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
FileProxyProteinSequenceCreator(File file, CompoundSet<AminoAcidCompound> compoundSet, SequenceParserInterface sequenceParser) 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.biojava.nbio.core.sequence.io.util

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

Modifier and Type	Method and Description
static <C extends Compound> String	IOUtils.getGCGType(CompoundSet<C> cs) Determines GCG type

Uses of CompoundSet in org.biojava.nbio.core.sequence.loader

Methods in org.biojava.nbio.core.sequence.loader that return CompoundSet

Modifier and Type	Method and Description
CompoundSet<C>	UniprotProxySequenceReader.getCompoundSet()
CompoundSet<C>	StringProxySequenceReader.getCompoundSet()
CompoundSet<C>	SequenceFileProxyLoader.getCompoundSet()

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

Modifier and Type	Method and Description
static <C extends Compound> UniprotProxySequenceReader<C>	UniprotProxySequenceReader.parseUniprotXMLString(String xml, CompoundSet<C> compoundSet) The passed in xml is parsed as a DOM object so we know everything about the protein.
void	UniprotProxySequenceReader.setCompoundSet(CompoundSet<C> compoundSet)
void	StringProxySequenceReader.setCompoundSet(CompoundSet<C> compoundSet)
void	SequenceFileProxyLoader.setCompoundSet(CompoundSet<C> compoundSet)

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

Constructor and Description
GenbankProxySequenceReader(String genbankDirectoryCache, String accessionID, CompoundSet<C> compoundSet)
SequenceFileProxyLoader(File file, SequenceParserInterface sequenceParser, long sequenceStartIndex, int sequenceLength, CompoundSet<C> compoundSet)
StringProxySequenceReader(String sequence, CompoundSet<C> compoundSet)
UniprotProxySequenceReader(Document document, CompoundSet<C> compoundSet) The xml is passed in as a DOM object so we know everything about the protein.
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.biojava.nbio.core.sequence.storage

Methods in org.biojava.nbio.core.sequence.storage that return CompoundSet

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

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

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

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

Constructor and Description
ArrayListSequenceReader(List<C> compounds, CompoundSet<C> compoundSet)
ArrayListSequenceReader(String sequence, CompoundSet<C> compoundSet)
BitArrayWorker(CompoundSet<C> compoundSet, int length)
BitArrayWorker(CompoundSet<C> compoundSet, int[] sequence)
BitArrayWorker(String sequence, CompoundSet<C> compoundSet)
FourBitArrayWorker(CompoundSet<C> compoundSet, int length)
FourBitArrayWorker(CompoundSet<C> compoundSet, int[] sequence)
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
TwoBitArrayWorker(CompoundSet<C> compoundSet, int length)
TwoBitArrayWorker(CompoundSet<C> compoundSet, int[] sequence)
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.biojava.nbio.core.sequence.template

Classes in org.biojava.nbio.core.sequence.template that implement CompoundSet

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

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

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

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

Modifier and Type	Method and Description
void	SequenceReader.setCompoundSet(CompoundSet<C> compoundSet)
void	AbstractSequence.setCompoundSet(CompoundSet<C> compoundSet)

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

Constructor and Description
AbstractCompoundTranslator(SequenceCreatorInterface<T> creator, CompoundSet<F> fromCompoundSet, CompoundSet<T> toCompoundSet)
AbstractCompoundTranslator(SequenceCreatorInterface<T> creator, CompoundSet<F> fromCompoundSet, CompoundSet<T> toCompoundSet)
AbstractSequence(SequenceReader<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.biojava.nbio.core.sequence.transcription

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

Modifier and Type	Method and Description
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.biojava.nbio.core.sequence.transcription with parameters of type CompoundSet

Modifier and Type	Method and Description
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.biojava.nbio.core.sequence.transcription with parameters of type CompoundSet

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)
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons) Deprecated. Retained for backwards compatability, setting RNAToAminoAcidTranslator.stopAtStopCodons to false
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons) Deprecated. Retained for backwards compatability, setting RNAToAminoAcidTranslator.stopAtStopCodons to false
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons) Deprecated. Retained for backwards compatability, setting RNAToAminoAcidTranslator.stopAtStopCodons to false
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons, boolean stopAtStopCodons) Deprecated.
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons, boolean stopAtStopCodons) Deprecated.
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator, CompoundSet<NucleotideCompound> nucleotides, CompoundSet<Table.Codon> codons, CompoundSet<AminoAcidCompound> aminoAcids, Table table, boolean trimStops, boolean initMetOnly, boolean translateNCodons, boolean stopAtStopCodons) Deprecated.
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)
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)
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 CompoundSet in org.biojava.nbio.core.sequence.views

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

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

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

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