Uses of Class
org.biojava.nbio.core.sequence.ProteinSequence

Packages that use ProteinSequence

Package	Description
org.biojava.nbio.aaproperties	Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
org.biojava.nbio.aaproperties.profeat	Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
org.biojava.nbio.aaproperties.profeat.convertor	Set of classes that enable the conversion protein sequences into various attributes.
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.io
org.biojava.nbio.genome
org.biojava.nbio.genome.parsers.geneid
org.biojava.nbio.ronn	BioJava provide a module biojava-protein-disorder for prediction disordered regions from a protein sequence.
org.biojava.nbio.structure.align.multiple.util
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.ws.hmmer

Uses of ProteinSequence in org.biojava.nbio.aaproperties

Methods in org.biojava.nbio.aaproperties with parameters of type ProteinSequence

Modifier and Type	Method and Description
Map<AminoAcidCompound,Double>	PeptidePropertiesImpl.getAAComposition(ProteinSequence sequence)
Map<AminoAcidCompound,Double>	IPeptideProperties.getAAComposition(ProteinSequence sequence) Returns the composition of the 20 standard amino acid in the sequence.
double	PeptidePropertiesImpl.getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced)
double	IPeptideProperties.getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced) Returns the absorbance (optical density) of sequence.
double	PeptidePropertiesImpl.getApliphaticIndex(ProteinSequence sequence)
double	IPeptideProperties.getApliphaticIndex(ProteinSequence sequence) Returns the apliphatic index of sequence.
double	PeptidePropertiesImpl.getAvgHydropathy(ProteinSequence sequence)
double	IPeptideProperties.getAvgHydropathy(ProteinSequence sequence) Returns the average hydropathy value of sequence.
double	PeptidePropertiesImpl.getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode)
double	IPeptideProperties.getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode) Returns the composition of specified amino acid in the sequence.
double	PeptidePropertiesImpl.getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced)
double	IPeptideProperties.getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced) Returns the extinction coefficient of sequence.
double	PeptidePropertiesImpl.getInstabilityIndex(ProteinSequence sequence)
double	IPeptideProperties.getInstabilityIndex(ProteinSequence sequence) Returns the instability index of sequence.
double	PeptidePropertiesImpl.getIsoelectricPoint(ProteinSequence sequence)
double	IPeptideProperties.getIsoelectricPoint(ProteinSequence seuqence)
double	PeptidePropertiesImpl.getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues)
double	IPeptideProperties.getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues) Returns the isoelectric point of sequence.
double	PeptidePropertiesImpl.getMolecularWeight(ProteinSequence sequence)
double	IPeptideProperties.getMolecularWeight(ProteinSequence sequence) Returns the molecular weight of sequence.
double	PeptidePropertiesImpl.getMolecularWeight(ProteinSequence sequence, File aminoAcidCompositionFile)
double	IPeptideProperties.getMolecularWeight(ProteinSequence sequence, File aminoAcidCompositionFile) Returns the molecular weight of sequence.
double	PeptidePropertiesImpl.getMolecularWeight(ProteinSequence sequence, File elementMassFile, File aminoAcidCompositionFile)
double	IPeptideProperties.getMolecularWeight(ProteinSequence sequence, File elementMassFile, File aminoAcidCompositionFile) Returns the molecular weight of sequence.
double	PeptidePropertiesImpl.getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable)
double	IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable) Returns the molecular weight of sequence.
double	PeptidePropertiesImpl.getNetCharge(ProteinSequence sequence)
double	IPeptideProperties.getNetCharge(ProteinSequence sequence)
double	PeptidePropertiesImpl.getNetCharge(ProteinSequence sequence, boolean useExpasyValues)
double	IPeptideProperties.getNetCharge(ProteinSequence sequence, boolean useExpasyValues)
double	PeptidePropertiesImpl.getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint)
double	IPeptideProperties.getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint) Returns the net charge of sequence at pH 7.

Uses of ProteinSequence in org.biojava.nbio.aaproperties.profeat

Methods in org.biojava.nbio.aaproperties.profeat with parameters of type ProteinSequence

Modifier and Type	Method and Description
static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>>	ProfeatProperties.getComposition(ProteinSequence sequence)
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>>	ProfeatPropertiesImpl.getComposition(ProteinSequence sequence)
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>>	IProfeatProperties.getComposition(ProteinSequence sequence)
static Map<IProfeatProperties.GROUPING,Double>	ProfeatProperties.getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
Map<IProfeatProperties.GROUPING,Double>	ProfeatPropertiesImpl.getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
Map<IProfeatProperties.GROUPING,Double>	IProfeatProperties.getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
static double	ProfeatProperties.getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) An adaptor method which returns the composition of the specific grouping for the given attribute.
double	ProfeatPropertiesImpl.getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group)
double	IProfeatProperties.getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) Returns the composition of the specific grouping for the given attribute.
static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>>	ProfeatProperties.getDistributionPosition(ProteinSequence sequence)
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>>	ProfeatPropertiesImpl.getDistributionPosition(ProteinSequence sequence)
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>>	IProfeatProperties.getDistributionPosition(ProteinSequence sequence)
static Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>	ProfeatProperties.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>	ProfeatPropertiesImpl.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>	IProfeatProperties.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
static Map<IProfeatProperties.DISTRIBUTION,Double>	ProfeatProperties.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group)
Map<IProfeatProperties.DISTRIBUTION,Double>	ProfeatPropertiesImpl.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group)
Map<IProfeatProperties.DISTRIBUTION,Double>	IProfeatProperties.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group)
static double	ProfeatProperties.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) An adaptor method which computes and return the position with respect to the sequence where the given distribution of the grouping can be found. Example: "1111122222" For the above example, position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0) position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
double	ProfeatPropertiesImpl.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution)
double	IProfeatProperties.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) Computes and return the position with respect to the sequence where the given distribution of the grouping can be found. Example: "1111122222" For the above example, position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0) position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>>	ProfeatProperties.getTransition(ProteinSequence sequence)
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>>	ProfeatPropertiesImpl.getTransition(ProteinSequence sequence)
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>>	IProfeatProperties.getTransition(ProteinSequence sequence)
static Map<IProfeatProperties.TRANSITION,Double>	ProfeatProperties.getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
Map<IProfeatProperties.TRANSITION,Double>	ProfeatPropertiesImpl.getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
Map<IProfeatProperties.TRANSITION,Double>	IProfeatProperties.getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
static double	ProfeatProperties.getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) An adaptor method which returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
double	ProfeatPropertiesImpl.getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition)
double	IProfeatProperties.getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.

Uses of ProteinSequence in org.biojava.nbio.aaproperties.profeat.convertor

Methods in org.biojava.nbio.aaproperties.profeat.convertor with parameters of type ProteinSequence

Modifier and Type	Method and Description
String	Convertor.convert(ProteinSequence sequence) Returns the converted sequence.

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

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

Modifier and Type	Method and Description
ProteinSequence	TranscriptSequence.getProteinSequence() Get the protein sequence
ProteinSequence	RNASequence.getProteinSequence() Get the ProteinSequence from the RNA sequence
ProteinSequence	TranscriptSequence.getProteinSequence(TranscriptionEngine engine) Get the protein sequence with user defined TranscriptEngine
ProteinSequence	RNASequence.getProteinSequence(TranscriptionEngine engine) Get the ProteinSequene from the RNA sequence with user defined transcription engine

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

Modifier and Type	Method and Description
ArrayList<ProteinSequence>	TranscriptSequence.getProteinCDSSequences() Return a list of protein sequences based on each CDS sequence where the phase shift between two CDS sequences is assigned to the CDS sequence that starts the triplet.

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

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

Modifier and Type	Method and Description
static LinkedHashMap<String,ProteinSequence>	FastaReaderHelper.readFastaProteinSequence(File file) Read a fasta file containing amino acids with setup that would handle most cases.
static LinkedHashMap<String,ProteinSequence>	FastaReaderHelper.readFastaProteinSequence(InputStream inStream) Read a fasta file containing amino acids with setup that would handle most cases.
static LinkedHashMap<String,ProteinSequence>	GenbankReaderHelper.readGenbankProteinSequence(File file) Read a Genbank file containing amino acids with setup that would handle most cases.
static LinkedHashMap<String,ProteinSequence>	GenbankReaderHelper.readGenbankProteinSequence(File file, boolean lazySequenceLoad) Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
static LinkedHashMap<String,ProteinSequence>	GenbankReaderHelper.readGenbankProteinSequence(InputStream inStream) Read a Genbank file containing amino acids with setup that would handle most cases.

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

Modifier and Type	Method and Description
static void	CasePreservingProteinSequenceCreator.setLowercaseToNull(ProteinSequence seq, Object[] out) Takes a ProteinSequence which was created by a CasePreservingProteinSequenceCreator.

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

Modifier and Type	Method and Description
static void	GenbankWriterHelper.writeProteinSequence(File file, Collection<ProteinSequence> proteinSequences) Write collection of protein sequences to a file
static void	FastaWriterHelper.writeProteinSequence(File file, Collection<ProteinSequence> proteinSequences) Write collection of protein sequences to a file
static void	GenbankWriterHelper.writeProteinSequence(OutputStream outputStream, Collection<ProteinSequence> proteinSequences) Write collection of protein sequences to a stream
static void	FastaWriterHelper.writeProteinSequence(OutputStream outputStream, Collection<ProteinSequence> proteinSequences) Write collection of protein sequences to a stream

Uses of ProteinSequence in org.biojava.nbio.genome

Methods in org.biojava.nbio.genome that return types with arguments of type ProteinSequence

Modifier and Type	Method and Description
static LinkedHashMap<String,ProteinSequence>	GeneFeatureHelper.getProteinSequences(Collection<ChromosomeSequence> chromosomeSequences)

Uses of ProteinSequence in org.biojava.nbio.genome.parsers.geneid

Methods in org.biojava.nbio.genome.parsers.geneid that return types with arguments of type ProteinSequence

Modifier and Type	Method and Description
LinkedHashMap<String,ProteinSequence>	GeneIDXMLReader.getProteinSequences()

Uses of ProteinSequence in org.biojava.nbio.ronn

Methods in org.biojava.nbio.ronn with parameters of type ProteinSequence

Modifier and Type	Method and Description
static FastaSequence	Jronn.convertProteinSequencetoFasta(ProteinSequence sequence) Utility method to convert a BioJava ProteinSequence object to the FastaSequence object used internally in JRonn.
static float[]	Jronn.getDisorderScores(ProteinSequence sequence) Calculates the probability value for each residue in the protein sequence, telling the probability that the residue belongs to disordered region.

Uses of ProteinSequence in org.biojava.nbio.structure.align.multiple.util

Methods in org.biojava.nbio.structure.align.multiple.util that return types with arguments of type ProteinSequence

Modifier and Type	Method and Description
static MultipleSequenceAlignment<ProteinSequence,AminoAcidCompound>	MultipleAlignmentTools.toProteinMSA(MultipleAlignment msta) Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid residues.

Uses of ProteinSequence in org.biojava.nbio.structure.io

Methods in org.biojava.nbio.structure.io that return ProteinSequence

Modifier and Type	Method and Description
static ProteinSequence	StructureSequenceMatcher.getProteinSequenceForStructure(Structure struct, Map<Integer,Group> groupIndexPosition) Generates a ProteinSequence corresponding to the sequence of struct, and maintains a mapping from the sequence back to the original groups.
ProteinSequence[]	FastaStructureParser.getSequences() Gets the protein sequences read from the Fasta file.
static ProteinSequence	StructureSequenceMatcher.removeGaps(ProteinSequence gapped) Removes all gaps ('-') from a protein sequence

Methods in org.biojava.nbio.structure.io with parameters of type ProteinSequence

Modifier and Type	Method and Description
static AFPChain	FastaAFPChainConverter.cpFastaToAfpChain(ProteinSequence first, ProteinSequence second, Structure structure, int cpSite) Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
static AFPChain	FastaAFPChainConverter.fastaToAfpChain(ProteinSequence sequence1, ProteinSequence sequence2, Structure structure1, Structure structure2) Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
static Structure	StructureSequenceMatcher.getSubstructureMatchingProteinSequence(ProteinSequence sequence, Structure wholeStructure) Get a substructure of wholeStructure containing only the Groups that are included in sequence.
static ResidueNumber[]	StructureSequenceMatcher.matchSequenceToStructure(ProteinSequence seq, Structure struct) Given a sequence and the corresponding Structure, get the ResidueNumber for each residue in the sequence.
static ProteinSequence	StructureSequenceMatcher.removeGaps(ProteinSequence gapped) Removes all gaps ('-') from a protein sequence

Method parameters in org.biojava.nbio.structure.io with type arguments of type ProteinSequence

Modifier and Type	Method and Description
static AFPChain	FastaAFPChainConverter.fastaToAfpChain(Map<String,ProteinSequence> sequences, Structure structure1, Structure structure2) Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment.

Constructor parameters in org.biojava.nbio.structure.io with type arguments of type ProteinSequence

Constructor and Description
FastaStructureParser(FastaReader<ProteinSequence,AminoAcidCompound> reader, AtomCache cache)
FastaStructureParser(File file, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(InputStream is, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)

Uses of ProteinSequence in org.biojava.nbio.ws.hmmer

Methods in org.biojava.nbio.ws.hmmer with parameters of type ProteinSequence

Modifier and Type	Method and Description
SortedSet<HmmerResult>	RemoteHmmerScan.scan(ProteinSequence sequence)
SortedSet<HmmerResult>	HmmerScan.scan(ProteinSequence sequence)
SortedSet<HmmerResult>	RemoteHmmerScan.scan(ProteinSequence sequence, URL serviceLocation) Scans a protein sequence for Pfam profile matches.