Uses of Class
org.biojava.nbio.core.sequence.ProteinSequence
Packages that use ProteinSequence
Package
Description
Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
Set of classes that enable the conversion protein sequences into various attributes.
BioJava provide a module biojava-protein-disorder for prediction disordered regions
from a protein sequence.
Input and Output of Structures
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Uses of ProteinSequence in org.biojava.nbio.aaproperties
Methods in org.biojava.nbio.aaproperties with parameters of type ProteinSequenceModifier and TypeMethodDescriptionIPeptideProperties.getAAComposition(ProteinSequence sequence) Returns the composition of the 20 standard amino acid in the sequence.PeptidePropertiesImpl.getAAComposition(ProteinSequence sequence) doubleIPeptideProperties.getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced) Returns the absorbance (optical density) of sequence.doublePeptidePropertiesImpl.getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced) doubleIPeptideProperties.getApliphaticIndex(ProteinSequence sequence) Returns the apliphatic index of sequence.doublePeptidePropertiesImpl.getApliphaticIndex(ProteinSequence sequence) doubleIPeptideProperties.getAromaticity(ProteinSequence sequence) Calculates the aromaticity value of a protein according to Lobry, 1994.doublePeptidePropertiesImpl.getAromaticity(ProteinSequence sequence) doubleIPeptideProperties.getAvgHydropathy(ProteinSequence sequence) Returns the average hydropathy value of sequence.doublePeptidePropertiesImpl.getAvgHydropathy(ProteinSequence sequence) doubleIPeptideProperties.getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode) Returns the composition of specified amino acid in the sequence.doublePeptidePropertiesImpl.getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode) doubleIPeptideProperties.getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced) Returns the extinction coefficient of sequence.doublePeptidePropertiesImpl.getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced) doubleIPeptideProperties.getInstabilityIndex(ProteinSequence sequence) Returns the instability index of sequence.doublePeptidePropertiesImpl.getInstabilityIndex(ProteinSequence sequence) doubleIPeptideProperties.getIsoelectricPoint(ProteinSequence seuqence) doubleIPeptideProperties.getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues) Returns the isoelectric point of sequence.doublePeptidePropertiesImpl.getIsoelectricPoint(ProteinSequence sequence) doublePeptidePropertiesImpl.getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues) doubleIPeptideProperties.getMolecularWeight(ProteinSequence sequence) Returns the molecular weight of sequence.doubleIPeptideProperties.getMolecularWeight(ProteinSequence sequence, File aminoAcidCompositionFile) Returns the molecular weight of sequence.doubleIPeptideProperties.getMolecularWeight(ProteinSequence sequence, File elementMassFile, File aminoAcidCompositionFile) Returns the molecular weight of sequence.doublePeptidePropertiesImpl.getMolecularWeight(ProteinSequence sequence) doublePeptidePropertiesImpl.getMolecularWeight(ProteinSequence sequence, File aminoAcidCompositionFile) doublePeptidePropertiesImpl.getMolecularWeight(ProteinSequence sequence, File elementMassFile, File aminoAcidCompositionFile) doubleIPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable) Returns the molecular weight of sequence.doublePeptidePropertiesImpl.getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable) doubleIPeptideProperties.getNetCharge(ProteinSequence sequence) doubleIPeptideProperties.getNetCharge(ProteinSequence sequence, boolean useExpasyValues) doubleIPeptideProperties.getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint) Returns the net charge of sequence at pH 7.doublePeptidePropertiesImpl.getNetCharge(ProteinSequence sequence) doublePeptidePropertiesImpl.getNetCharge(ProteinSequence sequence, boolean useExpasyValues) doublePeptidePropertiesImpl.getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint) -
Uses of ProteinSequence in org.biojava.nbio.aaproperties.profeat
Methods in org.biojava.nbio.aaproperties.profeat with parameters of type ProteinSequenceModifier and TypeMethodDescriptionIProfeatProperties.getComposition(ProteinSequence sequence) IProfeatProperties.getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) doubleIProfeatProperties.getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) Returns the composition of the specific grouping for the given attribute.ProfeatProperties.getComposition(ProteinSequence sequence) static Map<IProfeatProperties.GROUPING, Double> ProfeatProperties.getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) static doubleProfeatProperties.getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) An adaptor method which returns the composition of the specific grouping for the given attribute.ProfeatPropertiesImpl.getComposition(ProteinSequence sequence) ProfeatPropertiesImpl.getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) doubleProfeatPropertiesImpl.getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) Map<IProfeatProperties.ATTRIBUTE, Map<IProfeatProperties.GROUPING, Map<IProfeatProperties.DISTRIBUTION, Double>>> IProfeatProperties.getDistributionPosition(ProteinSequence sequence) IProfeatProperties.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) IProfeatProperties.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) doubleIProfeatProperties.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.GROUPING, Map<IProfeatProperties.DISTRIBUTION, Double>>> ProfeatProperties.getDistributionPosition(ProteinSequence sequence) ProfeatProperties.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) static Map<IProfeatProperties.DISTRIBUTION, Double> ProfeatProperties.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) static doubleProfeatProperties.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)Map<IProfeatProperties.ATTRIBUTE, Map<IProfeatProperties.GROUPING, Map<IProfeatProperties.DISTRIBUTION, Double>>> ProfeatPropertiesImpl.getDistributionPosition(ProteinSequence sequence) ProfeatPropertiesImpl.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) ProfeatPropertiesImpl.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) doubleProfeatPropertiesImpl.getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) IProfeatProperties.getTransition(ProteinSequence sequence) IProfeatProperties.getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) doubleIProfeatProperties.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.ProfeatProperties.getTransition(ProteinSequence sequence) static Map<IProfeatProperties.TRANSITION, Double> ProfeatProperties.getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) static doubleProfeatProperties.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.ProfeatPropertiesImpl.getTransition(ProteinSequence sequence) ProfeatPropertiesImpl.getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) doubleProfeatPropertiesImpl.getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) -
Uses of ProteinSequence in org.biojava.nbio.aaproperties.profeat.convertor
Methods in org.biojava.nbio.aaproperties.profeat.convertor with parameters of type ProteinSequenceModifier and TypeMethodDescriptionConvertor.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 ProteinSequenceModifier and TypeMethodDescriptionRNASequence.getProteinSequence()Get the ProteinSequence from the RNA sequenceRNASequence.getProteinSequence(TranscriptionEngine engine) Get the ProteinSequence from the RNA sequence with user-defined transcription engineTranscriptSequence.getProteinSequence()Get the protein sequenceTranscriptSequence.getProteinSequence(TranscriptionEngine engine) Get the protein sequence with user defined TranscriptEngineMethods in org.biojava.nbio.core.sequence that return types with arguments of type ProteinSequenceModifier and TypeMethodDescriptionTranscriptSequence.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 ProteinSequenceModifier and TypeMethodDescriptionprotected ProteinSequenceFastaStreamer.createSequence(ProteinSequence sequence) Create the sequence with the information from the header.Methods in org.biojava.nbio.core.sequence.io that return types with arguments of type ProteinSequenceModifier and TypeMethodDescriptionFastaStreamer.each()Enable iteration through the proteins in the file using syntax such as:FastaStreamer.getHeaderParser()static Map<String, ProteinSequence> FastaReaderHelper.readFastaProteinSequence(File file) Read a fasta file containing amino acids with setup that would handle most cases.static Map<String, ProteinSequence> FastaReaderHelper.readFastaProteinSequence(InputStream inStream) Read a fasta file containing amino acids with setup that would handle most cases.static Map<String, ProteinSequence> GenbankReaderHelper.readGenbankProteinSequence(File file) Read a Genbank file containing amino acids with setup that would handle most cases.static Map<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 Map<String, ProteinSequence> GenbankReaderHelper.readGenbankProteinSequence(InputStream inStream) Read a Genbank file containing amino acids with setup that would handle most cases.FastaStreamer.stream()Create a stream of protein sequences from the contents of the pathMethods in org.biojava.nbio.core.sequence.io with parameters of type ProteinSequenceModifier and TypeMethodDescriptionprotected ProteinSequenceFastaStreamer.createSequence(ProteinSequence sequence) Create the sequence with the information from the header.static voidCasePreservingProteinSequenceCreator.setLowercaseToNull(ProteinSequence seq, Object[] out) Takes aProteinSequencewhich was created by aCasePreservingProteinSequenceCreator.Method parameters in org.biojava.nbio.core.sequence.io with type arguments of type ProteinSequenceModifier and TypeMethodDescriptionFastaStreamer.withHeaderParser(SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser) static voidFastaWriterHelper.writeProteinSequence(File file, Collection<ProteinSequence> proteinSequences) Write collection of protein sequences to a filestatic voidFastaWriterHelper.writeProteinSequence(OutputStream outputStream, Collection<ProteinSequence> proteinSequences) Write collection of protein sequences to a streamstatic voidGenbankWriterHelper.writeProteinSequence(File file, Collection<ProteinSequence> proteinSequences) Write collection of protein sequences to a filestatic voidGenbankWriterHelper.writeProteinSequence(OutputStream outputStream, Collection<ProteinSequence> proteinSequences) Write collection of protein sequences to a stream -
Uses of ProteinSequence in org.biojava.nbio.core.util
Methods in org.biojava.nbio.core.util with parameters of type ProteinSequenceModifier and TypeMethodDescriptionstatic booleanSequenceTools.equalLengthSequences(ProteinSequence[] sequences) A method to check whether an array of sequences contains at least two sequences having an equal length. -
Uses of ProteinSequence in org.biojava.nbio.genome
Methods in org.biojava.nbio.genome that return types with arguments of type ProteinSequenceModifier and TypeMethodDescriptionstatic 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 -
Uses of ProteinSequence in org.biojava.nbio.genome.util
Methods in org.biojava.nbio.genome.util that return ProteinSequenceModifier and TypeMethodDescriptionstatic ProteinSequenceProteinMappingTools.convertDNAtoProteinSequence(String dnaSequence) Converts the DNA sequence to protein sequence.static ProteinSequenceProteinMappingTools.convertDNAtoProteinSequence(DNASequence dnaSequence) Converts the DNA sequence to protein sequence. -
Uses of ProteinSequence in org.biojava.nbio.ronn
Methods in org.biojava.nbio.ronn with parameters of type ProteinSequenceModifier and TypeMethodDescriptionstatic FastaSequenceJronn.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 ProteinSequenceModifier and TypeMethodDescriptionMultipleAlignmentTools.toProteinMSA(MultipleAlignment msta) Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid residues. -
Uses of ProteinSequence in org.biojava.nbio.structure.cluster
Methods in org.biojava.nbio.structure.cluster that return ProteinSequenceModifier and TypeMethodDescriptionSubunit.getProteinSequence()Get the protein sequence of the Subunit. -
Uses of ProteinSequence in org.biojava.nbio.structure.io
Methods in org.biojava.nbio.structure.io that return ProteinSequenceModifier and TypeMethodDescriptionstatic ProteinSequenceStructureSequenceMatcher.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.FastaStructureParser.getSequences()Gets the protein sequences read from the Fasta file.static ProteinSequenceStructureSequenceMatcher.removeGaps(ProteinSequence gapped) Removes all gaps ('-') from a protein sequenceMethods in org.biojava.nbio.structure.io with parameters of type ProteinSequenceModifier and TypeMethodDescriptionstatic AFPChainFastaAFPChainConverter.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 sitecpSiteresidues to the right.static AFPChainFastaAFPChainConverter.fastaToAfpChain(ProteinSequence sequence1, ProteinSequence sequence2, Structure structure1, Structure structure2) Returns an AFPChain corresponding to the alignment betweenstructure1andstructure2, which is given by the gapped protein sequencessequence1andsequence2.static StructureStructureSequenceMatcher.getSubstructureMatchingProteinSequence(ProteinSequence sequence, Structure wholeStructure) 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 ProteinSequenceStructureSequenceMatcher.removeGaps(ProteinSequence gapped) Removes all gaps ('-') from a protein sequenceMethod parameters in org.biojava.nbio.structure.io with type arguments of type ProteinSequenceModifier and TypeMethodDescriptionstatic AFPChainFastaAFPChainConverter.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 ProteinSequenceModifierConstructorDescriptionFastaStructureParser(File file, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache) FastaStructureParser(InputStream is, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache) FastaStructureParser(FastaReader<ProteinSequence, AminoAcidCompound> reader, AtomCache cache) -
Uses of ProteinSequence in org.biojava.nbio.ws.hmmer
Methods in org.biojava.nbio.ws.hmmer with parameters of type ProteinSequenceModifier and TypeMethodDescriptionHmmerScan.scan(ProteinSequence sequence) RemoteHmmerScan.scan(ProteinSequence sequence) RemoteHmmerScan.scan(ProteinSequence sequence, URL serviceLocation) Scans a protein sequence for Pfam profile matches.