Uses of Class
org.biojava.nbio.core.sequence.ProteinSequence
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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.core.util org.biojava.nbio.genome org.biojava.nbio.genome.parsers.geneid org.biojava.nbio.genome.util 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.cluster org.biojava.nbio.structure.io Input and Output of Structuresorg.biojava.nbio.ws.hmmer -
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Uses of ProteinSequence in org.biojava.nbio.aaproperties
Methods in org.biojava.nbio.aaproperties with parameters of type ProteinSequence Modifier and Type Method Description java.util.Map<AminoAcidCompound,java.lang.Double>
IPeptideProperties. getAAComposition(ProteinSequence sequence)
Returns the composition of the 20 standard amino acid in the sequence.java.util.Map<AminoAcidCompound,java.lang.Double>
PeptidePropertiesImpl. getAAComposition(ProteinSequence sequence)
double
IPeptideProperties. getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced)
Returns the absorbance (optical density) of sequence.double
PeptidePropertiesImpl. getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced)
double
IPeptideProperties. getApliphaticIndex(ProteinSequence sequence)
Returns the apliphatic index of sequence.double
PeptidePropertiesImpl. getApliphaticIndex(ProteinSequence sequence)
double
IPeptideProperties. getAvgHydropathy(ProteinSequence sequence)
Returns the average hydropathy value of sequence.double
PeptidePropertiesImpl. getAvgHydropathy(ProteinSequence sequence)
double
IPeptideProperties. getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode)
Returns the composition of specified amino acid in the sequence.double
PeptidePropertiesImpl. getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode)
double
IPeptideProperties. getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced)
Returns the extinction coefficient of sequence.double
PeptidePropertiesImpl. getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced)
double
IPeptideProperties. getInstabilityIndex(ProteinSequence sequence)
Returns the instability index of sequence.double
PeptidePropertiesImpl. getInstabilityIndex(ProteinSequence sequence)
double
IPeptideProperties. getIsoelectricPoint(ProteinSequence seuqence)
double
IPeptideProperties. getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues)
Returns the isoelectric point of sequence.double
PeptidePropertiesImpl. getIsoelectricPoint(ProteinSequence sequence)
double
PeptidePropertiesImpl. getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues)
double
IPeptideProperties. getMolecularWeight(ProteinSequence sequence)
Returns the molecular weight of sequence.double
IPeptideProperties. getMolecularWeight(ProteinSequence sequence, java.io.File aminoAcidCompositionFile)
Returns the molecular weight of sequence.double
IPeptideProperties. getMolecularWeight(ProteinSequence sequence, java.io.File elementMassFile, java.io.File aminoAcidCompositionFile)
Returns the molecular weight of sequence.double
PeptidePropertiesImpl. getMolecularWeight(ProteinSequence sequence)
double
PeptidePropertiesImpl. getMolecularWeight(ProteinSequence sequence, java.io.File aminoAcidCompositionFile)
double
PeptidePropertiesImpl. getMolecularWeight(ProteinSequence sequence, java.io.File elementMassFile, java.io.File aminoAcidCompositionFile)
double
IPeptideProperties. getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable)
Returns the molecular weight of sequence.double
PeptidePropertiesImpl. getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable)
double
IPeptideProperties. getNetCharge(ProteinSequence sequence)
double
IPeptideProperties. getNetCharge(ProteinSequence sequence, boolean useExpasyValues)
double
IPeptideProperties. getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint)
Returns the net charge of sequence at pH 7.double
PeptidePropertiesImpl. getNetCharge(ProteinSequence sequence)
double
PeptidePropertiesImpl. getNetCharge(ProteinSequence sequence, boolean useExpasyValues)
double
PeptidePropertiesImpl. getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint)
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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 Description java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>>
IProfeatProperties. getComposition(ProteinSequence sequence)
java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>
IProfeatProperties. getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
double
IProfeatProperties. getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group)
Returns the composition of the specific grouping for the given attribute.static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>>
ProfeatProperties. getComposition(ProteinSequence sequence)
static java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>
ProfeatProperties. 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.java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>>
ProfeatPropertiesImpl. getComposition(ProteinSequence sequence)
java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>
ProfeatPropertiesImpl. getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
double
ProfeatPropertiesImpl. getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group)
java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>>>
IProfeatProperties. getDistributionPosition(ProteinSequence sequence)
java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>>
IProfeatProperties. getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>
IProfeatProperties. getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group)
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 java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>>>
ProfeatProperties. getDistributionPosition(ProteinSequence sequence)
static java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>>
ProfeatProperties. getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
static java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>
ProfeatProperties. 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)java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>>>
ProfeatPropertiesImpl. getDistributionPosition(ProteinSequence sequence)
java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>>
ProfeatPropertiesImpl. getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>
ProfeatPropertiesImpl. getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group)
double
ProfeatPropertiesImpl. getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution)
java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>>
IProfeatProperties. getTransition(ProteinSequence sequence)
java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>
IProfeatProperties. getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
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.static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>>
ProfeatProperties. getTransition(ProteinSequence sequence)
static java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>
ProfeatProperties. 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.java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>>
ProfeatPropertiesImpl. getTransition(ProteinSequence sequence)
java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>
ProfeatPropertiesImpl. getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
double
ProfeatPropertiesImpl. getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition)
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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 Description java.lang.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 Description ProteinSequence
RNASequence. getProteinSequence()
Get the ProteinSequence from the RNA sequenceProteinSequence
RNASequence. getProteinSequence(TranscriptionEngine engine)
Get the ProteinSequene from the RNA sequence with user defined transcription engineProteinSequence
TranscriptSequence. getProteinSequence()
Get the protein sequenceProteinSequence
TranscriptSequence. getProteinSequence(TranscriptionEngine engine)
Get the protein sequence with user defined TranscriptEngineMethods in org.biojava.nbio.core.sequence that return types with arguments of type ProteinSequence Modifier and Type Method Description java.util.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 Description static java.util.LinkedHashMap<java.lang.String,ProteinSequence>
FastaReaderHelper. readFastaProteinSequence(java.io.File file)
Read a fasta file containing amino acids with setup that would handle most cases.static java.util.LinkedHashMap<java.lang.String,ProteinSequence>
FastaReaderHelper. readFastaProteinSequence(java.io.InputStream inStream)
Read a fasta file containing amino acids with setup that would handle most cases.static java.util.LinkedHashMap<java.lang.String,ProteinSequence>
GenbankReaderHelper. readGenbankProteinSequence(java.io.File file)
Read a Genbank file containing amino acids with setup that would handle most cases.static java.util.LinkedHashMap<java.lang.String,ProteinSequence>
GenbankReaderHelper. readGenbankProteinSequence(java.io.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 java.util.LinkedHashMap<java.lang.String,ProteinSequence>
GenbankReaderHelper. readGenbankProteinSequence(java.io.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 Description static void
CasePreservingProteinSequenceCreator. setLowercaseToNull(ProteinSequence seq, java.lang.Object[] out)
Takes aProteinSequence
which was created by aCasePreservingProteinSequenceCreator
.Method parameters in org.biojava.nbio.core.sequence.io with type arguments of type ProteinSequence Modifier and Type Method Description static void
FastaWriterHelper. writeProteinSequence(java.io.File file, java.util.Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a filestatic void
FastaWriterHelper. writeProteinSequence(java.io.OutputStream outputStream, java.util.Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a streamstatic void
GenbankWriterHelper. writeProteinSequence(java.io.File file, java.util.Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a filestatic void
GenbankWriterHelper. writeProteinSequence(java.io.OutputStream outputStream, java.util.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 ProteinSequence Modifier and Type Method Description static boolean
SequenceTools. 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 ProteinSequence Modifier and Type Method Description static java.util.LinkedHashMap<java.lang.String,ProteinSequence>
GeneFeatureHelper. getProteinSequences(java.util.Collection<ChromosomeSequence> chromosomeSequences)
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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 Description java.util.LinkedHashMap<java.lang.String,ProteinSequence>
GeneIDXMLReader. getProteinSequences()
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Uses of ProteinSequence in org.biojava.nbio.genome.util
Methods in org.biojava.nbio.genome.util that return ProteinSequence Modifier and Type Method Description static ProteinSequence
ProteinMappingTools. convertDNAtoProteinSequence(java.lang.String dnaSequence)
Converts the DNA sequence to protein sequence.static ProteinSequence
ProteinMappingTools. 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 ProteinSequence Modifier and Type Method 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 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.cluster
Methods in org.biojava.nbio.structure.cluster that return ProteinSequence Modifier and Type Method Description ProteinSequence
Subunit. 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 ProteinSequence Modifier and Type Method Description static ProteinSequence
StructureSequenceMatcher. getProteinSequenceForStructure(Structure struct, java.util.Map<java.lang.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 sequenceMethods in org.biojava.nbio.structure.io with parameters of type ProteinSequence Modifier and Type Method 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 sitecpSite
residues to the right.static AFPChain
FastaAFPChainConverter. fastaToAfpChain(ProteinSequence sequence1, ProteinSequence sequence2, Structure structure1, Structure structure2)
Returns an AFPChain corresponding to the alignment betweenstructure1
andstructure2
, which is given by the gapped protein sequencessequence1
andsequence2
.static Structure
StructureSequenceMatcher. 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 ProteinSequence
StructureSequenceMatcher. removeGaps(ProteinSequence gapped)
Removes all gaps ('-') from a protein sequenceMethod parameters in org.biojava.nbio.structure.io with type arguments of type ProteinSequence Modifier and Type Method Description static AFPChain
FastaAFPChainConverter. fastaToAfpChain(java.util.Map<java.lang.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 Description FastaStructureParser(java.io.File file, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(java.io.InputStream is, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(FastaReader<ProteinSequence,AminoAcidCompound> reader, AtomCache cache)
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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 Description java.util.SortedSet<HmmerResult>
HmmerScan. scan(ProteinSequence sequence)
java.util.SortedSet<HmmerResult>
RemoteHmmerScan. scan(ProteinSequence sequence)
java.util.SortedSet<HmmerResult>
RemoteHmmerScan. scan(ProteinSequence sequence, java.net.URL serviceLocation)
Scans a protein sequence for Pfam profile matches.
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