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

Packages that use ProteinSequence

Package	Description
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.util

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 sequence
ProteinSequence	RNASequence.getProteinSequence(TranscriptionEngine engine)	Get the ProteinSequence from the RNA sequence with user-defined transcription engine
ProteinSequence	TranscriptSequence.getProteinSequence()	Get the protein sequence
ProteinSequence	TranscriptSequence.getProteinSequence(TranscriptionEngine engine)	Get the protein sequence with user defined TranscriptEngine

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

Modifier and Type	Method	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 ProteinSequence

Modifier and Type	Method	Description
protected ProteinSequence	FastaStreamer.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 ProteinSequence

Modifier and Type	Method	Description
Iterable<ProteinSequence>	FastaStreamer.each()	Enable iteration through the proteins in the file using syntax such as:
protected SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound>	FastaStreamer.getHeaderParser()
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.
Stream<ProteinSequence>	FastaStreamer.stream()	Create a stream of protein sequences from the contents of the path

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

Modifier and Type	Method	Description
protected ProteinSequence	FastaStreamer.createSequence(ProteinSequence sequence)	Create the sequence with the information from the header.
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	Description
FastaStreamer	FastaStreamer.withHeaderParser(SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser)
static void	FastaWriterHelper.writeProteinSequence(File file, Collection<ProteinSequence> proteinSequences)	Write collection of protein sequences to a file
static void	FastaWriterHelper.writeProteinSequence(OutputStream outputStream, Collection<ProteinSequence> proteinSequences)	Write collection of protein sequences to a stream
static void	GenbankWriterHelper.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

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.