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

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