Uses of Class org.biojava.nbio.core.sequence.ProteinSequence (biojava-core 6.0.0 API)

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 ProteinSequene 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 types with arguments of type ProteinSequence
Modifier and Type	Method	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	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	Description
`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.