Uses of Class
org.expasy.mzjava.proteomics.mol.Protein

Packages that use Protein

Package	Description
org.expasy.mzjava.core.mol.polymer.prot
org.expasy.mzjava.proteomics.io.mol
org.expasy.mzjava.proteomics.mol
org.expasy.mzjava.proteomics.mol.digest
org.expasy.mzjava.proteomics.ms.dbsearch

Uses of Protein in org.expasy.mzjava.core.mol.polymer.prot

Methods in org.expasy.mzjava.core.mol.polymer.prot that return Protein

Modifier and Type	Method and Description
static Protein	ProteinFactory.newProtein(org.biojava3.core.sequence.ProteinSequence proteinSequence)
static Protein	ProteinFactory.newProtein(String accessionId, org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.AminoAcidCompound> aaCompoundSequence)
static Protein	ProteinFactory.newUniprotProtein(String accessionId)
Protein	BioJavaFastaProteinReader.next()

Uses of Protein in org.expasy.mzjava.proteomics.io.mol

Methods in org.expasy.mzjava.proteomics.io.mol that return Protein

Modifier and Type	Method and Description
Protein	FastaProteinReader.next()

Uses of Protein in org.expasy.mzjava.proteomics.mol

Methods in org.expasy.mzjava.proteomics.mol that return Protein

Modifier and Type	Method and Description
Protein	Protein.Builder.build()

Uses of Protein in org.expasy.mzjava.proteomics.mol.digest

Methods in org.expasy.mzjava.proteomics.mol.digest with parameters of type Protein

Modifier and Type	Method and Description
List<Peptide>	ProteinDigester.digest(Protein protein) Digest protein
Collection<Peptide>	ProteinDigester.digest(Protein protein, Collection<Peptide> digests) Digest protein given a container for digests
boolean	DigestionController.interruptDigestion(Protein protein, int proteinBoundsCount, int inclusiveLowerBoundIndex, int inclusiveUpperBoundIndex) Control digestion flow given the potential digest bounds
boolean	LengthDigestionController.interruptDigestion(Protein protein, int proteinBoundsCount, int inclusiveLowerBoundIndex, int inclusiveUpperBoundIndex)
boolean	AcceptAllDigestionController.interruptDigestion(Protein protein, int proteinCleavageSiteCount, int inclusiveLowerBoundIndex, int inclusiveUpperBoundIndex) Control digestion flow given the potential digest bounds
boolean	DigestionController.makeDigest(Protein protein, int inclusiveProteinLowerIndex, int exclusiveProteinUpperIndex, int missedCleavagesCount) Make a peptide digest from the given protein.
boolean	LengthDigestionController.makeDigest(Protein protein, int inclusiveProteinLowerIndex, int exclusiveProteinUpperIndex, int missedCleavagesCount)
boolean	AcceptAllDigestionController.makeDigest(Protein protein, int inclusiveProteinLowerIndex, int exclusiveProteinUpperIndex, int missedCleavagesCount) Make a peptide digest from the given protein.
boolean	DigestionController.retainDigest(Protein protein, Peptide digest, int digestIndex) Process DigestedPeptide with/without missed cleavages
boolean	LengthDigestionController.retainDigest(Protein protein, Peptide digest, int digestIndex)
boolean	AcceptAllDigestionController.retainDigest(Protein protein, Peptide digest, int digestIndex) Process DigestedPeptide with/without missed cleavages

Uses of Protein in org.expasy.mzjava.proteomics.ms.dbsearch

Method parameters in org.expasy.mzjava.proteomics.ms.dbsearch with type arguments of type Protein

Modifier and Type	Method and Description
PeptideSpectrumDB.DigestDSL	PeptideSpectrumDB.DigestSourceDSL.setProteinSource(IterativeReader<Protein> reader) Set the IterativeReader reader as the protein source.

Constructor parameters in org.expasy.mzjava.proteomics.ms.dbsearch with type arguments of type Protein

Constructor and Description
ArrayDigestDB.Builder(IterativeReader<Protein> reader, Protease protease, int missedCleavages) Create a bulder that build a ArrayDigestDB that digests proteins from the reader using the protease with missedCleavages missed cleavages.
ArrayDigestDB(IterativeReader<Protein> proteinReader, ProteinDigester proteinDigester, DigestDB.AmbiguousAminoAcidAction ambiguousAminoAcidAction) Construct a new ArrayDigestDB.