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

Packages that use PeptideBuilder

Package	Description
org.expasy.mzjava.proteomics.avro.io
org.expasy.mzjava.proteomics.mol

Uses of PeptideBuilder in org.expasy.mzjava.proteomics.avro.io

Methods in org.expasy.mzjava.proteomics.avro.io with parameters of type PeptideBuilder

Modifier and Type	Method and Description
void	AbstractAminoAcidSequenceReader.readSequence(PeptideBuilder builder, org.apache.avro.io.Decoder in)

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

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

Modifier and Type	Method and Description
PeptideBuilder	PeptideBuilder.add(AminoAcid aminoAcid) Add an amino acid
PeptideBuilder	PeptideBuilder.addModification(int index, Modification modification) Add a the modification to the side chain of residue at index
PeptideBuilder	PeptideBuilder.addModification(ModAttachment modAttachment, Modification modification) Add a the modification to either end of the the peptide.
PeptideBuilder	PeptideBuilder.addModificationToAll(Collection<Modification> modifications, AminoAcid aminoAcid) Add all of the Modification's in modifications to all amino acids that are equal to aminoAcid
PeptideBuilder	PeptideBuilder.addModificationToAll(Modification modification, AminoAcid aminoAcid) Add the modification to all amino acids that are equal to aminoAcid
PeptideBuilder	Protein.getPeptideBuilder(int fromInclusive, int toExclusive) Create a PeptideBuilder that has the sequence initialised by copying this Protein's amino acids starting at fromInclusive to toExclusive.
PeptideBuilder	PeptideBuilder.parseAndAdd(String peptideSequence) Parse the peptideSequence string and add the sequence and modifications to this builder