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

Packages that use AminoAcidSequence

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

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

Classes in org.expasy.mzjava.proteomics.avro.io with type parameters of type AminoAcidSequence

Modifier and Type	Class and Description
class	AbstractAminoAcidSequenceReader<O extends AminoAcidSequence>
class	AbstractAminoAcidSequenceWriter<O extends AminoAcidSequence>

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

Modifier and Type	Method and Description
void	AbstractAminoAcidSequenceWriter.writeSequence(AminoAcidSequence sequence, org.apache.avro.io.Encoder out)

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

Subclasses of AminoAcidSequence in org.expasy.mzjava.proteomics.mol

Modifier and Type	Class and Description
class	Peptide
class	PeptideFragment

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

Modifier and Type	Method and Description
boolean	AminoAcidSequence.hasSameSequence(AminoAcidSequence sequence) Returns true if this and sequence have the same AA sequence even if the two sequences have different modifications.

Constructors in org.expasy.mzjava.proteomics.mol with parameters of type AminoAcidSequence

Constructor and Description
AminoAcidSequence(AminoAcidSequence src, int fromInclusive, int toExclusive) Constructor that copies the residues and modifications from src.
AminoAcidSequence(AminoAcidSequence src, Set<AminoAcid> oldAAs, AminoAcid newAA) Constructor that copies the source AminoAcidSequence and replaces any amino acids in oldAAs with newAA.
Peptide(AminoAcidSequence src) Copy constructor.
Peptide(AminoAcidSequence src, int beginIndex, int endIndex) Constructs a Peptide by copying the residues and modifications from src.
PeptideFragment(FragmentType fragmentType, AminoAcidSequence src, int beginIndex, int endIndex) Constructor that copies the residues and modifications from src.

Uses of AminoAcidSequence in org.expasy.mzjava.proteomics.ms.spectrum

Methods in org.expasy.mzjava.proteomics.ms.spectrum with parameters of type AminoAcidSequence

Modifier and Type	Method and Description
PepFragAnnotation.Builder	PepFragAnnotation.Builder.setFragment(AminoAcidSequence fragment) Set the fragment

Constructors in org.expasy.mzjava.proteomics.ms.spectrum with parameters of type AminoAcidSequence

Constructor and Description
PepFragAnnotation.Builder(IonType ionType, int charge, AminoAcidSequence fragment) Construct a new Builder
PepFragAnnotation(IonType ionType, int charge, AminoAcidSequence sequence) Construct a PepFragAnnotation