Uses of Package
org.expasy.mzjava.proteomics.mol

Packages that use org.expasy.mzjava.proteomics.mol

Package	Description
org.expasy.mzjava.core.mol.polymer.prot
org.expasy.mzjava.proteomics.avro.io
org.expasy.mzjava.proteomics.io.mol
org.expasy.mzjava.proteomics.io.mol.fasta
org.expasy.mzjava.proteomics.io.ms.ident
org.expasy.mzjava.proteomics.io.ms.ident.pepxml
org.expasy.mzjava.proteomics.io.ms.spectrum
org.expasy.mzjava.proteomics.io.ms.spectrum.msp
org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt
org.expasy.mzjava.proteomics.mol
org.expasy.mzjava.proteomics.mol.digest
org.expasy.mzjava.proteomics.ms.consensus
org.expasy.mzjava.proteomics.ms.dbsearch
org.expasy.mzjava.proteomics.ms.fragment
org.expasy.mzjava.proteomics.ms.ident
org.expasy.mzjava.proteomics.ms.spectrum

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.core.mol.polymer.prot

Class and Description
Protein

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.avro.io

Class and Description
AminoAcidSequence Abstract amino acid sequence base class.
Peptide
PeptideBuilder A builder for constructing Peptides
PeptideFragment

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.io.mol

Class and Description
Protein
Protein.Builder

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.io.mol.fasta

Class and Description
Protein.Builder

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.io.ms.ident

Class and Description
AminoAcid Enum that represents the 21 Proteinogenic amino acids and 3 B, Z and X to represent amino acids for which there is ambiguity.

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.io.ms.ident.pepxml

Class and Description
AminoAcid Enum that represents the 21 Proteinogenic amino acids and 3 B, Z and X to represent amino acids for which there is ambiguity.

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.io.ms.spectrum

Class and Description
Peptide

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.io.ms.spectrum.msp

Class and Description
Peptide

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt

Class and Description
Peptide

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.mol

Class and Description
AAMassCalculator
AminoAcid Enum that represents the 21 Proteinogenic amino acids and 3 B, Z and X to represent amino acids for which there is ambiguity.
AminoAcidSequence Abstract amino acid sequence base class.
ModifiedPeptideFactory This factory creates modified Peptides given an Peptide source and a set of targeted AAs/variable modifications.
ModifiedPeptideFactory.Builder
Peptide
PeptideBuilder A builder for constructing Peptides
PeptideFragment
Protein
Protein.Builder

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.mol.digest

Class and Description
AminoAcid Enum that represents the 21 Proteinogenic amino acids and 3 B, Z and X to represent amino acids for which there is ambiguity.
Peptide
Protein

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.ms.consensus

Class and Description
Peptide

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.ms.dbsearch

Class and Description
Peptide
Protein

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.ms.fragment

Class and Description
AminoAcid Enum that represents the 21 Proteinogenic amino acids and 3 B, Z and X to represent amino acids for which there is ambiguity.
Peptide
PeptideFragment

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.ms.ident

Class and Description
AminoAcid Enum that represents the 21 Proteinogenic amino acids and 3 B, Z and X to represent amino acids for which there is ambiguity.
Peptide

Classes in org.expasy.mzjava.proteomics.mol used by org.expasy.mzjava.proteomics.ms.spectrum

Class and Description
AminoAcidSequence Abstract amino acid sequence base class.
Peptide
PeptideFragment