Package org.expasy.mzjava.proteomics.ms.dbsearch

Interface Summary

Interface	Description
DigestDB	A database that stores digested peptides
PeptideSpectrumCache
PeptideSpectrumDB.DigestDSL	Fluent interface for configuring the protein digestion and fragmentation.
PeptideSpectrumDB.DigestSourceDSL	Fluent interface for configuring the protein source
PeptideSpectrumDB.EndDSL
PeptideSpectrumDB.FragmentDSL	Fluent interface for configuring the protein digestion and fragmentation.
PeptideSpectrumDB.StartDSL	Fluent interface that starts the build.

Class Summary

Class	Description
ArrayDigestDB	A peptide digest db that stores peptide digests in ram and is backed by an array.
ArrayDigestDB.Builder	Builder
Digest	A wrapper for Peptide that has a set to hold the ids of the proteins that the peptide belongs to.
PeptideSpectrumDB	PeptideSpectrumDB is a facade that collects together all the classes that are required by a peptide spectrum database.
SoftRefPepSpectrumCache	PeptideSpectrum cache that is memory-sensitive.

Enum Summary

Enum	Description
DigestDB.AmbiguousAminoAcidAction	The action to take if a peptide that have amino acids that are ambiguous (Z, B etc) are returned by the digester