Uses of Interface
org.expasy.mzjava.core.mol.SymbolSequence

Packages that use SymbolSequence

Package	Description
org.expasy.mzjava.proteomics.mol
org.expasy.mzjava.proteomics.mol.digest
org.expasy.mzjava.proteomics.ms.ident

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

Classes in org.expasy.mzjava.proteomics.mol that implement SymbolSequence

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

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

Modifier and Type	Method and Description
boolean	AminoAcidSequence.hasSameSequence(SymbolSequence<AminoAcid> sequence) Returns true if this and sequence have the same AA sequence.

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

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

Modifier and Type	Method and Description
int	CleavageSiteFinderImpl.countCleavageSites(SymbolSequence<AminoAcid> aaSeq)
int	Protease.countCleavageSites(SymbolSequence<AminoAcid> aaSeq)
int	ProteinDigester.countCleavageSites(SymbolSequence<AminoAcid> aaSeq)
int	CleavageSiteFinder.countCleavageSites(SymbolSequence<AminoAcid> aaSeq) Get the number of potential cleavage sites
int	CleavageSiteFinderImpl.find(SymbolSequence<AminoAcid> aaSeq, com.google.common.base.Optional<CleavageSiteVisitor> visitor) Find potential cleavage sites over the given amino-acid sequence
void	CleavageSiteFinderImpl.find(SymbolSequence<AminoAcid> aaSeq, gnu.trove.list.TIntList sites)
void	Protease.find(SymbolSequence<AminoAcid> aaSeq, gnu.trove.list.TIntList sites)
void	CleavageSiteFinder.find(SymbolSequence<AminoAcid> aaSeq, gnu.trove.list.TIntList sites) Find potential cleavage sites over the given amino-acid sequence
void	CleavageSiteVisitor.visit(SymbolSequence<AminoAcid> aaSeq, int index)

Uses of SymbolSequence in org.expasy.mzjava.proteomics.ms.ident

Classes in org.expasy.mzjava.proteomics.ms.ident that implement SymbolSequence

Modifier and Type	Class and Description
class	PeptideMatch PeptideMatch stores the match information from a peptide spectrum match

Constructors in org.expasy.mzjava.proteomics.ms.ident with parameters of type SymbolSequence

Constructor and Description
PeptideMatch(SymbolSequence<AminoAcid> sequence) Create a peptide match given an amino acid esequence