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

Packages that use AminoAcid

Package	Description
org.expasy.mzjava.proteomics.io.ms.ident
org.expasy.mzjava.proteomics.io.ms.ident.pepxml
org.expasy.mzjava.proteomics.mol
org.expasy.mzjava.proteomics.mol.digest
org.expasy.mzjava.proteomics.ms.fragment
org.expasy.mzjava.proteomics.ms.ident

Uses of AminoAcid in org.expasy.mzjava.proteomics.io.ms.ident

Fields in org.expasy.mzjava.proteomics.io.ms.ident with type parameters of type AminoAcid

Modifier and Type	Field and Description
protected List<AminoAcid>	MODaPsmReader.fixedModResidues

Methods in org.expasy.mzjava.proteomics.io.ms.ident that return types with arguments of type AminoAcid

Modifier and Type	Method and Description
List<AminoAcid>	MODaPsmReader.PeptideInfoParser.getSequence()

Methods in org.expasy.mzjava.proteomics.io.ms.ident with parameters of type AminoAcid

Modifier and Type	Method and Description
protected double	PepXmlReader.adjustMass(Double mass, AminoAcid residue)

Constructor parameters in org.expasy.mzjava.proteomics.io.ms.ident with type arguments of type AminoAcid

Constructor and Description
MODaPsmReader(List<AminoAcid> fixedModResidues, com.google.common.collect.Multimap<Integer,Modification> sideChainFixedModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termFixedModMap)

Uses of AminoAcid in org.expasy.mzjava.proteomics.io.ms.ident.pepxml

Methods in org.expasy.mzjava.proteomics.io.ms.ident.pepxml that return types with arguments of type AminoAcid

Modifier and Type	Method and Description
Map<AminoAcid,Set<AminoacidModificationHashable>>	ModificationMap.getAminoacidModificationMap()

Methods in org.expasy.mzjava.proteomics.io.ms.ident.pepxml with parameters of type AminoAcid

Modifier and Type	Method and Description
Set<AminoacidModificationHashable>	ModificationMap.getAminoacidModificationSet(AminoAcid aa)

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

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

Modifier and Type	Method and Description
AminoAcid	AminoAcidSequence.getSymbol(int index)
AminoAcid	Protein.getSymbol(int index)
static AminoAcid	AminoAcid.valueOf(char aa)
static AminoAcid	AminoAcid.valueOf(String name) Returns the enum constant of this type with the specified name.
static AminoAcid[]	AminoAcid.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in org.expasy.mzjava.proteomics.mol that return types with arguments of type AminoAcid

Modifier and Type	Method and Description
Set<AminoAcid>	AminoAcidSequence.getAmbiguousAminoAcids() Returns a set containing all the amino acids that are ambiguous.

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

Modifier and Type	Method and Description
PeptideBuilder	PeptideBuilder.add(AminoAcid aminoAcid) Add an amino acid
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
int[]	AminoAcidSequence.getSymbolIndexes(AminoAcid symbol) Returns an array containing the indexes of where symbol is found in this sequence.
Peptide	Peptide.replace(Set<AminoAcid> oldAAs, AminoAcid newAa)

Method parameters in org.expasy.mzjava.proteomics.mol with type arguments of type AminoAcid

Modifier and Type	Method and Description
ModifiedPeptideFactory.Builder	ModifiedPeptideFactory.Builder.addTarget(Set<AminoAcid> aas, ModAttachment attachment, Modification mod)
ModifiedPeptideFactory.Builder	ModifiedPeptideFactory.Builder.addTarget(Set<AminoAcid> aas, Modification mod)
int	AminoAcidSequence.countAminoAcidsIn(Set<AminoAcid> aminoAcidSet) Counts sums the number of times each of the amino acid in aminoAcidSet is contained in this Peptide.
boolean	AminoAcidSequence.hasSameSequence(SymbolSequence<AminoAcid> sequence) Returns true if this and sequence have the same AA sequence.
Peptide	Peptide.replace(Set<AminoAcid> oldAAs, AminoAcid newAa)

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

Constructor and Description
AminoAcidSequence(AminoAcid[] residues) Constructs an AminoAcidSequence by copying the residues.
AminoAcidSequence(AminoAcid firstResidue, AminoAcid... residues) Construct an AminoAcidSequence by copying the residues
AminoAcidSequence(AminoAcid firstResidue, AminoAcid... residues) Construct an AminoAcidSequence by copying the residues
AminoAcidSequence(AminoAcidSequence src, Set<AminoAcid> oldAAs, AminoAcid newAA) Constructor that copies the source AminoAcidSequence and replaces any amino acids in oldAAs with newAA.
Peptide(AminoAcid firstResidue, AminoAcid... residues) Construct an Peptide by copying the residues.
Peptide(AminoAcid firstResidue, AminoAcid... residues) Construct an Peptide by copying the residues.
Peptide(Peptide peptide, Set<AminoAcid> oldAAs, AminoAcid newAa)
PeptideBuilder(AminoAcid... seq) Construct a PeptideBuilder initialised to contain the amino acids from seq
PeptideBuilder(AminoAcid[] residues, int fromInclusive, int toExclusive) Constructs an PeptideBuilder by copying the residues from residues starting at fromInclusive to toExclusive.
PeptideFragment(FragmentType fragmentType, AminoAcid firstResidue, AminoAcid... residues) Construct an PeptideFragment by copying the residues
PeptideFragment(FragmentType fragmentType, AminoAcid firstResidue, AminoAcid... residues) Construct an PeptideFragment by copying the residues
Protein(String accessionId, AminoAcid... aas) Create an instance from a list of AminoAcids

Constructor parameters in org.expasy.mzjava.proteomics.mol with type arguments of type AminoAcid

Constructor and Description
AminoAcidSequence(AminoAcidSequence src, Set<AminoAcid> oldAAs, AminoAcid newAA) Constructor that copies the source AminoAcidSequence and replaces any amino acids in oldAAs with newAA.
AminoAcidSequence(List<AminoAcid> residues, com.google.common.collect.Multimap<Integer,Modification> sideChainModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termModMap) Constructs an AminoAcidSequence from the list of residues with the modifications contained in side chain and term mod map.
Peptide(List<AminoAcid> residues) Constructs an Peptide by copying the residues.
Peptide(List<AminoAcid> residues, com.google.common.collect.Multimap<Integer,Modification> sideChainModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termModMap) Constructs an Peptide from the list of residues with the modifications contained in side chain and term mod map.
Peptide(Peptide peptide, Set<AminoAcid> oldAAs, AminoAcid newAa)
PeptideBuilder(List<AminoAcid> sequence) Construct a PeptideBuilder initialised to contain the amino acids from sequence
PeptideFragment(FragmentType fragmentType, List<AminoAcid> residues, com.google.common.collect.Multimap<Integer,Modification> sideChainModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termModMap) Constructs an PeptideFragment from the list of residues with the modifications contained in side chain and term mod map.

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

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

Modifier and Type	Method and Description
ProteinDigester.Builder	ProteinDigester.Builder.addFixedMod(AminoAcid target, Modification mod)

Method parameters in org.expasy.mzjava.proteomics.mol.digest with type arguments of type AminoAcid

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 AminoAcid in org.expasy.mzjava.proteomics.ms.fragment

Method parameters in org.expasy.mzjava.proteomics.ms.fragment with type arguments of type AminoAcid

Modifier and Type	Method and Description
static PeptideNeutralLossPeakGenerator	PeptideNeutralLossPeakGenerator.newModificationLossGenerator(Mass loss, Set<AminoAcid> aminoAcids, Set<Modification> modifications, Set<ModAttachment> modAttachments, Set<IonType> ionTypes, double peakIntensity)

Constructor parameters in org.expasy.mzjava.proteomics.ms.fragment with type arguments of type AminoAcid

Constructor and Description
PeptideNeutralLossPeakGenerator(Mass massShift, Set<AminoAcid> affectedAA, Set<IonType> ionTypes, double peakIntensity)

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

Methods in org.expasy.mzjava.proteomics.ms.ident that return AminoAcid

Modifier and Type	Method and Description
AminoAcid	ModificationMatch.getResidue()
AminoAcid	PeptideMatch.getSymbol(int index)

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

Constructor and Description
ModificationMatch(double massShift, AminoAcid residue, Integer position, ModAttachment modAttachment) Create a ModificationMatch given a mass shift
ModificationMatch(Modification modification, AminoAcid residue, int position, ModAttachment modAttachment) Create a ModificationMatch given a modification.
PeptideMatch(AminoAcid... sequence) Create a peptide match given an amino acid sequence

Constructor parameters in org.expasy.mzjava.proteomics.ms.ident with type arguments of type AminoAcid

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