Serialized Form

Package org.expasy.jpl.core.mol

Class org.expasy.jpl.core.mol.AbstractMolecularSymbolManager extends Object implements Serializable

serialVersionUID: 464351627831125436L

Serialized Fields

symbol2molecules

Map<K,V> symbol2molecules

map molecular symbols to their (pooled) molecule instance

alphabet

org.expasy.jpl.commons.collection.symbol.AlphabetImpl<T> alphabet

molecular symbol alphabet

type

org.expasy.jpl.commons.collection.symbol.Symbol.SymbolType<T> type

the symbol type

molecularMap

Map<K,V> molecularMap

data molecular map

Package org.expasy.jpl.core.mol.chem

Class org.expasy.jpl.core.mol.chem.MassCalculator extends Object implements Serializable

serialVersionUID: 8998920858136140710L

Serialized Fields

MODIF_MANAGER

ModifContainerManager MODIF_MANAGER

accuracy

MassCalculator.Accuracy accuracy

Package org.expasy.jpl.core.mol.chem.api

Class org.expasy.jpl.core.mol.chem.api.AbstractMassCalc extends Object implements Serializable

serialVersionUID: 478466207779720942L

Serialized Fields

monoAndAvgMasses

double[] monoAndAvgMasses

Package org.expasy.jpl.core.mol.chem.impl

Class org.expasy.jpl.core.mol.chem.impl.ChargedParticleImpl extends Object implements Serializable

serialVersionUID: -4705805530470603425L

Serialized Fields

id

String id

mass

double mass

charge

int charge

Class org.expasy.jpl.core.mol.chem.impl.Element extends Object implements Serializable

serialVersionUID: -4036045099620467092L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream s)
                  throws IOException,
                         ClassNotFoundException

Throws:

IOException

ClassNotFoundException

readResolve

private Object readResolve()
                    throws InvalidObjectException

Throws:

InvalidObjectException

Serialized Fields

name

String name

The element name. Must be non-null.

Class org.expasy.jpl.core.mol.chem.impl.IonizableGroup extends Object implements Serializable

serialVersionUID: 3195269340240878040L

Serialized Fields

ionizableEntities

List<E> ionizableEntities

ionizable group

Class org.expasy.jpl.core.mol.chem.impl.IonizableMolecule extends Object implements Serializable

serialVersionUID: 476403395848654822L

Serialized Fields

molecule

Molecule molecule

ionizableGroup

IonizableGroup ionizableGroup

sorted (by ascending pKas) list of acido-basic couple

Class org.expasy.jpl.core.mol.chem.impl.Isotope extends Object implements Serializable

serialVersionUID: -6673856178026212306L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream s)
                  throws IOException,
                         ClassNotFoundException

Throws:

IOException

ClassNotFoundException

readResolve

private Object readResolve()
                    throws InvalidObjectException

Throws:

InvalidObjectException

Serialized Fields

atom

Element atom

The isotope atom instance. Must be non-null.

massNumber

int massNumber

The number of mass A (number of nucleon = neutron + proton). Must be non-null.

Class org.expasy.jpl.core.mol.chem.impl.ModifiedMolecule extends Object implements Serializable

serialVersionUID: 1777966030328925095L

Serialized Fields

molecule

Molecule molecule

modif

Modification modif

monoMass

double monoMass

avgMass

double avgMass

format

ModifFormat format

Package org.expasy.jpl.core.mol.modif

Class org.expasy.jpl.core.mol.modif.IonizableModification extends Object implements Serializable

serialVersionUID: 476403395848654822L

Serialized Fields

modif

Modification modif

ionizableGroup

IonizableGroup ionizableGroup

sorted (by ascending pKas) list of acido-basic couple

Class org.expasy.jpl.core.mol.modif.LossModification extends Object implements Serializable

serialVersionUID: 7571575506001763382L

Serialized Fields

loss

Modification loss

a ModificationFactory.valueOf(Double) or .valueOf(Molecule)

Class org.expasy.jpl.core.mol.modif.ModifFormat extends Object implements Serializable

serialVersionUID: 8043728064683551770L

Serialized Fields

formatter

NumberFormat formatter

the print formatter for doubles

modifFormat

ModifFormat.Format modifFormat

massCalc

MassCalculator massCalc

Class org.expasy.jpl.core.mol.modif.ModificationFactory extends Object implements Serializable

serialVersionUID: -6674345629500727988L

Serialized Fields

label

String label

the modification identifier.

value

Object value

the value can be a [@code Double} or a Molecule

type

Modification.ModifType type

Package org.expasy.jpl.core.mol.monomer.aa

Class org.expasy.jpl.core.mol.monomer.aa.AAManager extends AbstractMolecularSymbolManager<AminoAcid> implements Serializable

serialVersionUID: -1568100586628959134L

Class org.expasy.jpl.core.mol.monomer.aa.AASymbol extends org.expasy.jpl.commons.collection.symbol.AbstractSymbol<AminoAcid> implements Serializable

serialVersionUID: 4259061422415942712L

Class org.expasy.jpl.core.mol.monomer.aa.AATermManager extends AbstractMolecularSymbolManager<AminoAcidTerm> implements Serializable

serialVersionUID: 4378886567105390681L

Class org.expasy.jpl.core.mol.monomer.aa.AATermSymbol extends org.expasy.jpl.commons.collection.symbol.AbstractSymbol<AminoAcidTerm> implements Serializable

serialVersionUID: -2761434939025664621L

Package org.expasy.jpl.core.mol.monomer.nuc

Class org.expasy.jpl.core.mol.monomer.nuc.DeoxyRiboNucManager extends AbstractMolecularSymbolManager<DeoxyRiboNucleotide> implements Serializable

serialVersionUID: 2179149659492263852L

Class org.expasy.jpl.core.mol.monomer.nuc.DeoxyRiboNucSymbol extends org.expasy.jpl.commons.collection.symbol.AbstractSymbol<DeoxyRiboNucleotide> implements Serializable

serialVersionUID: -3616122847621899607L

Class org.expasy.jpl.core.mol.monomer.nuc.RiboNucManager extends AbstractMolecularSymbolManager<RiboNucleotide> implements Serializable

serialVersionUID: 8000431430611602344L

Class org.expasy.jpl.core.mol.monomer.nuc.RiboNucSymbol extends org.expasy.jpl.commons.collection.symbol.AbstractSymbol<RiboNucleotide> implements Serializable

serialVersionUID: 3409478140144167553L

Package org.expasy.jpl.core.mol.polymer

Class org.expasy.jpl.core.mol.polymer.AbstractBioPolymer extends Object implements Serializable

serialVersionUID: 2856989788180915333L

Serialized Fields

symbolSeq

org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl<E> symbolSeq

modifContainer

BioPolymerModifContainer modifContainer

modifFormat

ModifFormat modifFormat

isforceDoubleDisplay

boolean isforceDoubleDisplay

if true, possible modifications will be displayed in double format

massCalc

AbstractBioPolymer.PolymerMassCalc massCalc

molecular masses

head

Molecule head

head functional group

tail

Molecule tail

tail functional group

numberOfProtons

int numberOfProtons

numberOfElectrons

int numberOfElectrons

common

Molecule common

the monomer common structure (NHCHCO for proteins)

Class org.expasy.jpl.core.mol.polymer.AbstractBioPolymer.PolymerMassCalc extends AbstractMassCalc<AbstractBioPolymer<E extends Molecule>> implements Serializable

serialVersionUID: 6245736657408334228L

Package org.expasy.jpl.core.mol.polymer.modif

Class org.expasy.jpl.core.mol.polymer.modif.BioPolymerModifContainer extends Object implements Serializable

serialVersionUID: -8714514970974814080L

Serialized Fields

modifsByIndex

Map<K,V> modifsByIndex

to access modifs by index

modifsByName

ModifContainer modifsByName

to access modifs by name

bioSeqLength

int bioSeqLength

Class org.expasy.jpl.core.mol.polymer.modif.ModifContainer extends Object implements Serializable

serialVersionUID: -374939639840817841L

Serialized Fields

modifs

org.expasy.jpl.commons.base.record.RecordsCount<T> modifs

It is an Adapter of Object over CountableRecords. It stores the number of occurrences of each existing modifs.

byLabel

Map<K,V> byLabel

Modifs stored by label

Class org.expasy.jpl.core.mol.polymer.modif.ModifContainerManager extends Object implements Serializable

serialVersionUID: 2907680500563209831L

Package org.expasy.jpl.core.mol.polymer.pept

Class org.expasy.jpl.core.mol.polymer.pept.Peptide extends AbstractBioPolymer<AminoAcid> implements Serializable

serialVersionUID: -8677344826437804990L

Serialized Fields

proteins

Set<E> proteins

a peptide may come from many proteins

nTerm

NTerminus nTerm

cTerm

CTerminus cTerm

Class org.expasy.jpl.core.mol.polymer.pept.PeptideResidueManager.BadPeptideElementException extends Exception implements Serializable

serialVersionUID: -474866637545710341L

Class org.expasy.jpl.core.mol.polymer.pept.PeptideTypeImpl extends Object implements Serializable

serialVersionUID: 2520968900418058040L

Serialized Fields

nterm

Set<E> nterm

cterm

Set<E> cterm

Package org.expasy.jpl.core.mol.polymer.pept.fragmenter

Class org.expasy.jpl.core.mol.polymer.pept.fragmenter.PeptideFragmentationException extends Exception implements Serializable

serialVersionUID: 1L

Package org.expasy.jpl.core.mol.polymer.pept.term

Class org.expasy.jpl.core.mol.polymer.pept.term.CTermManager extends AbstractMolecularSymbolManager<CTerminus> implements Serializable

serialVersionUID: -2058181709120509333L

Class org.expasy.jpl.core.mol.polymer.pept.term.CTermSymbol extends org.expasy.jpl.commons.collection.symbol.AbstractSymbol<CTerminus> implements Serializable

serialVersionUID: 4517626442133419261L

Class org.expasy.jpl.core.mol.polymer.pept.term.NTermManager extends AbstractMolecularSymbolManager<NTerminus> implements Serializable

serialVersionUID: 5396180008399563980L

Class org.expasy.jpl.core.mol.polymer.pept.term.NTermSymbol extends org.expasy.jpl.commons.collection.symbol.AbstractSymbol<NTerminus> implements Serializable

serialVersionUID: 1268537699355046734L

Package org.expasy.jpl.core.mol.polymer.prot

Class org.expasy.jpl.core.mol.polymer.prot.Protein extends Object implements Serializable

serialVersionUID: -6615532036684291974L

Serialized Fields

accNumber

String accNumber

sequence

String sequence

peptides

Set<E> peptides

Package org.expasy.jpl.core.ms.lc

Class org.expasy.jpl.core.ms.lc.IncompatibleRTUnitException extends Exception implements Serializable

serialVersionUID: -7301924210617288411L

Class org.expasy.jpl.core.ms.lc.RetentionTime extends Object implements Serializable

serialVersionUID: -1200233371180565964L

Serialized Fields

id

long id

value

double value

unit

RetentionTime.RTUnit unit

Package org.expasy.jpl.core.ms.spectrum

Class org.expasy.jpl.core.ms.spectrum.BinnedPeakListImpl extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

peakList

PeakList peakList

the binned spectrum

dataset

org.expasy.jpl.commons.collection.stat.HistogramDataSet dataset

the bin peak list

mzMin

double mzMin

minimun and maximum mzs

mzMax

double mzMax

minimun and maximum mzs

binWidth

double binWidth

the interval length in daltons

size

int size

number of intervals (bins)

profile

BitSet profile

bins profile

intensities

double[] intensities

bins intensities

stdError

double stdError

The standard error of a method of measurement is the standard deviation of the sampling distribution associated with the estimation method. Here, the measure error in a MS/MS experiment is usually assumed to follow a normal distribution, and the propagation of uncertainty is computed using this assumption. http://en.wikipedia.org/wiki/Standard_error_%28statistics%29

ppm

double ppm

The relative error of the measure (stdError is an absolute error)

annotations

FragmentAnnotations annotations

bins annotations

Class org.expasy.jpl.core.ms.spectrum.InvalidPeakListException extends Exception implements Serializable

serialVersionUID: 1L

Class org.expasy.jpl.core.ms.spectrum.PeakListImpl extends Object implements Serializable

serialVersionUID: 4777319220046253097L

Serialized Fields

mzs

double[] mzs

peptides masses/charge ratios

intensities

double[] intensities

peaks intensities

annotations

FragmentAnnotations annotations

ion type, number of residues, charge, neutral loss

msLevel

int msLevel

the MS level

precursor

Peak precursor

the precursor peak (for fragmentation)

Package org.expasy.jpl.core.ms.spectrum.annot

Class org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationDecorator extends org.expasy.jpl.commons.base.AbstractDecorator<FragmentAnnotation> implements Serializable

serialVersionUID: -2015610224312560075L

Class org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationGeneric extends Object implements Serializable

serialVersionUID: -2015610224312560075L

Serialized Fields

id

String id

Deprecated.

annot

org.expasy.jpl.commons.base.record.DataTable.Record annot

Deprecated.

Class org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationImpl extends Object implements Serializable

serialVersionUID: -2015610224312560075L

Serialized Fields

id

String id

the identifier

ionType

PeptideType ionType

the fragment type

charge

int charge

the fragment charge

resNumber

int resNumber

the number of fragment residues

aa

AminoAcid aa

the amino acid if immonium type

c13Number

int c13Number

the number of isotope 13 carbon atoms

modifs

org.expasy.jpl.commons.base.record.RecordsCount<T> modifs

modifications

isNeutralLoss

boolean isNeutralLoss

return true if has a neutral loss

modifFormat

FragmentAnnotationImpl.ModifFormat modifFormat

Class org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotations extends Object implements Serializable

serialVersionUID: 5141237305266001606L

Serialized Fields

peakAnnotationIndices

int[] peakAnnotationIndices

Indices give starting positions for each peak annotation(s) in list below : i.e. peakAnnotationIndex[2]=10, peakAnnotationIndex[3]=14 means that the 3rd peak has 4 annotations in annotations list from indices 10 to 13

annotations

List<E> annotations

The list of annotations

higherMzAnnotatedPeakIndex

int higherMzAnnotatedPeakIndex

link needed for updating purpose

Package org.expasy.jpl.core.ms.spectrum.peak

Class org.expasy.jpl.core.ms.spectrum.peak.AnnotatedPeak extends Object implements Serializable

serialVersionUID: -600747873943224986L

Serialized Fields

peak

Peak peak

the sequence-based peak

annot

FragmentAnnotationImpl annot

Class org.expasy.jpl.core.ms.spectrum.peak.InvalidPeakException extends Exception implements Serializable

serialVersionUID: 1L

Class org.expasy.jpl.core.ms.spectrum.peak.PeakImpl extends Object implements Serializable

serialVersionUID: 8626703305620811095L

Serialized Fields

id

long id

id of the peak (persistence use)

mz

double mz

mz of the peak

charge

int charge

number of electrical charges (0 if unknown)

intensity

double intensity

intensity of signal

peptide

Peptide peptide

the sequence peptide

rt

RetentionTime rt

retention time

msLevel

int msLevel

the Mass-Spectrometry level

Package org.expasy.jpl.core.ms.spectrum.stat

Class org.expasy.jpl.core.ms.spectrum.stat.PeakListMZPrecComparator.MissingPrecursorException extends RuntimeException implements Serializable

serialVersionUID: 4003147006084075668L