Uses of Class
org.expasy.mzjava.core.mol.Composition

Packages that use Composition

Package	Description
org.expasy.mzjava.avro.io
org.expasy.mzjava.core.mol
org.expasy.mzjava.glycomics.io.mol.glycoct
org.expasy.mzjava.glycomics.mol
org.expasy.mzjava.glycomics.ms.spectrum
org.expasy.mzjava.proteomics.mol
org.expasy.mzjava.proteomics.mol.modification
org.expasy.mzjava.proteomics.mol.modification.unimod
org.expasy.mzjava.proteomics.ms.spectrum

Uses of Composition in org.expasy.mzjava.avro.io

Methods in org.expasy.mzjava.avro.io that return Composition

Modifier and Type	Method and Description
Composition	CompositionReader.read(org.apache.avro.io.Decoder in)

Methods in org.expasy.mzjava.avro.io with parameters of type Composition

Modifier and Type	Method and Description
void	CompositionWriter.write(Composition composition, org.apache.avro.io.Encoder out)

Uses of Composition in org.expasy.mzjava.core.mol

Methods in org.expasy.mzjava.core.mol that return Composition

Modifier and Type	Method and Description
Composition	Composition.Builder.build() Build the composition
static Composition	Composition.parseComposition(String s) Creates a Composition by parsing the given string.
static Composition	Composition.subtractCompositions(Composition composition1, Composition composition2)

Methods in org.expasy.mzjava.core.mol with parameters of type Composition

Modifier and Type	Method and Description
Composition.Builder	Composition.Builder.addAll(Composition composition) Add all of the atoms in composition to this
static double	MassCalculator.calcIsotopeDelta(Composition composition)
static double	MassCalculator.calculateAverageMass(Composition composition) Calculates the sum of the average mass of each Atom in this Composition.
static Composition	Composition.subtractCompositions(Composition composition1, Composition composition2)

Constructors in org.expasy.mzjava.core.mol with parameters of type Composition

Constructor and Description
Composition(Composition... compositions) Constructs a composition that is the sum of the compositions

Uses of Composition in org.expasy.mzjava.glycomics.io.mol.glycoct

Methods in org.expasy.mzjava.glycomics.io.mol.glycoct that return types with arguments of type Composition

Modifier and Type	Method and Description
com.google.common.base.Optional<Composition>	GlycoCtResolver.getLinkageComposition(String glycoCtCode)
com.google.common.base.Optional<Composition>	DefaultGlycoCtResolver.getLinkageComposition(String glycoCtCode) Returns the appropriate LinkageComposition instance for the given GlycoCT code.

Uses of Composition in org.expasy.mzjava.glycomics.mol

Fields in org.expasy.mzjava.glycomics.mol declared as Composition

Modifier and Type	Field and Description
protected Composition	GlycanNode.composition

Methods in org.expasy.mzjava.glycomics.mol that return Composition

Modifier and Type	Method and Description
Composition	GlycanNode.getComposition() Return the composition of the GlycanNode
Composition	GlycanFragment.getEndComposition() Return the composition of the end of the glycan.
Composition	Glycan.getEndComposition() Return the composition of the end of the glycan.
Composition	GlycanMassCalculator.getGlycosidicDeltaComposition(IonType ionType) Return the composition that the glycan have lost during the glycosidic fragmentation depending on the ion type.
Composition	DefaultGlycanMassCalculator.getGlycosidicDeltaComposition(IonType ionType) Return the value of mass that the glycan have lost during the glycosidic fragmentation depending on the ion type.

Methods in org.expasy.mzjava.glycomics.mol that return types with arguments of type Composition

Modifier and Type	Method and Description
com.google.common.base.Optional<Composition>	GlycosidicLinkage.getAnomericComposition()
com.google.common.base.Optional<Composition>	Linkage.getLinkedComposition() Return the composition of the linkage.
com.google.common.base.Optional<Composition>	SubstituentLinkage.getLinkedComposition()
com.google.common.base.Optional<Composition>	GlycosidicLinkage.getLinkedComposition()

Methods in org.expasy.mzjava.glycomics.mol with parameters of type Composition

Modifier and Type	Method and Description
Monosaccharide	GlycanFragment.Builder.setCleavedRoot(Monosaccharide root, FragmentType fragmentType, Composition endComposition, CutIndexes cutIndexes) Set the cleaved root of the Glycan Fragments.
Monosaccharide	GlycanFragment.Builder.setRoot(Monosaccharide root, FragmentType fragmentType, Composition endComposition) Set the root of the Glycan Fragments.
Monosaccharide	Glycan.Builder.setRoot(Monosaccharide monosaccharide, com.google.common.base.Optional<Anomericity> endAnomericity, String databaseIdentifier, Composition endComposition) Set the root of the Glycan.

Constructors in org.expasy.mzjava.glycomics.mol with parameters of type Composition

Constructor and Description
Glycan(Monosaccharide root, com.google.common.base.Optional<Anomericity> reducingEndAnomericity, String databaseIdentifier, Composition endComposition)
GlycanFragment(Monosaccharide root, FragmentType fragmentType, Composition endComposition)
GlycanFragment(Monosaccharide root, FragmentType fragmentType, List<GlycanNode> nodes, List<SEdge> edges, org.expasy.mzjava.glycomics.mol.IdentityEdgeMultimap<Monosaccharide,Monosaccharide,org.expasy.mzjava.glycomics.mol.GlycosidicEdge> monosaccharideEdgeMultimap, org.expasy.mzjava.glycomics.mol.IdentityEdgeMultimap<Monosaccharide,Substituent,org.expasy.mzjava.glycomics.mol.SubstituentEdge> substituentEdgeMultimap, Composition endComposition, Map<CleavedMonosaccharide,IonType> monosaccharideIonTypeMap, Map<SEdge,IonType> edgeIonTypeMap)
GlycanNode(String name, Composition composition)
GlycosidicLinkage(Anomericity anomericity, Integer anomericCarbon, Integer linkedCarbon, Composition anomericComposition, Composition linkedComposition)
Monosaccharide(String name, Composition composition, MonosaccharideSuperclass monosaccharideSuperclass, MonosaccharideClass monosaccharideClass, RingType ring, int firstCarbonRing, int lastCarbonRing)
Substituent(String name, Composition composition)
SubstituentLinkage(Integer linkedCarbon, Composition linkedComposition)

Constructor parameters in org.expasy.mzjava.glycomics.mol with type arguments of type Composition

Constructor and Description
GlycosidicLinkage(com.google.common.base.Optional<Anomericity> anomericity, com.google.common.base.Optional<Integer> anomericCarbon, com.google.common.base.Optional<Integer> linkedCarbon, com.google.common.base.Optional<Composition> anomericComposition, com.google.common.base.Optional<Composition> linkedComposition)
GlycosidicLinkage(com.google.common.base.Optional<Anomericity> anomericity, com.google.common.base.Optional<Integer> anomericCarbon, com.google.common.base.Optional<Integer> linkedCarbon, com.google.common.base.Optional<Composition> anomericComposition, com.google.common.base.Optional<Composition> linkedComposition)
SubstituentLinkage(com.google.common.base.Optional<Integer> linkedCarbon, com.google.common.base.Optional<Composition> linkedComposition)

Uses of Composition in org.expasy.mzjava.glycomics.ms.spectrum

Fields in org.expasy.mzjava.glycomics.ms.spectrum declared as Composition

Modifier and Type	Field and Description
static Composition	GlycanFragAnnotation.EMPTY_COMPOSITION

Methods in org.expasy.mzjava.glycomics.ms.spectrum that return Composition

Modifier and Type	Method and Description
Composition	GlycanFragAnnotation.getIsotopeComposition() Return the Composition that contains the isotopes.

Methods in org.expasy.mzjava.glycomics.ms.spectrum with parameters of type Composition

Modifier and Type	Method and Description
GlycanFragAnnotation.FragBuilder	GlycanFragAnnotation.FragBuilder.addIsotopeComposition(Composition isotopeComposition) Add all the atoms from isotopeComposition

Constructors in org.expasy.mzjava.glycomics.ms.spectrum with parameters of type Composition

Constructor and Description
GlycanFragAnnotation(int charge, GlycanFragment fragment, Composition isotopeComposition, Mass neutralLoss)

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

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

Modifier and Type	Method and Description
Composition	AminoAcid.getCompositionOfMonomer() Returns the composition of this amino acid when it is part of a polymer.
Composition	AAMassCalculator.getDeltaComposition(IonType ionType)

Uses of Composition in org.expasy.mzjava.proteomics.mol.modification

Subclasses of Composition in org.expasy.mzjava.proteomics.mol.modification

Modifier and Type	Class and Description
class	NeutralLoss

Uses of Composition in org.expasy.mzjava.proteomics.mol.modification.unimod

Methods in org.expasy.mzjava.proteomics.mol.modification.unimod that return Composition

Modifier and Type	Method and Description
Composition	UnimodMod.getComposition() Returns the Composition associated with this UnimodMod.

Uses of Composition in org.expasy.mzjava.proteomics.ms.spectrum

Fields in org.expasy.mzjava.proteomics.ms.spectrum declared as Composition

Modifier and Type	Field and Description
static Composition	PepFragAnnotation.EMPTY_COMPOSITION

Methods in org.expasy.mzjava.proteomics.ms.spectrum that return Composition

Modifier and Type	Method and Description
Composition	PepFragAnnotation.getIsotopeComposition() Return the Composition that contains the isotopes.

Methods in org.expasy.mzjava.proteomics.ms.spectrum with parameters of type Composition

Modifier and Type	Method and Description
PepFragAnnotation.Builder	PepFragAnnotation.Builder.addIsotopeComposition(Composition isotopeComposition) Add all the atoms from isotopeComposition