Uses of Class
org.expasy.mzjava.glycomics.mol.Substituent

Packages that use Substituent

Package	Description
org.expasy.mzjava.glycomics.io.mol.glycoct
org.expasy.mzjava.glycomics.mol

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

Methods in org.expasy.mzjava.glycomics.io.mol.glycoct that return Substituent

Modifier and Type	Method and Description
Substituent	GlycoCtResolver.getSubstituent(String glycoCtCode)
protected Substituent	GlycoCTReader.getSubstituent(String glycoctResidueLine)
Substituent	DefaultGlycoCtResolver.getSubstituent(String glycoCtCode) Search for the substituent that resolves the GlycoCT code in input.

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

Fields in org.expasy.mzjava.glycomics.mol with type parameters of type Substituent

Modifier and Type	Field and Description
protected org.expasy.mzjava.glycomics.mol.IdentityEdgeMultimap<Monosaccharide,Substituent,org.expasy.mzjava.glycomics.mol.SubstituentEdge>	SaccharideGraph.substituentEdgeMultimap

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

Modifier and Type	Method and Description
Substituent	SaccharideGraph.AbstractBuilder.add(Substituent substituent, List<Monosaccharide> parents, SubstituentLinkage linkage) Add a hyper edge from parents to substituent.
Substituent	SaccharideGraph.AbstractBuilder.add(Substituent substituent, Monosaccharide parent, SubstituentLinkage linkage) Adda substituent to parent
Substituent	DefaultSubstituentLookup.getNew(String name) Search for a substituent with the input name the list of known substituents.
Substituent	SubstituentLookup.getNew(String name) Search for a substituent with the input name the list of known substituents.

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

Modifier and Type	Method and Description
NodeSet<Substituent>	SaccharideGraph.getSubstituentChildren(Monosaccharide parent) Returns all children of parent that are Substituents
protected Map<String,Substituent>	DefaultSubstituentLookup.parse(Reader in, Map<String,Substituent> substituentLookupMap) Parser for the Substituent Lookup file
List<Substituent>	DefaultSubstituentLookup.values() Return a list of the substituents specified in Substituent Lookup file.
List<Substituent>	SubstituentLookup.values() Return a list of the substituents specified in Substituent Lookup file.

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

Modifier and Type	Method and Description
Monosaccharide	SaccharideGraph.AbstractBuilder.add(Monosaccharide monosaccharide, Substituent substituent, Monosaccharide parent, GlycosidicLinkage glycoLinkage, SubstituentLinkage substituentLinkage) Add monosaccharide and substituent to the Glycan being built.
protected int	SaccharideGraph.add(Substituent child, List<Monosaccharide> parents, SubstituentLinkage linkage)
Substituent	SaccharideGraph.AbstractBuilder.add(Substituent substituent, List<Monosaccharide> parents, SubstituentLinkage linkage) Add a hyper edge from parents to substituent.
protected int	SaccharideGraph.add(Substituent child, Monosaccharide parent, SubstituentLinkage linkage)
Substituent	SaccharideGraph.AbstractBuilder.add(Substituent substituent, Monosaccharide parent, SubstituentLinkage linkage) Adda substituent to parent
Monosaccharide	GlycanFragment.Builder.addCleavedMonosaccharide(Monosaccharide cleavedMonosaccharide, Substituent substituent, Monosaccharide parent, GlycosidicLinkage glycoLinkage, SubstituentLinkage substituentLinkage, CutIndexes cutIndexes, IonType ionType) Add cleavedMonosaccharide and substituent to the Glycan being built.

Method parameters in org.expasy.mzjava.glycomics.mol with type arguments of type Substituent

Modifier and Type	Method and Description
protected Map<String,Substituent>	DefaultSubstituentLookup.parse(Reader in, Map<String,Substituent> substituentLookupMap) Parser for the Substituent Lookup file

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

Constructor and Description
Substituent(Substituent src)

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

Constructor and Description

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)