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

Packages that use Monosaccharide

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

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

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

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

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

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

Modifier and Type	Field and Description
protected Monosaccharide	SaccharideGraph.root

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

Modifier and Type	Field and Description
protected org.expasy.mzjava.glycomics.mol.IdentityEdgeMultimap<Monosaccharide,Monosaccharide,org.expasy.mzjava.glycomics.mol.GlycosidicEdge>	SaccharideGraph.monosaccharideEdgeMultimap
protected org.expasy.mzjava.glycomics.mol.IdentityEdgeMultimap<Monosaccharide,Monosaccharide,org.expasy.mzjava.glycomics.mol.GlycosidicEdge>	SaccharideGraph.monosaccharideEdgeMultimap
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 Monosaccharide

Modifier and Type	Method and Description
Monosaccharide	SaccharideGraph.AbstractBuilder.add(Monosaccharide monosaccharide, List<Monosaccharide> parents, GlycosidicLinkage linkage) Adda hyper edge from the list of parents to the monosaccharide.
Monosaccharide	SaccharideGraph.AbstractBuilder.add(Monosaccharide monosaccharide, Monosaccharide parent, GlycosidicLinkage linkage) Add a Monosaccharide to the Glycan.
Monosaccharide	SaccharideGraph.AbstractBuilder.add(Monosaccharide monosaccharide, Substituent substituent, Monosaccharide parent, GlycosidicLinkage glycoLinkage, SubstituentLinkage substituentLinkage) Add monosaccharide and substituent to the Glycan being built.
Monosaccharide	GlycanFragment.Builder.addCleavedMonosaccharide(Monosaccharide cleavedMonosaccharide, List<Monosaccharide> parents, GlycosidicLinkage linkage, CutIndexes cutIndexes, IonType ionType) Add an hyper edge from the list of parents to the cleavedMonosaccharide.
Monosaccharide	GlycanFragment.Builder.addCleavedMonosaccharide(Monosaccharide cleavedMonosaccharide, Monosaccharide parent, GlycosidicLinkage linkage, CutIndexes cutIndexes, IonType ionType) Add a Monosaccharide to the Glycan.
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.
Monosaccharide	CleavedMonosaccharide.getMonosaccharide()
Monosaccharide	DefaultMonosaccharideLookup.getNew(String name) Search for a monosaccharide with the input name the list of known monosaccharides.
Monosaccharide	MonosaccharideLookup.getNew(String name) Search for a monosaccharide with the input name the list of known monosaccharides.
Monosaccharide	SEdge.getParent()
Monosaccharide	SaccharideGraph.getRoot() Return the root of this SaccharideGraph
Monosaccharide	GlycanFragment.Builder.setCleavedRoot(Monosaccharide root, FragmentType fragmentType, Composition endComposition, CutIndexes cutIndexes) Set the cleaved root of the Glycan Fragments.
Monosaccharide	GlycanFragment.Builder.setCleavedRoot(Monosaccharide root, FragmentType fragmentType, CutIndexes cutIndexes) Set the cleaved root of the Glycan Fragments.
Monosaccharide	GlycanFragment.Builder.setRoot(Monosaccharide root, FragmentType fragmentType) Set the 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) Set the root of the Glycan.
Monosaccharide	Glycan.Builder.setRoot(Monosaccharide monosaccharide, com.google.common.base.Optional<Anomericity> endAnomericity, String databaseIdentifier, Composition endComposition) Set the root of the Glycan.

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

Modifier and Type	Method and Description
Set<Monosaccharide>	CutDescriptor.getCleavedNodes() Return a set of all the cleaved monosaccharides in the CutDescriptor.
NodeSet<Monosaccharide>	SaccharideGraph.getMonosaccharideChildren(Monosaccharide parent) Returns all children of parent that are Monosaccharides
List<Monosaccharide>	SEdge.getParents()
protected Map<String,Monosaccharide>	DefaultMonosaccharideLookup.parse(Reader in, Map<String,Monosaccharide> monosaccharideLookupMap) Parser for the Monosaccharide Lookup file
List<Monosaccharide>	DefaultMonosaccharideLookup.values() Return a list of the monosaccharides specified in Monosaccharide Lookup file.
List<Monosaccharide>	MonosaccharideLookup.values() Return a list of the monosaccharides specified in Monosaccharide Lookup file.

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

Modifier and Type	Method and Description
void	LinkageAcceptor.accept(Monosaccharide parent, Monosaccharide child, GlycosidicLinkage glycosidicLinkage)
protected int	SaccharideGraph.add(Monosaccharide child, List<Monosaccharide> parents, GlycosidicLinkage linkage)
Monosaccharide	SaccharideGraph.AbstractBuilder.add(Monosaccharide monosaccharide, List<Monosaccharide> parents, GlycosidicLinkage linkage) Adda hyper edge from the list of parents to the monosaccharide.
protected int	SaccharideGraph.add(Monosaccharide child, Monosaccharide parent, GlycosidicLinkage linkage)
Monosaccharide	SaccharideGraph.AbstractBuilder.add(Monosaccharide monosaccharide, Monosaccharide parent, GlycosidicLinkage linkage) Add a Monosaccharide to the Glycan.
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, Monosaccharide parent, SubstituentLinkage linkage)
Substituent	SaccharideGraph.AbstractBuilder.add(Substituent substituent, Monosaccharide parent, SubstituentLinkage linkage) Adda substituent to parent
SEdge	GlycanFragment.Builder.addCleavedEdge(Monosaccharide attachPoint, SEdge edge, IonType ionType) Add a cleaved edge to the fragment.
void	CutDescriptor.addCleavedMonosaccharide(Monosaccharide monosaccharide, CutIndexes cutIndexes) Add a cleaved monosaccharide edge to the CutDescriptor.
Monosaccharide	GlycanFragment.Builder.addCleavedMonosaccharide(Monosaccharide cleavedMonosaccharide, List<Monosaccharide> parents, GlycosidicLinkage linkage, CutIndexes cutIndexes, IonType ionType) Add an hyper edge from the list of parents to the cleavedMonosaccharide.
Monosaccharide	GlycanFragment.Builder.addCleavedMonosaccharide(Monosaccharide cleavedMonosaccharide, Monosaccharide parent, GlycosidicLinkage linkage, CutIndexes cutIndexes, IonType ionType) Add a Monosaccharide to the Glycan.
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.
boolean	SaccharideGraph.canFragmentCrossRing(Monosaccharide monosaccharide) Return a boolean value that show if the glycan is fragmentable.
int	TraversalComparator.compare(Monosaccharide child1, GlycosidicLinkage linkage1, Monosaccharide child2, GlycosidicLinkage linkage2) Compares two children of a node in a SaccharideGraph for order.
boolean	CutDescriptor.contains(Monosaccharide monosaccharide) Check if the CutDescriptor contains the specified monosaccharide.
Set<CutIndexes>	CrossRingCutType.get(Monosaccharide monosaccharide) Return an array of Crossring indexes.
Set<CutIndexes>	AllCrossRingCutType.get(Monosaccharide monosaccharide) Return an array of all possible Crossiring cleavage indexes for the specific input.
CutIndexes[]	GlycanMassCalculator.getAllInternalTypeCleavage(Monosaccharide monosaccharide) Return all possible type of internal cleavage for the monosaccharide of interest Before call this method be sure that the molecularMass it is correct.
CutIndexes[]	DefaultGlycanMassCalculator.getAllInternalTypeCleavage(Monosaccharide monosaccharide) Return all possible type of internal cleavage for the monosaccharide of interest Before call this method be sure that the molecularMass it is correct.
NodeSet<GlycanNode>	SaccharideGraph.getChildren(Monosaccharide parent) Returns a the children of parent
double	GlycanMassCalculator.getCrossRingLossMass(IonType ionType, int anomericCarbon, Monosaccharide cleavedMonosaccaride, CutIndexes cutIndexes) Return the value of mass that the glycan have lost during the crossring fragmentation depending on the ion type.
double	DefaultGlycanMassCalculator.getCrossRingLossMass(IonType ionType, int attachCarbon, Monosaccharide cleavedMonosaccaride, CutIndexes cutIndexes) Return the value of mass that the glycan have lost during the crossring fragmentation depending on the ion type.
CutIndexes	CutDescriptor.getCutIndexesForMonosaccharide(Monosaccharide monosaccharide) Return the CutIndex related with the specified monosaccharide.
NodeSet<Monosaccharide>	SaccharideGraph.getMonosaccharideChildren(Monosaccharide parent) Returns all children of parent that are Monosaccharides
NodeSet<Substituent>	SaccharideGraph.getSubstituentChildren(Monosaccharide parent) Returns all children of parent that are Substituents
boolean	SaccharideGraph.isLeaf(Monosaccharide monosaccharide) Returns true if the specified monosaccharide is a leaf in the saccharide.
Monosaccharide	GlycanFragment.Builder.setCleavedRoot(Monosaccharide root, FragmentType fragmentType, Composition endComposition, CutIndexes cutIndexes) Set the cleaved root of the Glycan Fragments.
Monosaccharide	GlycanFragment.Builder.setCleavedRoot(Monosaccharide root, FragmentType fragmentType, CutIndexes cutIndexes) Set the cleaved root of the Glycan Fragments.
Monosaccharide	GlycanFragment.Builder.setRoot(Monosaccharide root, FragmentType fragmentType) Set the 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) Set the root of the Glycan.
Monosaccharide	Glycan.Builder.setRoot(Monosaccharide monosaccharide, com.google.common.base.Optional<Anomericity> endAnomericity, String databaseIdentifier, Composition endComposition) Set the root of the Glycan.

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

Modifier and Type	Method and Description
protected int	SaccharideGraph.add(Monosaccharide child, List<Monosaccharide> parents, GlycosidicLinkage linkage)
Monosaccharide	SaccharideGraph.AbstractBuilder.add(Monosaccharide monosaccharide, List<Monosaccharide> parents, GlycosidicLinkage linkage) Adda hyper edge from the list of parents to the monosaccharide.
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.
Monosaccharide	GlycanFragment.Builder.addCleavedMonosaccharide(Monosaccharide cleavedMonosaccharide, List<Monosaccharide> parents, GlycosidicLinkage linkage, CutIndexes cutIndexes, IonType ionType) Add an hyper edge from the list of parents to the cleavedMonosaccharide.
protected boolean	SaccharideGraph.AbstractBuilder.checkMonosaccharidesPresence(List<Monosaccharide> monosaccharides) Check for the presence of all cleaved monosaccharides inside the graph.
protected void	SaccharideGraph.doBFS(LinkageAcceptor linkageAcceptor, Deque<Monosaccharide> deque, Comparator<org.expasy.mzjava.glycomics.mol.GlycosidicEdge> traversalComparator)
protected void	SaccharideGraph.doDFS(LinkageAcceptor linkageAcceptor, Deque<Monosaccharide> deque, Comparator<org.expasy.mzjava.glycomics.mol.GlycosidicEdge> traversalComparator)
protected Map<String,Monosaccharide>	DefaultMonosaccharideLookup.parse(Reader in, Map<String,Monosaccharide> monosaccharideLookupMap) Parser for the Monosaccharide Lookup file

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

Constructor and Description
CleavedMonosaccharide(Monosaccharide monosaccharide, CutIndexes cutIndexes)
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)
Monosaccharide(Monosaccharide src)
SaccharideGraph(Monosaccharide root)

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

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)
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)
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)