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

Packages that use CutIndexes

Package	Description
org.expasy.mzjava.glycomics.mol

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

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

Modifier and Type	Method and Description
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.
CutIndexes	CleavedMonosaccharide.getCutIndexes()
CutIndexes	CutDescriptor.getCutIndexesForMonosaccharide(Monosaccharide monosaccharide) Return the CutIndex related with the specified monosaccharide.

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

Modifier and Type	Method and Description
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.

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

Modifier and Type	Method and Description
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	Monosaccharide.checkLinkedCarbon(CutIndexes cutIndexes, CutDirection cutDirection, int carbonNumber) Check if a carbon of the ring is in the fragment specified by the cutIndexes and the cutDirection.
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.
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.

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

Constructor and Description
CleavedMonosaccharide(Monosaccharide monosaccharide, CutIndexes cutIndexes)