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

Packages that use Glycan

Package	Description
org.expasy.mzjava.glycomics.io.mol.glycoct
org.expasy.mzjava.glycomics.mol
org.expasy.mzjava.glycomics.ms.fragment
org.expasy.mzjava.glycomics.ms.spectrum

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

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

Modifier and Type	Method and Description
protected Glycan	GlycoCTReader.glycoctListsToSugar(String databaseIdentifier, List<String> residuesList, List<String> linkagesList)
Glycan	GlycoCTReader.read(String glycoct, String databaseIdentifier)

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

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

Modifier and Type	Method and Description
Glycan	Glycan.Builder.build() Build the Glycan.

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

Modifier and Type	Method and Description
List<CutDescriptor>	CutDescriptorGenerator.generateCutDescriptor(Glycan glycan, int glycosidicCut, int crossringCut)
List<CutDescriptor>	CutDescriptorGenerator.generateCutDescriptor(Glycan glycan, int glycosidicCut, int crossringCut, CrossRingCutType crossRingCutType)

Uses of Glycan in org.expasy.mzjava.glycomics.ms.fragment

Methods in org.expasy.mzjava.glycomics.ms.fragment with parameters of type Glycan

Modifier and Type	Method and Description
GlycanSpectrum	GlycanFragmenter.fragment(Glycan glycan, int precursorCharge) Generate a GlycanSpectrum from the fragment in input.
GlycanSpectrum	GlycanFragmenter.fragment(Glycan glycan, int precursorCharge, CrossRingCutType crossRingCutType) Generate a GlycanSpectrum from the fragment in input.
GlycanSpectrum	GlycanFragmenter.fragment(Glycan glycan, int precursorCharge, int[] fragmentCharges, CrossRingCutType crossRingCutType) Generate a GlycanSpectrum from the fragment in input.
GlycanSpectrum	GlycanFragmenter.fragment(Glycan glycan, int precursorCharge, List<GlycanFragment> fragmentList, int[] fragmentCharges) Generate a GlycanSpectrum from the fragment in input.
List<AnnotatedPeak<A>>	GlycanPeakGenerator.generatePeaks(Glycan precursor, GlycanFragment fragment, int[] charges, List<AnnotatedPeak<GlycanFragAnnotation>> annotatedPeaks) Generate peaks that are observed for the fragment at the supplied charge states.
List<AnnotatedPeak<GlycanFragAnnotation>>	GlycanFragmentPeakGenerator.generatePeaks(Glycan precursor, GlycanFragment fragment, int[] charges, List<AnnotatedPeak<GlycanFragAnnotation>> annotatedPeaks) Generate peaks that are observed for the fragment at the supplied charge states.

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

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

Modifier and Type	Method and Description
Glycan	GlycanSpectrum.getGlycan() Returns the glycan used for creating the spectrum.

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

Constructor and Description
GlycanSpectrum(Glycan glycan, int charge) Constructor for GlycanSpectrum.
GlycanSpectrum(Glycan glycan, int charge, int initialCapacity, double constantIntensity, PeakList.Precision precision) Constructor for GlycanSpectrum.
GlycanSpectrum(Glycan glycan, int charge, int initialCapacity, PeakList.Precision precision) Constructor for GlycanSpectrum.
GlycanSpectrum(Glycan glycan, int charge, PeakList.Precision precision) Constructor for GlycanSpectrum.
GlycanSpectrum(Spectrum<GlycanFragAnnotation> src, Glycan glycan, int charge) Constructor for GlycanSpectrum.