org.expasy.mzjava.glycomics.mol

Class GlycanFragment

java.lang.Object

org.expasy.mzjava.glycomics.mol.SaccharideGraph

org.expasy.mzjava.glycomics.mol.GlycanFragment

public class GlycanFragment
extends SaccharideGraph

Version:

sqrt -1

Author:

Oliver Horlacher, Davide Alocci

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GlycanFragment.Builder A builder to build Glycosidic Fragments.

Nested classes/interfaces inherited from class org.expasy.mzjava.glycomics.mol.SaccharideGraph

SaccharideGraph.AbstractBuilder<G extends SaccharideGraph>, SaccharideGraph.Traversal

Field Summary

Fields inherited from class org.expasy.mzjava.glycomics.mol.SaccharideGraph

edges, monosaccharideEdgeMultimap, nodes, postOrder, preOrder, root, substituentEdgeMultimap

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	GlycanFragment(Monosaccharide root, FragmentType fragmentType, Composition endComposition)
protected	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)

Method Summary

Methods

Modifier and Type	Method and Description
double	calculateMolecularMass() Return the mass of the this fragment.
boolean	equals(Object o)
Set<SEdge>	getCleavedEdges() Return a set of cleaved edge in the fragment
Set<CleavedMonosaccharide>	getCleavedNodes() Return a set of cleaved nodes in the fragment
Composition	getEndComposition() Return the composition of the end of the glycan.
FragmentType	getFragmentType() Return the fragment type.
IonType	getIonType(CleavedMonosaccharide cleavedMonosaccharide)
IonType	getIonType(SEdge edge)
Set<IonType>	getIonTypes()
int	hashCode()

Methods inherited from class org.expasy.mzjava.glycomics.mol.SaccharideGraph

add, add, add, add, calculateTotalSaccharideMass, canFragmentCrossRing, containsNode, copyEdgeList, doBFS, doDFS, forEachLinkage, forEachLinkage, getChildren, getGlycoLinkage, getMonosaccharideChildren, getNode, getParent, getRoot, getSubstituentChildren, getSubstituentLinkage, hasHyperEdges, isEmpty, isLeaf, order, populatePrePostOrder, size

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GlycanFragment

protected 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

protected GlycanFragment(Monosaccharide root,
              FragmentType fragmentType,
              Composition endComposition)

Method Detail

calculateMolecularMass

public double calculateMolecularMass()

Return the mass of the this fragment.

Returns:

the mass of the fragment.

getCleavedNodes

public Set<CleavedMonosaccharide> getCleavedNodes()

Return a set of cleaved nodes in the fragment

Returns:

a set

getCleavedEdges

public Set<SEdge> getCleavedEdges()

Return a set of cleaved edge in the fragment

Returns:

a set

getFragmentType

public FragmentType getFragmentType()

Return the fragment type.

Returns:

the fragment type.

getEndComposition

public Composition getEndComposition()

Return the composition of the end of the glycan.

Returns:

the composition of the end of the glycan.

getIonType

public IonType getIonType(SEdge edge)

getIonType

public IonType getIonType(CleavedMonosaccharide cleavedMonosaccharide)

getIonTypes

public Set<IonType> getIonTypes()

equals

public boolean equals(Object o)

Overrides:

equals in class SaccharideGraph

hashCode

public int hashCode()

Overrides:

hashCode in class SaccharideGraph