org.expasy.mzjava.glycomics.mol

Class Glycan

java.lang.Object

org.expasy.mzjava.glycomics.mol.SaccharideGraph

org.expasy.mzjava.glycomics.mol.Glycan

public class Glycan
extends SaccharideGraph

Data structure to represent a Glycan.

The glycan is represented as a rooted directed acyclic graph.

To represent uncertainty in linkage Glycans can have hyper edges that connect 1..n parent nodes to 1 child node.

Glycans are immutable, Glycans are constructed using the builder pattern:

     Glycan.Builder builder = new Glycan.Builder()
     Monosaccharide glc = builder.setRoot(MonosaccharideLookup.getNew("Glc"), Optional.absent(), "A");
     Monosaccharide gal = builder.add(MonosaccharideLookup.getNew("Gal"), glc, new GlycosidicLinkage(Optional.absent(), Optional.absent(), Optional.absent(), Optional.absent(), Optional.absent()));
     Glycan glycan = builder.build();
 

Version:

sqrt -1

Author:

Oliver Horlacher, Davide Alocci

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Glycan.Builder A builder to build Glycans.

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	Glycan(Monosaccharide root, com.google.common.base.Optional<Anomericity> reducingEndAnomericity, String databaseIdentifier, Composition endComposition)

Method Summary

Methods

Modifier and Type	Method and Description
double	calculateMass() Return the molecular mass of this glycan.
double	calculateMz(int charge) Return the mass/charge of this glycan.
boolean	equals(Object o)
String	getDatabaseIdentifier() Return the database identifier associated with this glycan.
Composition	getEndComposition() Return the composition of the end of the glycan.
List<GlycanFragment>	getFragment(CutDescriptor cutDescriptor)
com.google.common.base.Optional<Anomericity>	getReducingEndAnomericity()
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

Glycan

protected Glycan(Monosaccharide root,
      com.google.common.base.Optional<Anomericity> reducingEndAnomericity,
      String databaseIdentifier,
      Composition endComposition)

Method Detail

getEndComposition

public Composition getEndComposition()

Return the composition of the end of the glycan.

Returns:

the composition of the end of the glycan.

calculateMass

public double calculateMass()

Return the molecular mass of this glycan.

Returns:

the molecular mass of this glycan.

calculateMz

public double calculateMz(int charge)

Return the mass/charge of this glycan.

Parameters:

charge - the specific charge for the calculation.

Returns:

the mass/charge of this glycan.

getDatabaseIdentifier

public String getDatabaseIdentifier()

Return the database identifier associated with this glycan.

Returns:

the database identifier associated with this glycan

getReducingEndAnomericity

public com.google.common.base.Optional<Anomericity> getReducingEndAnomericity()

getFragment

public List<GlycanFragment> getFragment(CutDescriptor cutDescriptor)

equals

public boolean equals(Object o)

Overrides:

equals in class SaccharideGraph

hashCode

public int hashCode()

Overrides:

hashCode in class SaccharideGraph