org.expasy.mzjava.glycomics.mol

Class SaccharideGraph.AbstractBuilder<G extends SaccharideGraph>

java.lang.Object

org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder<G>

Direct Known Subclasses:

Glycan.Builder, GlycanFragment.Builder

Enclosing class:

SaccharideGraph

protected abstract static class SaccharideGraph.AbstractBuilder<G extends SaccharideGraph>
extends Object

A builder to build Glycan. This builder is not reusable.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	SaccharideGraph.AbstractBuilder.BuildSate

Field Summary

Fields

Modifier and Type	Field and Description
protected SaccharideGraph.AbstractBuilder.BuildSate	buildSate
protected G	graph

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SaccharideGraph.AbstractBuilder()

Method Summary

Methods

Modifier and Type	Method and Description
Monosaccharide	add(Monosaccharide monosaccharide, List<Monosaccharide> parents, GlycosidicLinkage linkage) Adda hyper edge from the list of parents to the monosaccharide.
Monosaccharide	add(Monosaccharide monosaccharide, Monosaccharide parent, GlycosidicLinkage linkage) Add a Monosaccharide to the Glycan.
Monosaccharide	add(Monosaccharide monosaccharide, Substituent substituent, Monosaccharide parent, GlycosidicLinkage glycoLinkage, SubstituentLinkage substituentLinkage) Add monosaccharide and substituent to the Glycan being built.
Substituent	add(Substituent substituent, List<Monosaccharide> parents, SubstituentLinkage linkage) Add a hyper edge from parents to substituent.
Substituent	add(Substituent substituent, Monosaccharide parent, SubstituentLinkage linkage) Adda substituent to parent
protected void	checkIsBuilding()
protected boolean	checkMonosaccharidesPresence(List<Monosaccharide> monosaccharides) Check for the presence of all cleaved monosaccharides inside the graph.
int	getId(GlycanNode node) Return the id of the node
GlycanNode	getNode(int nodeId) Return the nodeId'th node that was added

Methods inherited from class java.lang.Object

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

Field Detail

graph

protected G extends SaccharideGraph graph

buildSate

protected SaccharideGraph.AbstractBuilder.BuildSate buildSate

Constructor Detail

SaccharideGraph.AbstractBuilder

protected SaccharideGraph.AbstractBuilder()

Method Detail

add

public Monosaccharide add(Monosaccharide monosaccharide,
                 Monosaccharide parent,
                 GlycosidicLinkage linkage)

Add a Monosaccharide to the Glycan. The monosaccharide is attached to the pattern via the linkage. If the parent has not been added to this glycan an IllegalStateException is thrown.

Parameters:

monosaccharide - the monosaccharide to add

parent - Monosaccharide to which monosaccharide is to be added

linkage - the linkage

Returns:

the passed in monosaccharide

add

public Monosaccharide add(Monosaccharide monosaccharide,
                 Substituent substituent,
                 Monosaccharide parent,
                 GlycosidicLinkage glycoLinkage,
                 SubstituentLinkage substituentLinkage)

Add monosaccharide and substituent to the Glycan being built. The monosaccharide is attached to the parent using the glycoLinkage and the substituent is attached to the monosaccharide using the substituentLinkage.

This method addes two nodes and two edges to the Glycan being built.

     substituent <-- substituentLinkage -- monosaccharide <-- glycoLinkage <-- parent
 

If the parent has not been added to this glycan an IllegalStateException is thrown.

Parameters:

monosaccharide - the Monosaccharide to add

substituent - the monosaccharide's Substituent

parent - the parent to which the monosaccharide is to be attached

glycoLinkage - the linkage between parent and monosaccharide

substituentLinkage - the linkage between monosaccharide and substituent

Returns:

the monosaccharide

add

public Monosaccharide add(Monosaccharide monosaccharide,
                 List<Monosaccharide> parents,
                 GlycosidicLinkage linkage)

Adda hyper edge from the list of parents to the monosaccharide.

Parameters:

monosaccharide - the monosaccharide to add

parents - the list of parents

linkage - the linkage between the parents and the monosaccharide

Returns:

the monosaccharide

add

public Substituent add(Substituent substituent,
              Monosaccharide parent,
              SubstituentLinkage linkage)

Adda substituent to parent

Parameters:

substituent - teh substituent to add

parent - the parent

linkage - the linkage between parent and substituent

Returns:

the substituent

add

public Substituent add(Substituent substituent,
              List<Monosaccharide> parents,
              SubstituentLinkage linkage)

Add a hyper edge from parents to substituent.

Parameters:

substituent - the substituent to add

parents - the list of parents to add the substituent to

linkage - the linkage between the parents and the substituent

Returns:

the substituent

getNode

public GlycanNode getNode(int nodeId)

Return the nodeId'th node that was added

Parameters:

nodeId - the id of the node

Returns:

the nodeId'th node that was added

getId

public int getId(GlycanNode node)

Return the id of the node

Parameters:

node - the node

Returns:

the id of the node

checkIsBuilding

protected void checkIsBuilding()

checkMonosaccharidesPresence

protected boolean checkMonosaccharidesPresence(List<Monosaccharide> monosaccharides)

Check for the presence of all cleaved monosaccharides inside the graph.

Parameters:

monosaccharides - list of monosaccharides.

Returns:

a boolean value.