org.expasy.mzjava.glycomics.mol

Class GlycanFragment.Builder

java.lang.Object

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

org.expasy.mzjava.glycomics.mol.GlycanFragment.Builder

Enclosing class:

GlycanFragment

public static class GlycanFragment.Builder
extends SaccharideGraph.AbstractBuilder<GlycanFragment>

A builder to build Glycosidic Fragments. This builder is not reusable.

Nested Class Summary

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

SaccharideGraph.AbstractBuilder.BuildSate

Field Summary

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

buildSate, graph

Constructor Summary

Constructors

Constructor and Description
GlycanFragment.Builder()

Method Summary

Methods

Modifier and Type	Method and Description
SEdge	addCleavedEdge(Monosaccharide attachPoint, SEdge edge, IonType ionType) Add a cleaved edge to the fragment.
Monosaccharide	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	addCleavedMonosaccharide(Monosaccharide cleavedMonosaccharide, Monosaccharide parent, GlycosidicLinkage linkage, CutIndexes cutIndexes, IonType ionType) Add a Monosaccharide to the Glycan.
Monosaccharide	addCleavedMonosaccharide(Monosaccharide cleavedMonosaccharide, Substituent substituent, Monosaccharide parent, GlycosidicLinkage glycoLinkage, SubstituentLinkage substituentLinkage, CutIndexes cutIndexes, IonType ionType) Add cleavedMonosaccharide and substituent to the Glycan being built.
GlycanFragment	build() Build the Glycosidic Fragments Fragment.
Monosaccharide	setCleavedRoot(Monosaccharide root, FragmentType fragmentType, Composition endComposition, CutIndexes cutIndexes) Set the cleaved root of the Glycan Fragments.
Monosaccharide	setCleavedRoot(Monosaccharide root, FragmentType fragmentType, CutIndexes cutIndexes) Set the cleaved root of the Glycan Fragments.
Monosaccharide	setRoot(Monosaccharide root, FragmentType fragmentType) Set the root of the Glycan Fragments.
Monosaccharide	setRoot(Monosaccharide root, FragmentType fragmentType, Composition endComposition) Set the root of the Glycan Fragments.

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

add, add, add, add, add, checkIsBuilding, checkMonosaccharidesPresence, getId, getNode

Methods inherited from class java.lang.Object

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

Constructor Detail

GlycanFragment.Builder

public GlycanFragment.Builder()

Method Detail

setRoot

public Monosaccharide setRoot(Monosaccharide root,
                     FragmentType fragmentType)

Set the root of the Glycan Fragments. Can only be called once.

Parameters:

root - the monosaccharide that is to be the root

fragmentType - the fragment type.

Returns:

the monosaccharide that becomes root.

setCleavedRoot

public Monosaccharide setCleavedRoot(Monosaccharide root,
                            FragmentType fragmentType,
                            CutIndexes cutIndexes)

Set the cleaved root of the Glycan Fragments. Can only be called once.

Parameters:

root - the monosaccharide that is to be the root

fragmentType - the fragment type.

cutIndexes - the cutIndex of the root.

Returns:

the monosaccharide that becomes root.

setCleavedRoot

public Monosaccharide setCleavedRoot(Monosaccharide root,
                            FragmentType fragmentType,
                            Composition endComposition,
                            CutIndexes cutIndexes)

Set the cleaved root of the Glycan Fragments. Can only be called once.

Parameters:

root - the monosaccharide that is to be the root

fragmentType - the fragment type.

endComposition - the composition of the end of the fragment.

cutIndexes - the cutIndex of the root.

Returns:

the monosaccharide that becomes root.

setRoot

public Monosaccharide setRoot(Monosaccharide root,
                     FragmentType fragmentType,
                     Composition endComposition)

Set the root of the Glycan Fragments. Can only be called once.

Parameters:

root - the monosaccharide that is to be the root

fragmentType - the fragment type.

endComposition - the composition of the end of the fragment.

Returns:

the monosaccharide that becomes root.

addCleavedMonosaccharide

public Monosaccharide addCleavedMonosaccharide(Monosaccharide cleavedMonosaccharide,
                                      Monosaccharide parent,
                                      GlycosidicLinkage linkage,
                                      CutIndexes cutIndexes,
                                      IonType ionType)

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

Parameters:

cleavedMonosaccharide - the cleavedMonosaccharide to add

parent - Monosaccharide to which cleavedMonosaccharide is to be added

linkage - the linkage

Returns:

the passed in cleavedMonosaccharide

addCleavedMonosaccharide

public Monosaccharide addCleavedMonosaccharide(Monosaccharide cleavedMonosaccharide,
                                      Substituent substituent,
                                      Monosaccharide parent,
                                      GlycosidicLinkage glycoLinkage,
                                      SubstituentLinkage substituentLinkage,
                                      CutIndexes cutIndexes,
                                      IonType ionType)

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

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

     substituent <-- substituentLinkage -- cleavedMonosaccharide <-- glycoLinkage <-- parent
 

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

Parameters:

cleavedMonosaccharide - the Monosaccharide to add

substituent - the cleaved monosaccharide substituent

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

glycoLinkage - the linkage between parent and cleavedMonosaccharide

substituentLinkage - the linkage between cleavedMonosaccharide and substituent

Returns:

the cleavedMonosaccharide

addCleavedMonosaccharide

public Monosaccharide addCleavedMonosaccharide(Monosaccharide cleavedMonosaccharide,
                                      List<Monosaccharide> parents,
                                      GlycosidicLinkage linkage,
                                      CutIndexes cutIndexes,
                                      IonType ionType)

Add an hyper edge from the list of parents to the cleavedMonosaccharide.

Parameters:

cleavedMonosaccharide - the cleavedMonosaccharide to add

parents - the list of parents

linkage - the linkage between the parents and the cleavedMonosaccharide

Returns:

the cleavedMonosaccharide

addCleavedEdge

public SEdge addCleavedEdge(Monosaccharide attachPoint,
                   SEdge edge,
                   IonType ionType)

Add a cleaved edge to the fragment.

Parameters:

attachPoint - the monosaccharide where the edge is attach. It could be the parent or the child.

edge - the cleaved edge

Returns:

the cleaved edge

build

public GlycanFragment build()

Build the Glycosidic Fragments Fragment.

Returns:

the new Glycosidic Fragments Fragment