org.expasy.mzjava.glycomics.mol

Class SaccharideGraph

java.lang.Object

org.expasy.mzjava.glycomics.mol.SaccharideGraph

Direct Known Subclasses:

Glycan, GlycanFragment

public class SaccharideGraph
extends Object

Version:

sqrt -1

Author:

Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	SaccharideGraph.AbstractBuilder<G extends SaccharideGraph> A builder to build Glycan.
static class	SaccharideGraph.Traversal

Field Summary

Fields

Modifier and Type	Field and Description
protected List<SEdge>	edges
protected org.expasy.mzjava.glycomics.mol.IdentityEdgeMultimap<Monosaccharide,Monosaccharide,org.expasy.mzjava.glycomics.mol.GlycosidicEdge>	monosaccharideEdgeMultimap
protected List<GlycanNode>	nodes
protected gnu.trove.map.TObjectIntMap<GlycanNode>	postOrder
protected gnu.trove.map.TObjectIntMap<GlycanNode>	preOrder
protected Monosaccharide	root
protected org.expasy.mzjava.glycomics.mol.IdentityEdgeMultimap<Monosaccharide,Substituent,org.expasy.mzjava.glycomics.mol.SubstituentEdge>	substituentEdgeMultimap

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SaccharideGraph(Monosaccharide root)

Method Summary

Methods

Modifier and Type	Method and Description
protected int	add(Monosaccharide child, List<Monosaccharide> parents, GlycosidicLinkage linkage)
protected int	add(Monosaccharide child, Monosaccharide parent, GlycosidicLinkage linkage)
protected int	add(Substituent child, List<Monosaccharide> parents, SubstituentLinkage linkage)
protected int	add(Substituent child, Monosaccharide parent, SubstituentLinkage linkage)
protected double	calculateTotalSaccharideMass() Returns the total mass of the Saccharide Graph.
boolean	canFragmentCrossRing(Monosaccharide monosaccharide) Return a boolean value that show if the glycan is fragmentable.
protected boolean	containsNode(GlycanNode node) This method check if a glycan contains a specific node.
List<SEdge>	copyEdgeList() Returns a new list of all the edges.
protected void	doBFS(LinkageAcceptor linkageAcceptor, Deque<Monosaccharide> deque, Comparator<org.expasy.mzjava.glycomics.mol.GlycosidicEdge> traversalComparator)
protected void	doDFS(LinkageAcceptor linkageAcceptor, Deque<Monosaccharide> deque, Comparator<org.expasy.mzjava.glycomics.mol.GlycosidicEdge> traversalComparator)
boolean	equals(Object o)
void	forEachLinkage(SaccharideGraph.Traversal traversal, LinkageAcceptor linkageAcceptor) Traverses the saccharide graph starting at the root.
void	forEachLinkage(SaccharideGraph.Traversal traversal, TraversalComparator traversalComparator, LinkageAcceptor linkageAcceptor) Traverses the saccharide graph starting at the root.
NodeSet<GlycanNode>	getChildren(Monosaccharide parent) Returns a the children of parent
com.google.common.base.Optional<GlycosidicLinkage>	getGlycoLinkage(GlycanNode parentNode, GlycanNode childNode) Return the linkage between parentNode and childNode
NodeSet<Monosaccharide>	getMonosaccharideChildren(Monosaccharide parent) Returns all children of parent that are Monosaccharides
GlycanNode	getNode(int nodeId) Returns the nodeId'th node that was added to this SaccharideGraph.
<A extends GlycanNode> GlycanNode	getParent(A child) Calculate the parent of a node.
Monosaccharide	getRoot() Return the root of this SaccharideGraph
NodeSet<Substituent>	getSubstituentChildren(Monosaccharide parent) Returns all children of parent that are Substituents
com.google.common.base.Optional<SubstituentLinkage>	getSubstituentLinkage(GlycanNode parentNode, GlycanNode childNode) Return the linkage between parentNode and childNode
int	hashCode()
boolean	hasHyperEdges() Returns true if the glycan has hyperedges.
boolean	isEmpty() Check if there is no nodes in the glycan.
boolean	isLeaf(Monosaccharide monosaccharide) Returns true if the specified monosaccharide is a leaf in the saccharide.
int	order() Return the number of monosaccharides and substituents in this glycan
protected void	populatePrePostOrder(GlycanNode node, Counter counter) Populate the pre and post order table
int	size() Return the size of the glycan as the number of monosaccharide.

Methods inherited from class java.lang.Object

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

Field Detail

root

protected final Monosaccharide root

nodes

protected final List<GlycanNode> nodes

edges

protected final List<SEdge> edges

monosaccharideEdgeMultimap

protected final org.expasy.mzjava.glycomics.mol.IdentityEdgeMultimap<Monosaccharide,Monosaccharide,org.expasy.mzjava.glycomics.mol.GlycosidicEdge> monosaccharideEdgeMultimap

substituentEdgeMultimap

protected final org.expasy.mzjava.glycomics.mol.IdentityEdgeMultimap<Monosaccharide,Substituent,org.expasy.mzjava.glycomics.mol.SubstituentEdge> substituentEdgeMultimap

preOrder

protected final gnu.trove.map.TObjectIntMap<GlycanNode> preOrder

postOrder

protected final gnu.trove.map.TObjectIntMap<GlycanNode> postOrder

Constructor Detail

SaccharideGraph

protected SaccharideGraph(Monosaccharide root)

Method Detail

add

protected int add(Monosaccharide child,
      List<Monosaccharide> parents,
      GlycosidicLinkage linkage)

add

protected int add(Monosaccharide child,
      Monosaccharide parent,
      GlycosidicLinkage linkage)

add

protected int add(Substituent child,
      List<Monosaccharide> parents,
      SubstituentLinkage linkage)

add

protected int add(Substituent child,
      Monosaccharide parent,
      SubstituentLinkage linkage)

getNode

public GlycanNode getNode(int nodeId)

Returns the nodeId'th node that was added to this SaccharideGraph.

Parameters:

nodeId - the node id

Returns:

the nodeId'th node that was added to this SaccharideGraph.

getRoot

public Monosaccharide getRoot()

Return the root of this SaccharideGraph

Returns:

the root of this SaccharideGraph

getGlycoLinkage

public com.google.common.base.Optional<GlycosidicLinkage> getGlycoLinkage(GlycanNode parentNode,
                                                                 GlycanNode childNode)

Return the linkage between parentNode and childNode

Parameters:

parentNode - the parent node

childNode - the childNode

Returns:

an Optional containing the linkage if one exists between parentNode and childNode, or an empty Optional if no linkage exists.

getSubstituentLinkage

public com.google.common.base.Optional<SubstituentLinkage> getSubstituentLinkage(GlycanNode parentNode,
                                                                        GlycanNode childNode)

Return the linkage between parentNode and childNode

Parameters:

parentNode - the parent node

childNode - the childNode

Returns:

an Optional containing the linkage if one exists between parentNode and childNode, or an empty Optional if no linkage exists.

getChildren

public NodeSet<GlycanNode> getChildren(Monosaccharide parent)

Returns a the children of parent

Parameters:

parent - the parent node

Returns:

a sorted set of all the children of parent

getMonosaccharideChildren

public NodeSet<Monosaccharide> getMonosaccharideChildren(Monosaccharide parent)

Returns all children of parent that are Monosaccharides

Parameters:

parent - the parent node

Returns:

all Monosaccharide children of parent

getSubstituentChildren

public NodeSet<Substituent> getSubstituentChildren(Monosaccharide parent)

Returns all children of parent that are Substituents

Parameters:

parent - the parent node

Returns:

all children of parent that are Substituents

order

public int order()

Return the number of monosaccharides and substituents in this glycan

Returns:

the number of monosaccharides and substituents in this glycan

copyEdgeList

public List<SEdge> copyEdgeList()

Returns a new list of all the edges.

Returns:

a new list of all the edges

hasHyperEdges

public boolean hasHyperEdges()

Returns true if the glycan has hyperedges.

Returns:

true if the glycan has hyperedges; false otherwise

isLeaf

public boolean isLeaf(Monosaccharide monosaccharide)

Returns true if the specified monosaccharide is a leaf in the saccharide.

Returns:

true if the specified monosaccharide is a leaf in the saccharide; false otherwise

getParent

public <A extends GlycanNode> GlycanNode getParent(A child)

Calculate the parent of a node. It use pre and post order so could be time consuming. In case that the node is a root it return the root it self.

Parameters:

child - a child in the graph.

Returns:

the parent of the child specified.

calculateTotalSaccharideMass

protected double calculateTotalSaccharideMass()

Returns the total mass of the Saccharide Graph.

Returns:

the total mass of the Saccharide Graph.

containsNode

protected boolean containsNode(GlycanNode node)

This method check if a glycan contains a specific node. It check for memory reference of the node. Don't use it for check if a glycan contains a type of monosaccahride.

Parameters:

node - a monosaccharide

Returns:

true if the monosaccharide is in the list of nodes. false otherwise

canFragmentCrossRing

public boolean canFragmentCrossRing(Monosaccharide monosaccharide)

Return a boolean value that show if the glycan is fragmentable.

Returns:

true if the glycan is fragmentable otherwise return false.

isEmpty

public boolean isEmpty()

Check if there is no nodes in the glycan.

Returns:

boolean value

size

public int size()

Return the size of the glycan as the number of monosaccharide.

Returns:

size of the fragment.

populatePrePostOrder

protected void populatePrePostOrder(GlycanNode node,
                        Counter counter)

Populate the pre and post order table

Parameters:

node - node of the saccharide graph.

counter - node counter.

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

forEachLinkage

public void forEachLinkage(SaccharideGraph.Traversal traversal,
                  LinkageAcceptor linkageAcceptor)

Traverses the saccharide graph starting at the root. The type of traversal is determined by traversal.

Parameters:

traversal - determines weather the traversal is depth or breadth first

linkageAcceptor - callback that gets called for every edge that is traversed

forEachLinkage

public void forEachLinkage(SaccharideGraph.Traversal traversal,
                  TraversalComparator traversalComparator,
                  LinkageAcceptor linkageAcceptor)

Traverses the saccharide graph starting at the root. The type of traversal is determined by traversal. The order in which the children are traversed can be controlled using the traversalComparator.

Parameters:

traversal - determines weather the traversal is depth or breadth first

traversalComparator - allows control of the order in which a nodes children are traversed

linkageAcceptor - callback that gets called for every edge that is traversed

doDFS

protected void doDFS(LinkageAcceptor linkageAcceptor,
         Deque<Monosaccharide> deque,
         Comparator<org.expasy.mzjava.glycomics.mol.GlycosidicEdge> traversalComparator)

doBFS

protected void doBFS(LinkageAcceptor linkageAcceptor,
         Deque<Monosaccharide> deque,
         Comparator<org.expasy.mzjava.glycomics.mol.GlycosidicEdge> traversalComparator)