org.expasy.mzjava.glycomics.mol

Class CutDescriptor

java.lang.Object

org.expasy.mzjava.glycomics.mol.CutDescriptor

public class CutDescriptor
extends Object

Version:

sqrt -1.

Author:

Davide Alocci

Constructor Summary

Constructors

Constructor and Description
CutDescriptor()
CutDescriptor(Set<CleavedMonosaccharide> cleavedMonosaccharidesSet, Set<SEdge> cleavedEdges)

Method Summary

Methods

Modifier and Type	Method and Description
void	addCleavedEdge(SEdge edge) Add a cleaved edge to the CutDescriptor.
void	addCleavedEdges(Set<SEdge> edges) Add a set of cleaved edge to the CutDescriptor.
void	addCleavedMonosaccharide(Monosaccharide monosaccharide, CutIndexes cutIndexes) Add a cleaved monosaccharide edge to the CutDescriptor.
void	addCleavedMonosaccharides(Set<CleavedMonosaccharide> cleavedMonosaccharides) Add a collection of cleaved monosaccharides edge to the CutDescriptor.
boolean	contains(Monosaccharide monosaccharide) Check if the CutDescriptor contains the specified monosaccharide.
boolean	contains(SEdge edge) Check if the CutDescriptor contains the specified edge.
boolean	equals(Object o)
Set<SEdge>	getCleavedEdges() Return a set of all the cleaved edges in the CutDescriptor.
Set<CleavedMonosaccharide>	getCleavedMonosaccharides() Return a set of all the cleaved monosaccharides in the CutDescriptor with their CutIndex.
Set<Monosaccharide>	getCleavedNodes() Return a set of all the cleaved monosaccharides in the CutDescriptor.
CutIndexes	getCutIndexesForMonosaccharide(Monosaccharide monosaccharide) Return the CutIndex related with the specified monosaccharide.
int	getNumberOfCut() Return the actual number of cuts in the CutDescriptor.
int	hashCode()
boolean	isEmpty() Return true if the CutDescriptor is empty.

Methods inherited from class java.lang.Object

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

Constructor Detail

CutDescriptor

public CutDescriptor()

CutDescriptor

public CutDescriptor(Set<CleavedMonosaccharide> cleavedMonosaccharidesSet,
             Set<SEdge> cleavedEdges)

Method Detail

addCleavedEdge

public void addCleavedEdge(SEdge edge)

Add a cleaved edge to the CutDescriptor.

Parameters:

edge - cleaved edge.

addCleavedEdges

public void addCleavedEdges(Set<SEdge> edges)

Add a set of cleaved edge to the CutDescriptor.

Parameters:

edges - cleaved edge.

addCleavedMonosaccharide

public void addCleavedMonosaccharide(Monosaccharide monosaccharide,
                            CutIndexes cutIndexes)

Add a cleaved monosaccharide edge to the CutDescriptor.

Parameters:

monosaccharide - cleaved monosaccharide.

cutIndexes - type of cut for the monosaccharide.

addCleavedMonosaccharides

public void addCleavedMonosaccharides(Set<CleavedMonosaccharide> cleavedMonosaccharides)

Add a collection of cleaved monosaccharides edge to the CutDescriptor. It use an IdentityHashMap because the software use the references to check the equaly.

Parameters:

cleavedMonosaccharides - a set of CleavedMonosaccharides.

contains

public boolean contains(Monosaccharide monosaccharide)

Check if the CutDescriptor contains the specified monosaccharide. Return true if the monosaccharide is already present in the CutDescriptor.

Parameters:

monosaccharide - a monosaccharide

Returns:

true if the monosaccharide is in the CutDescriptor. false otherwise

contains

public boolean contains(SEdge edge)

Check if the CutDescriptor contains the specified edge. Return true if the edge is already present in the CutDescriptor.

Parameters:

edge - a edge

Returns:

true if the edge is in the CutDescriptor. false otherwise

getCutIndexesForMonosaccharide

public CutIndexes getCutIndexesForMonosaccharide(Monosaccharide monosaccharide)

Return the CutIndex related with the specified monosaccharide.

Parameters:

monosaccharide - a monosaccharide.

Returns:

CutIndex related with the specified monosaccharide.

isEmpty

public boolean isEmpty()

Return true if the CutDescriptor is empty.

Returns:

true if the CutDescriptor is empty. false otherwise

getNumberOfCut

public int getNumberOfCut()

Return the actual number of cuts in the CutDescriptor.

Returns:

a integer

getCleavedNodes

public Set<Monosaccharide> getCleavedNodes()

Return a set of all the cleaved monosaccharides in the CutDescriptor.

Returns:

a set of monosaccharides.

getCleavedMonosaccharides

public Set<CleavedMonosaccharide> getCleavedMonosaccharides()

Return a set of all the cleaved monosaccharides in the CutDescriptor with their CutIndex.

Returns:

a set of CleavedMonosaccharides.

getCleavedEdges

public Set<SEdge> getCleavedEdges()

Return a set of all the cleaved edges in the CutDescriptor.

Returns:

a set of edges.

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object