org.pistoiaalliance.helm.HELMSimilarityLibrary.utils

Class Vertex

java.lang.Object

org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

public class Vertex
extends Object

Vertex class is a data model for a vertex in a Graph. It is based on the monomer notation.

Author:

bueltel

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Vertex.Type

Field Summary

Fields

Modifier and Type	Field and Description
Vertex.Type	monomerType

Constructor Summary

Constructors

Constructor and Description
Vertex()
Vertex(org.helm.notation2.parser.notation.polymer.MonomerNotation monomer)
Vertex(org.helm.notation2.parser.notation.polymer.MonomerNotation monomer, Vertex.Type monomerType, boolean isNonNatural, boolean hasUniqueUnit, int index)
Vertex(Vertex vertex)
Vertex(Vertex vertex, Vertex.Type monomerType)

Method Summary

Modifier and Type	Method and Description
void	addBothNeighbours(Vertex vertex)
void	addNeighbour(Vertex vertex)
boolean	equals(Vertex otherVertex)
int	getIndex()
org.helm.notation2.parser.notation.polymer.MonomerNotation	getMonomer()
List<Vertex>	getNeighbourList()
Vertex	getParent()
boolean	hasUniqueUnit()
boolean	isChem()
boolean	isNonNatural()
boolean	isPeptide()
boolean	isRNA()
boolean	isVisited()
void	setHasUniqueUnit(boolean hasUniqueUnit)
void	setIndex(int idx)
void	setMonomer(org.helm.notation2.parser.notation.polymer.MonomerNotation monomer)
void	setNeighbourList(List<Vertex> neighbourList)
void	setNonNatural()
void	setParent(Vertex parent)
void	setVisited(boolean visited)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

monomerType

public Vertex.Type monomerType

Constructor Detail

Vertex

public Vertex()

Vertex

public Vertex(Vertex vertex)

Vertex

public Vertex(Vertex vertex,
              Vertex.Type monomerType)

Vertex

public Vertex(org.helm.notation2.parser.notation.polymer.MonomerNotation monomer)

Vertex

public Vertex(org.helm.notation2.parser.notation.polymer.MonomerNotation monomer,
              Vertex.Type monomerType,
              boolean isNonNatural,
              boolean hasUniqueUnit,
              int index)

Method Detail

getMonomer

public org.helm.notation2.parser.notation.polymer.MonomerNotation getMonomer()

addNeighbour

public void addNeighbour(Vertex vertex)

addBothNeighbours

public void addBothNeighbours(Vertex vertex)

isVisited

public boolean isVisited()

setVisited

public void setVisited(boolean visited)

setMonomer

public void setMonomer(org.helm.notation2.parser.notation.polymer.MonomerNotation monomer)

setIndex

public void setIndex(int idx)

getIndex

public int getIndex()

getNeighbourList

public List<Vertex> getNeighbourList()

setNeighbourList

public void setNeighbourList(List<Vertex> neighbourList)

getParent

public Vertex getParent()

setParent

public void setParent(Vertex parent)

isPeptide

public boolean isPeptide()

isRNA

public boolean isRNA()

isChem

public boolean isChem()

isNonNatural

public boolean isNonNatural()

setNonNatural

public void setNonNatural()

hasUniqueUnit

public boolean hasUniqueUnit()

setHasUniqueUnit

public void setHasUniqueUnit(boolean hasUniqueUnit)

toString

public String toString()

Overrides:

toString in class Object

equals

public boolean equals(Vertex otherVertex)