Package de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml

Class Entry

java.lang.Object

de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Entry

public class Entry
extends Object

Constructor Summary

Constructors

Constructor	Description
Entry(Id id, KeggId name, EntryType type, Url link, IdRef map, Collection<KeggId> reactions, Collection<IdRef> components, Graphics graphics)

Method Summary

Modifier and Type	Method	Description
void	addComponent(IdRef component)
Node	addGraphNode(Graph graph)
void	addReaction(KeggId reaction)
Collection<IdRef>	getComponents()
static Collection<Entry>	getEntryElementsFromGraphNodes(de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.KgmlIdGenerator idGenerator, List<Node> nodes, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, HashMap<Entry,Node> entry2graphNode)
static Entry	getEntryFromKgmlEntryElement(Collection<IdRef> mapLinksWhichNeedToBeUpdated, Collection<IdRef> componentsWhichNeedToBeUpdated, org.jdom2.Element entryElement, String sourcePathwayId)
Graphics	getGraphics()
Id	getId()
org.jdom2.Element	getKgmlEntryElement(boolean addSourcePathwayInformation)
Url	getLink()
IdRef	getMapRef()
KeggId	getName()
Collection<KeggId>	getReactions()
Node	getSourceGraphNode()	In case this entry has been created from a Graph node, the souce graph node may be retrieved with this function.
String	getSourcePathwayKeggId()
EntryType	getType()
String	getVisibleName()
boolean	hasCompoundName()
boolean	hasGlycanName()
boolean	isPartOfGroup()
void	removeReaction(Reaction r)
void	setGraphics(Graphics graphics)
void	setIsPartOfGroup(boolean partOfGroup)
void	setLink(String url)
void	setMapRef(IdRef map)
void	setSourcePathwayKeggId(String id)
void	setType(EntryType et)
String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

Entry

public Entry(Id id,
KeggId name,
EntryType type,
Url link,
IdRef map,
Collection<KeggId> reactions,
Collection<IdRef> components,
Graphics graphics)

Method Details

setSourcePathwayKeggId

public void setSourcePathwayKeggId(String id)

getSourcePathwayKeggId

public String getSourcePathwayKeggId()

hasGlycanName

public boolean hasGlycanName()

hasCompoundName

public boolean hasCompoundName()

getType

public EntryType getType()

getName

public KeggId getName()

getId

public Id getId()

getMapRef

public IdRef getMapRef()

setMapRef

public void setMapRef(IdRef map)

getGraphics

public Graphics getGraphics()

setGraphics

public void setGraphics(Graphics graphics)

getEntryFromKgmlEntryElement

public static Entry getEntryFromKgmlEntryElement(Collection<IdRef> mapLinksWhichNeedToBeUpdated,
Collection<IdRef> componentsWhichNeedToBeUpdated,
org.jdom2.Element entryElement,
String sourcePathwayId)

getReactions

public Collection<KeggId> getReactions()

addReaction

public void addReaction(KeggId reaction)

getComponents

public Collection<IdRef> getComponents()

addComponent

public void addComponent(IdRef component)

getLink

public Url getLink()

getKgmlEntryElement

public org.jdom2.Element getKgmlEntryElement(boolean addSourcePathwayInformation)

addGraphNode

public Node addGraphNode(Graph graph)

toString

public String toString()

Overrides:

toString in class Object

getEntryElementsFromGraphNodes

public static Collection<Entry> getEntryElementsFromGraphNodes(de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.KgmlIdGenerator idGenerator,
List<Node> nodes,
Collection<Gml2PathwayWarningInformation> warnings,
Collection<Gml2PathwayErrorInformation> errors,
HashMap<Entry,Node> entry2graphNode)

getSourceGraphNode

public Node getSourceGraphNode()

In case this entry has been created from a Graph node, the souce graph node may be retrieved with this function. More than one Entry may be created from a single Graph node.

Returns:

Souce Graph Node (if Entry is created from a Graph)

setIsPartOfGroup

public void setIsPartOfGroup(boolean partOfGroup)

isPartOfGroup

public boolean isPartOfGroup()

getVisibleName

public String getVisibleName()

setLink

public void setLink(String url)

setType

public void setType(EntryType et)

removeReaction

public void removeReaction(Reaction r)