Uses of Class
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Entry

Packages that use Entry

Package	Description
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes

Uses of Entry in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type with type arguments of type Entry

Modifier and Type	Method	Description
static void	KeggReactionIdAttributeEditor.editReactions(Reaction r, Pathway p, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, HashMap<Entry,Node> entry2graphNode, Graph graph)

Uses of Entry in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui with type arguments of type Entry

Constructor	Description
CompoundListEditor(Reaction currReaction, Pathway p, boolean sub, boolean enz, boolean prod, HashMap<Entry,Node> entry2graphNode)

Uses of Entry in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui with type arguments of type Entry

Constructor	Description
SrcTargetEditor(String title, Relation initialRelation, List<Entry> entries, HashMap<Entry,Node> entry2graphNode)
SrcTargetEditor(String title, Relation initialRelation, List<Entry> entries, HashMap<Entry,Node> entry2graphNode)
SubtypeCompoundEditor(String title, Relation initialRelation, List<Entry> entries, HashMap<Entry,Node> entry2graphNode)
SubtypeCompoundEditor(String title, Relation initialRelation, List<Entry> entries, HashMap<Entry,Node> entry2graphNode)

Uses of Entry in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg with type arguments of type Entry

Constructor	Description
ReactionLabel(Reaction r, HashMap<Entry,Node> entry2graphNode, Pathway p, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, Graph graph)
RelationLabel(Relation r, HashMap<Entry,Node> entry2graphNode, Pathway pathway, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, Graph graph)

Uses of Entry in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml that return Entry

Modifier and Type	Method	Description
static Entry	Entry.getEntryFromKgmlEntryElement(Collection<IdRef> mapLinksWhichNeedToBeUpdated, Collection<IdRef> componentsWhichNeedToBeUpdated, org.jdom2.Element entryElement, String sourcePathwayId)
Entry	Relation.getSourceEntry()
Entry	Relation.getTargetEntry()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml that return types with arguments of type Entry

Modifier and Type	Method	Description
Collection<Entry>	Pathway.findMultipleEntries(ArrayList<Entry> validEntries)
static Collection<Entry>	Reaction.getDistanceSubset(Collection<Entry> substratesOrProducts, Node b, HashMap<Entry,Node> entry2graphNode)
Collection<Entry>	Pathway.getEntries()
Collection<Entry>	Reaction.getEntriesRepresentingThisReaction(Collection<Entry> entryElements)
static Collection<Entry>	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)
Collection<Entry>	Reaction.getProducts()
Collection<Entry>	Reaction.getSubstrates()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml with parameters of type Entry

Modifier and Type	Method	Description
void	Relation.addSubtypeRef(Entry e)
static void	Graphics.processDefaultNodeDesign(Node n, Entry entry)
void	Reaction.removePossibleEntry(Entry invalidEntry)
void	Relation.removeSubtypeRef(Entry e)
void	Relation.setSourceEntry(Entry e)
void	Relation.setTargetEntry(Entry e)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml with type arguments of type Entry

Modifier and Type	Method	Description
Collection<Entry>	Pathway.findMultipleEntries(ArrayList<Entry> validEntries)
Collection<NodeCombination>	Reaction.getDesiredNodeCombinations(HashMap<Entry,Node> entry2graphNode, Collection<Entry> entryElements, Collection<Relation> relationElements, Collection<NodeCombination> relationNodeCombinations)
Collection<NodeCombination>	Reaction.getDesiredNodeCombinations(HashMap<Entry,Node> entry2graphNode, Collection<Entry> entryElements, Collection<Relation> relationElements, Collection<NodeCombination> relationNodeCombinations)
Collection<NodeCombination>	Relation.getDesiredNodeCombinations(HashMap<Entry,Node> entry2graphNode, Collection<Entry> entries)
Collection<NodeCombination>	Relation.getDesiredNodeCombinations(HashMap<Entry,Node> entry2graphNode, Collection<Entry> entries)
static Collection<Entry>	Reaction.getDistanceSubset(Collection<Entry> substratesOrProducts, Node b, HashMap<Entry,Node> entry2graphNode)
static Collection<Entry>	Reaction.getDistanceSubset(Collection<Entry> substratesOrProducts, Node b, HashMap<Entry,Node> entry2graphNode)
Collection<Entry>	Reaction.getEntriesRepresentingThisReaction(Collection<Entry> entryElements)
static Collection<Entry>	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 Pathway	Pathway.getPathwayFromGraph(Graph graph, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, HashMap<Entry,Node> entry2graphNode)
static Collection<Reaction>	Reaction.getReactionElementsFromGraphEdges(Collection<Entry> entries, Collection<Edge> graphEdges, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors)
static Collection<Reaction>	Reaction.getReactionElementsFromGraphNodes(Collection<Entry> entries, List<Node> graphNodes, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors)
static Reaction	Reaction.getReactionFromKgmlReactionElement(org.jdom2.Element reactionElement, Collection<Entry> entryElements, String clusterIdForHiddenCompounds)
static Collection<Relation>	Relation.getRelationElementsFromGraph(Collection<Entry> entries, Graph graph, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors)
static Relation	Relation.getRelationFromKgmlRelationElement(org.jdom2.Element relationElement, Collection<Entry> entryElements, String clusterIdForHiddenCompounds)
static Subtype	Subtype.getSubtypeFromKgmlSubtypeElement(org.jdom2.Element subtypeElement, Collection<Entry> entries, String clusterIdForHiddenCompounds)
void	Pathway.mergeMultipleEntriesOfType(EntryType et, ArrayList<Entry> validEntries)
void	Pathway.removeMergeTheseEntriesIfPossible(Collection<Entry> removeMergeTheseEntries)
void	Reaction.setProducts(Collection<Entry> products)
void	Reaction.setSubstrates(Collection<Entry> substrates)

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml with type arguments of type Entry

Constructor	Description
Pathway(KeggId name, MapOrg org, MapNumber number, String title, Url image, Url link, Collection<Entry> entries, Collection<Reaction> reactions, Collection<Relation> relations)
Reaction(String name, ReactionType type, Collection<Entry> substrates, Collection<Entry> products)
Reaction(String name, ReactionType type, Collection<Entry> substrates, Collection<Entry> products, String elementID)

Uses of Entry in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes that return Entry

Modifier and Type	Method	Description
Entry	KeggId.getEntry()
Entry	IdRef.getRef()
Entry	KeggId.getReference()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes with parameters of type Entry

Modifier and Type	Method	Description
void	IdRef.setRef(Entry ref)
void	KeggId.setReference(Entry entryRef)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes with parameters of type Entry

Constructor	Description
IdRef(Entry ref, String id)