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

Class Reaction

java.lang.Object

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

public class Reaction
extends Object

Constructor Summary

Constructors

Constructor	Description
Reaction(String name, ReactionType type, Collection<Entry> substrates, Collection<Entry> products)
Reaction(String name, ReactionType type, Collection<Entry> substrates, Collection<Entry> products, String elementID)

Method Summary

Modifier and Type	Method	Description
Collection<NodeCombination>	getDesiredNodeCombinations(HashMap<Entry,Node> entry2graphNode, Collection<Entry> entryElements, Collection<Relation> relationElements, Collection<NodeCombination> relationNodeCombinations)
static Collection<Entry>	getDistanceSubset(Collection<Entry> substratesOrProducts, Node b, HashMap<Entry,Node> entry2graphNode)
String	getElementID()
Collection<Entry>	getEntriesRepresentingThisReaction(Collection<Entry> entryElements)
String	getId()
org.jdom2.Element	getKgmlReactionElement()
Collection<Entry>	getProducts()
static Collection<Reaction>	getReactionElementsFromGraphEdges(Collection<Entry> entries, Collection<Edge> graphEdges, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors)
static Collection<Reaction>	getReactionElementsFromGraphNodes(Collection<Entry> entries, List<Node> graphNodes, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors)
static Reaction	getReactionFromKgmlReactionElement(org.jdom2.Element reactionElement, Collection<Entry> entryElements, String clusterIdForHiddenCompounds)
Collection<Entry>	getSubstrates()
ReactionType	getType()
static void	processEdgeReactionInformation(Edge e, ArrayList<ReactionAndInfo> reactionsRequestingThisNodeCombination, ArrayList<ReactionAndInfo> reactionsRequestingThisInverseNodeCombination)
void	removePossibleEntry(Entry invalidEntry)
void	setId(String name)
void	setProducts(Collection<Entry> products)
void	setSubstrates(Collection<Entry> substrates)
void	setType(ReactionType reactionType)
String	toString()
String	toStringWithDetails(boolean html, boolean fullHtml)

Methods inherited from class java.lang.Object

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

Constructor Details

Reaction

public Reaction(String name,
ReactionType type,
Collection<Entry> substrates,
Collection<Entry> products)

Reaction

public Reaction(String name,
ReactionType type,
Collection<Entry> substrates,
Collection<Entry> products,
String elementID)

Method Details

getId

public String getId()

setId

public void setId(String name)

getType

public ReactionType getType()

getSubstrates

public Collection<Entry> getSubstrates()

getProducts

public Collection<Entry> getProducts()

getElementID

public String getElementID()

getReactionFromKgmlReactionElement

public static Reaction getReactionFromKgmlReactionElement(org.jdom2.Element reactionElement,
Collection<Entry> entryElements,
String clusterIdForHiddenCompounds)

getKgmlReactionElement

public org.jdom2.Element getKgmlReactionElement()

getEntriesRepresentingThisReaction

public Collection<Entry> getEntriesRepresentingThisReaction(Collection<Entry> entryElements)

getDesiredNodeCombinations

public Collection<NodeCombination> getDesiredNodeCombinations(HashMap<Entry,Node> entry2graphNode,
Collection<Entry> entryElements,
Collection<Relation> relationElements,
Collection<NodeCombination> relationNodeCombinations)

getDistanceSubset

public static Collection<Entry> getDistanceSubset(Collection<Entry> substratesOrProducts,
Node b,
HashMap<Entry,Node> entry2graphNode)

toString

public String toString()

Overrides:

toString in class Object

processEdgeReactionInformation

public static void processEdgeReactionInformation(Edge e,
ArrayList<ReactionAndInfo> reactionsRequestingThisNodeCombination,
ArrayList<ReactionAndInfo> reactionsRequestingThisInverseNodeCombination)

getReactionElementsFromGraphEdges

public static Collection<Reaction> getReactionElementsFromGraphEdges(Collection<Entry> entries,
Collection<Edge> graphEdges,
Collection<Gml2PathwayWarningInformation> warnings,
Collection<Gml2PathwayErrorInformation> errors)

getReactionElementsFromGraphNodes

public static Collection<Reaction> getReactionElementsFromGraphNodes(Collection<Entry> entries,
List<Node> graphNodes,
Collection<Gml2PathwayWarningInformation> warnings,
Collection<Gml2PathwayErrorInformation> errors)

toStringWithDetails

public String toStringWithDetails(boolean html,
boolean fullHtml)

setType

public void setType(ReactionType reactionType)

setSubstrates

public void setSubstrates(Collection<Entry> substrates)

setProducts

public void setProducts(Collection<Entry> products)

removePossibleEntry

public void removePossibleEntry(Entry invalidEntry)