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

Class Pathway

java.lang.Object

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

public class Pathway
extends Object

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
Collection<Entry>	findMultipleEntries(ArrayList<Entry> validEntries)
Collection<Reaction>	findReaction(String reactionId)
Collection<Reaction>	findReaction(Collection<String> reactionIds)
Collection<Relation>	findRelations(String relationSrcTgtIds)
Collection<Entry>	getEntries()
Graph	getGraph()
void	getGraph(Graph graph)
org.jdom2.Document	getKgmlDocument()	Use getPathwayFromKGML to read a KGML document and to create pathway object.
MapOrg	getMapOrg()
KeggId	getName()
static int	getNextID()
static Pathway	getPathwayFromGraph(Graph graph, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, HashMap<Entry,Node> entry2graphNode)
static Pathway	getPathwayFromKGML(InputStream in)
static Pathway	getPathwayFromKGML(Reader in)
static Pathway	getPathwayFromKGML(org.jdom2.Element kgmlRoot)
Collection<Reaction>	getReactions()
Collection<Relation>	getRelations()
String	getTitle()
void	mergeMultipleEntriesOfType(EntryType et, ArrayList<Entry> validEntries)
void	removeMergeTheseEntriesIfPossible(Collection<Entry> removeMergeTheseEntries)
static void	resetIdGen()
static void	showKgmlErrors(Collection<Gml2PathwayErrorInformation> errors, Collection<Gml2PathwayWarningInformation> warnings)
static void	testGML2Pathway2GML()
static int	testShowPathwayComparison(Pathway p1, Pathway p2, boolean showMessage)	Compare two pathways
static void	testShowPathwayInfo(Pathway p)

Methods inherited from class java.lang.Object

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

Constructor Details

Pathway

public Pathway(KeggId name,
MapOrg org,
MapNumber number,
String title,
Url image,
Url link,
Collection<Entry> entries,
Collection<Reaction> reactions,
Collection<Relation> relations)

Method Details

getName

public KeggId getName()

getMapOrg

public MapOrg getMapOrg()

getTitle

public String getTitle()

testGML2Pathway2GML

public static void testGML2Pathway2GML()

testShowPathwayInfo

public static void testShowPathwayInfo(Pathway p)

testShowPathwayComparison

public static int testShowPathwayComparison(Pathway p1,
Pathway p2,
boolean showMessage)

Compare two pathways

Parameters:

p1 - Pathway 1

p2 - Pathway 2

showMessage - If true, the differences will be shown in a task panel

Returns:

Number of differences, 0 if p1 and p2 appear to be the same.

getEntries

public Collection<Entry> getEntries()

getReactions

public Collection<Reaction> getReactions()

getRelations

public Collection<Relation> getRelations()

getPathwayFromKGML

public static Pathway getPathwayFromKGML(org.jdom2.Element kgmlRoot)

getPathwayFromKGML

public static Pathway getPathwayFromKGML(InputStream in)

getPathwayFromKGML

public static Pathway getPathwayFromKGML(Reader in)

getKgmlDocument

public org.jdom2.Document getKgmlDocument()

Use getPathwayFromKGML to read a KGML document and to create pathway object. Use this method to create KGML document from a pathway object.

Returns:

A JDOM XML Document containing the pathway information of this object.

getGraph

public Graph getGraph()

getGraph

public void getGraph(Graph graph)

getPathwayFromGraph

public static Pathway getPathwayFromGraph(Graph graph,
Collection<Gml2PathwayWarningInformation> warnings,
Collection<Gml2PathwayErrorInformation> errors,
HashMap<Entry,Node> entry2graphNode)

findReaction

public Collection<Reaction> findReaction(String reactionId)

findReaction

public Collection<Reaction> findReaction(Collection<String> reactionIds)

findRelations

public Collection<Relation> findRelations(String relationSrcTgtIds)

showKgmlErrors

public static void showKgmlErrors(Collection<Gml2PathwayErrorInformation> errors,
Collection<Gml2PathwayWarningInformation> warnings)

getNextID

public static int getNextID()

resetIdGen

public static void resetIdGen()

findMultipleEntries

public Collection<Entry> findMultipleEntries(ArrayList<Entry> validEntries)

mergeMultipleEntriesOfType

public void mergeMultipleEntriesOfType(EntryType et,
ArrayList<Entry> validEntries)

removeMergeTheseEntriesIfPossible

public void removeMergeTheseEntriesIfPossible(Collection<Entry> removeMergeTheseEntries)