Package de.ipk_gatersleben.ag_nw.graffiti

Class GraphHelperBio

java.lang.Object

de.ipk_gatersleben.ag_nw.graffiti.GraphHelperBio

All Implemented Interfaces:

HelperClass

public class GraphHelperBio
extends Object
implements HelperClass

Author:

Christian Klukas

Constructor Summary

Constructors

Constructor	Description
GraphHelperBio()

Method Summary

Modifier and Type	Method	Description
static Edge	addEdgeCopyIfNotExistant(Edge refEdge, Node a, Node b)
static Edge	addEdgeIfNotExistant(Graph graph, Node nodeA, Node nodeB, boolean directed, CollectionAttribute graphicsAttributeForEdge)
static Node	addMapNode(Graph superGraph, KeggPathwayEntry kpe)
static void	connectNodesWithSameLabel(List<Node> nodes)
static ArrayList<Node>	getEnzymeNodes(Graph g)
static String	getKeggName(GraphElement ge, String resultIfNotAvailable)
static String	getKeggType(GraphElement ge, String resultIfNotAvailable)
static ArrayList<Edge>	getMapLinkEdges(Graph g)
static ArrayList<Node>	getMapLinkNodes(Graph g)
static boolean	isMapLink(Edge e)
static void	mergeNodesWithSameLabel(List<Node> nodes, boolean selectOnlyTrueOrMergeIsFalse, boolean extendSelection, boolean considerCluster)
static void	mergeNodesWithSameLabel(List<Node> nodes, boolean selectOnlyTrueOrMergeIsFalse, boolean extendSelection, boolean considerCluster, boolean considerPositionPlusMinus10, boolean retainClusterIDs)
static void	setKeggType(GraphElement ge, String keggType)

Methods inherited from class java.lang.Object

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

Constructor Details

GraphHelperBio

public GraphHelperBio()

Method Details

getKeggType

public static String getKeggType(GraphElement ge,
String resultIfNotAvailable)

setKeggType

public static void setKeggType(GraphElement ge,
String keggType)

getKeggName

public static String getKeggName(GraphElement ge,
String resultIfNotAvailable)

isMapLink

public static boolean isMapLink(Edge e)

getMapLinkEdges

public static ArrayList<Edge> getMapLinkEdges(Graph g)

getEnzymeNodes

public static ArrayList<Node> getEnzymeNodes(Graph g)

getMapLinkNodes

public static ArrayList<Node> getMapLinkNodes(Graph g)

addEdgeIfNotExistant

public static Edge addEdgeIfNotExistant(Graph graph,
Node nodeA,
Node nodeB,
boolean directed,
CollectionAttribute graphicsAttributeForEdge)

addEdgeCopyIfNotExistant

public static Edge addEdgeCopyIfNotExistant(Edge refEdge,
Node a,
Node b)

addMapNode

public static Node addMapNode(Graph superGraph,
KeggPathwayEntry kpe)

mergeNodesWithSameLabel

public static void mergeNodesWithSameLabel(List<Node> nodes,
boolean selectOnlyTrueOrMergeIsFalse,
boolean extendSelection,
boolean considerCluster)

mergeNodesWithSameLabel

public static void mergeNodesWithSameLabel(List<Node> nodes,
boolean selectOnlyTrueOrMergeIsFalse,
boolean extendSelection,
boolean considerCluster,
boolean considerPositionPlusMinus10,
boolean retainClusterIDs)

connectNodesWithSameLabel

public static void connectNodesWithSameLabel(List<Node> nodes)