public class Graph
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.util.Vector |
allGraphs |
static boolean |
countGraphs |
java.util.HashMap<java.lang.String,Edge> |
EdgeHash |
java.util.Vector<Edge> |
Edges |
java.lang.String |
globalComment |
java.util.Vector |
metaNodes |
java.lang.String |
name |
java.util.HashMap<java.lang.String,Node> |
NodeHash |
java.util.HashMap<java.lang.String,java.lang.Integer> |
NodeIndexHash |
java.util.Vector<Node> |
Nodes |
java.util.HashSet |
selectedIds |
java.lang.String |
startId |
boolean |
useIDsForOutput |
boolean |
writeHangingNodes |
Constructor and Description |
---|
Graph() |
Modifier and Type | Method and Description |
---|---|
void |
addConnections(Graph gr) |
void |
addConnectionsAlongSequence(Graph gr) |
void |
addEdge(Edge e) |
void |
addEdgeIdUnique(Edge e) |
void |
addEdges(Graph gr) |
void |
addMetanodeConnections(Graph gr,
boolean nodeIntersectionView,
boolean showIntersections) |
void |
addNode(Node n) |
void |
addNodes(Graph gr) |
void |
addNodesFromEdges() |
void |
assignEdgeIds() |
void |
calcNodesInOut() |
java.lang.String |
correct(java.lang.String id) |
void |
createIndexNodeHash() |
java.util.Vector |
edgesConnectingSubGraphs(Graph meta1,
Graph meta2,
Graph grglobal,
boolean nodeIntersectionView) |
Edge |
getCreateEdge(java.lang.String id) |
Node |
getCreateNode(java.lang.String id) |
java.util.Vector<Edge> |
getEdge(Node source,
Node target,
boolean directedGraph) |
Edge |
getEdge(java.lang.String id) |
Edge |
getEdgeByLabel(java.lang.String label) |
int |
getEdgeIndex(java.lang.String id) |
Graph |
getHangingNodes() |
double[][] |
getIncidenceMatrix() |
Node |
getNode(java.lang.String id) |
Node |
getNodeByLabel(java.lang.String label) |
int |
getNodeIndex(java.lang.String id) |
Graph |
getNodesByLabelInclusion(java.lang.String label) |
Graph |
getSelectedNodes() |
boolean |
identicalEdges(Graph gr) |
boolean |
identicalNodes(Graph gr) |
boolean |
identicalTo(Graph gr) |
java.util.Vector |
includesEdges(Graph gr) |
java.util.Vector |
includesNodes(Graph gr) |
float |
includesNodesPercentage(Graph gr) |
Graph |
intersection(Graph gr) |
static void |
main(java.lang.String[] args) |
Graph |
makeCopy() |
void |
makeEdgeDoubleSense(java.lang.String edgeId)
Add an edge from edgeId.Target to edgeId.Source.
|
static void |
printGraphList() |
void |
recreateNodeEdgeHash() |
void |
removeEdge(java.lang.String id) |
void |
removeNode(java.lang.String id) |
void |
removeNodes(Graph gr) |
void |
removeObsoleteEdges() |
void |
saveAsCytoscapeGML(java.lang.String fn) |
void |
saveAsCytoscapeSif(java.lang.String fn) |
void |
saveAsCytoscapeXGMML(java.lang.String fn) |
void |
subtractNodes(Graph gr) |
java.lang.String |
toString() |
public java.lang.String name
public boolean useIDsForOutput
public boolean writeHangingNodes
public java.lang.String startId
public java.lang.String globalComment
public java.util.Vector<Node> Nodes
public java.util.Vector<Edge> Edges
public java.util.HashMap<java.lang.String,Node> NodeHash
public java.util.HashMap<java.lang.String,java.lang.Integer> NodeIndexHash
public java.util.HashMap<java.lang.String,Edge> EdgeHash
public java.util.HashSet selectedIds
public static boolean countGraphs
public static java.util.Vector allGraphs
public java.util.Vector metaNodes
public static void main(java.lang.String[] args)
public void saveAsCytoscapeSif(java.lang.String fn)
public java.lang.String correct(java.lang.String id)
public void saveAsCytoscapeXGMML(java.lang.String fn)
public void saveAsCytoscapeGML(java.lang.String fn)
public Node getNode(java.lang.String id)
public Edge getEdge(java.lang.String id)
public Node getNodeByLabel(java.lang.String label)
public Graph getNodesByLabelInclusion(java.lang.String label)
public int getNodeIndex(java.lang.String id)
public int getEdgeIndex(java.lang.String id)
public Node getCreateNode(java.lang.String id)
public Edge getCreateEdge(java.lang.String id)
public Graph makeCopy()
public void subtractNodes(Graph gr)
public void addNodes(Graph gr)
public void addNode(Node n)
public void addEdge(Edge e)
public void addEdgeIdUnique(Edge e)
public void removeNodes(Graph gr)
public void removeNode(java.lang.String id)
public void removeEdge(java.lang.String id)
public void addEdges(Graph gr)
public void removeObsoleteEdges()
public void addNodesFromEdges()
public void addConnections(Graph gr)
public void addConnectionsAlongSequence(Graph gr)
public void addMetanodeConnections(Graph gr, boolean nodeIntersectionView, boolean showIntersections)
public Edge getEdgeByLabel(java.lang.String label)
public java.util.Vector edgesConnectingSubGraphs(Graph meta1, Graph meta2, Graph grglobal, boolean nodeIntersectionView)
public void assignEdgeIds()
public Graph getHangingNodes()
public void calcNodesInOut()
public boolean identicalNodes(Graph gr)
public boolean identicalEdges(Graph gr)
public boolean identicalTo(Graph gr)
public java.util.Vector includesNodes(Graph gr)
public java.util.Vector includesEdges(Graph gr)
public float includesNodesPercentage(Graph gr)
public Graph getSelectedNodes()
public static void printGraphList()
public void makeEdgeDoubleSense(java.lang.String edgeId)
edgeId
- public void createIndexNodeHash()
public double[][] getIncidenceMatrix()
public java.lang.String toString()
toString
in class java.lang.Object
public void recreateNodeEdgeHash()