edu.iastate.metnet.graphmodel
Class NetworkEditHelper

java.lang.Object
  edu.iastate.metnet.graphmodel.NetworkEditHelper

public class NetworkEditHelper
extends java.lang.Object

helper function for NetworkEditForm

Author:

Jie Li

Field Summary

(package private) static org.apache.log4j.Logger

logger log4j facility

Constructor Summary

NetworkEditHelper(org.jgraph.JGraph jGraph)
default constructor

Method Summary

java.lang.Object[]	captureGraphModel(org.jgraph.JGraph graph) capture the graph model represented in the current graph, do not consider the bridge interaction right now
java.util.Map	createBounds(org.jgraph.graph.CellView view, java.awt.Color color, int x, int y) create the box for the label
java.util.Map	createLines(org.jgraph.graph.CellView view, java.awt.Color color) create an line
MetnetInteraction	getCurrentInteraction()
MetnetLiveEntity	getCurrentLiveEntity()
MetnetPathway	getCurrentPathway()
GraphValidity	getCurrentValidity()
org.jgraph.graph.Edge	getEdge(org.jgraph.JGraph graph, org.jgraph.graph.GraphCell sourceCell, org.jgraph.graph.GraphCell targetCell) get the JGraph edge based on JGraph node
org.jgraph.JGraph	getJGraph()
static java.util.Collection	getMitochondrionFamily() get the location belongs to mitochondrion.
static java.util.Collection	getNucleusFamily() get the location belongs to nucleus.
java.util.Collection	getPathwayList()
static java.util.Collection	getPlastidFamily() get the location belongs to plastid.
int	getPortObject()
java.util.List	getPredEdgeList(org.jgraph.graph.GraphModel model, org.jgraph.graph.GraphCell cell) get the predecessor edges
java.util.List	getPredEdgeList(org.jgraph.JGraph jGraph, org.jgraph.graph.GraphCell cell) get the predecessor edges
java.util.List	getPredNodeList(org.jgraph.JGraph jGraph, org.jgraph.graph.GraphCell cell) get the predecessor node list of the current node
org.jgraph.graph.DefaultGraphCell	getSourceNode(org.jgraph.graph.GraphModel model, org.jgraph.graph.GraphCell cell) get the source node list of the edge
org.jgraph.graph.DefaultGraphCell	getSourceNode(org.jgraph.JGraph jGraph, org.jgraph.graph.GraphCell cell) get the source node of the edge
java.util.List	getSuccEdgeList(org.jgraph.graph.GraphModel model, org.jgraph.graph.GraphCell cell) get the successor edge list
java.util.List	getSuccEdgeList(org.jgraph.JGraph jGraph, org.jgraph.graph.GraphCell cell) get the successor edges
org.jgraph.graph.DefaultGraphCell	getTargetNode(org.jgraph.graph.GraphModel model, org.jgraph.graph.GraphCell cell) get the target node list of the edge
org.jgraph.graph.DefaultGraphCell	getTargetNode(org.jgraph.JGraph jGraph, org.jgraph.graph.GraphCell cell) get the target node of the edge
boolean	isEdge(org.jgraph.graph.GraphModel model, java.lang.Object cell) detect if it is a vertex
boolean	isEdge(org.jgraph.JGraph jGraph, java.lang.Object cell) detect if it is a vertex
boolean	isVertex(org.jgraph.graph.GraphModel model, java.lang.Object cell) detect if it is a vertex
boolean	isVertex(org.jgraph.JGraph jGraph, java.lang.Object cell) detect if it is a vertex
java.lang.Integer	nextPortObject() create unique port number
void	reset() reset the UI and internal model
void	setCurrentInteraction(MetnetInteraction currentInteraction)
void	setCurrentLiveEntity(MetnetLiveEntity currentLiveEntity)
void	setCurrentPathway(MetnetPathway currentPathway)
void	setCurrentValidity(GraphValidity currentValidity)
void	setJGraph(org.jgraph.JGraph graph)
void	setPortObject(int portObject)
GraphValidity	validateGraph(org.jgraph.JGraph jGraph) we shoudl check the graph at the model level rather than from the user interface level which is hard to infer the graph structure

Methods inherited from class java.lang.Object

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

Field Detail

logger

static org.apache.log4j.Logger logger

log4j facility

Constructor Detail

NetworkEditHelper

public NetworkEditHelper(org.jgraph.JGraph jGraph)

default constructor

Parameters:

jGraph - the jgraph need to capture

Method Detail

reset

public void reset()

reset the UI and internal model

captureGraphModel

public java.lang.Object[] captureGraphModel(org.jgraph.JGraph graph)

capture the graph model represented in the current graph, do not consider the bridge interaction right now

Returns:

the graph model and the data mapping, and also the mapping from the model data to view data, also the coefficient map.

getEdge

public org.jgraph.graph.Edge getEdge(org.jgraph.JGraph graph,
                                     org.jgraph.graph.GraphCell sourceCell,
                                     org.jgraph.graph.GraphCell targetCell)

get the JGraph edge based on JGraph node

Parameters:

graph - the jgraph

sourceCell - the jgraph node

targetCell - the jgraph node

Returns:

the edge

getJGraph

public org.jgraph.JGraph getJGraph()

Returns:

the jGraph

isVertex

public boolean isVertex(org.jgraph.graph.GraphModel model,
                        java.lang.Object cell)

detect if it is a vertex

Parameters:

cell - the cell

Returns:

if it is a vertex

isVertex

public boolean isVertex(org.jgraph.JGraph jGraph,
                        java.lang.Object cell)

detect if it is a vertex

Parameters:

cell - the cell

Returns:

if it is a vertex

nextPortObject

public java.lang.Integer nextPortObject()

create unique port number

Returns:

unique port number

createBounds

public java.util.Map createBounds(org.jgraph.graph.CellView view,
                                  java.awt.Color color,
                                  int x,
                                  int y)

create the box for the label

Parameters:

view - the box view

color - the color

Returns:

the box attribute map

createLines

public java.util.Map createLines(org.jgraph.graph.CellView view,
                                 java.awt.Color color)

create an line

Parameters:

view - the cell view

color - the color

Returns:

the line attribute map

getTargetNode

public org.jgraph.graph.DefaultGraphCell getTargetNode(org.jgraph.graph.GraphModel model,
                                                       org.jgraph.graph.GraphCell cell)

get the target node list of the edge

Parameters:

model - the graph model

cell - the edge cell

Returns:

the target node

getTargetNode

public org.jgraph.graph.DefaultGraphCell getTargetNode(org.jgraph.JGraph jGraph,
                                                       org.jgraph.graph.GraphCell cell)

get the target node of the edge

Parameters:

jGraph - the jgraph

cell - the edge

Returns:

the target node

getSuccEdgeList

public java.util.List getSuccEdgeList(org.jgraph.graph.GraphModel model,
                                      org.jgraph.graph.GraphCell cell)

get the successor edge list

Parameters:

model - the graph model

cell - the graph element

Returns:

the successor edge list

getSuccEdgeList

public java.util.List getSuccEdgeList(org.jgraph.JGraph jGraph,
                                      org.jgraph.graph.GraphCell cell)

get the successor edges

Parameters:

jGraph - the jgraph

cell - the graph element

Returns:

the successor edge

getPredEdgeList

public java.util.List getPredEdgeList(org.jgraph.graph.GraphModel model,
                                      org.jgraph.graph.GraphCell cell)

get the predecessor edges

Parameters:

model - the graph model

cell - the graph element

Returns:

the edge list

getPredNodeList

public java.util.List getPredNodeList(org.jgraph.JGraph jGraph,
                                      org.jgraph.graph.GraphCell cell)

get the predecessor node list of the current node

Parameters:

jGraph - the graph

cell - the current node

Returns:

the predecessor node list

getPredEdgeList

public java.util.List getPredEdgeList(org.jgraph.JGraph jGraph,
                                      org.jgraph.graph.GraphCell cell)

get the predecessor edges

Parameters:

jGraph - the jgraph

cell - the graph element

Returns:

the edge list

getSourceNode

public org.jgraph.graph.DefaultGraphCell getSourceNode(org.jgraph.graph.GraphModel model,
                                                       org.jgraph.graph.GraphCell cell)

get the source node list of the edge

Parameters:

model - the graph model

cell - the edge

Returns:

the source node

getSourceNode

public org.jgraph.graph.DefaultGraphCell getSourceNode(org.jgraph.JGraph jGraph,
                                                       org.jgraph.graph.GraphCell cell)

get the source node of the edge

Parameters:

jGraph - the jgraph

cell - the edge

Returns:

the source node

isEdge

public boolean isEdge(org.jgraph.graph.GraphModel model,
                      java.lang.Object cell)

detect if it is a vertex

Parameters:

cell - the cell

Returns:

if it is a vertex

isEdge

public boolean isEdge(org.jgraph.JGraph jGraph,
                      java.lang.Object cell)

detect if it is a vertex

Parameters:

cell - the cell

Returns:

if it is a vertex

setJGraph

public void setJGraph(org.jgraph.JGraph graph)

Parameters:

graph - the jGraph to set

getPathwayList

public java.util.Collection getPathwayList()

Returns:

the pbidList

getCurrentInteraction

public MetnetInteraction getCurrentInteraction()

Returns:

the currentInteraction

setCurrentInteraction

public void setCurrentInteraction(MetnetInteraction currentInteraction)

Parameters:

currentInteraction - the currentInteraction to set

getCurrentLiveEntity

public MetnetLiveEntity getCurrentLiveEntity()

Returns:

the currentLiveEntity

setCurrentLiveEntity

public void setCurrentLiveEntity(MetnetLiveEntity currentLiveEntity)

Parameters:

currentLiveEntity - the currentLiveEntity to set

getCurrentPathway

public MetnetPathway getCurrentPathway()

Returns:

the currentPathway

setCurrentPathway

public void setCurrentPathway(MetnetPathway currentPathway)

Parameters:

currentPathway - the currentPathway to set

getPortObject

public int getPortObject()

Returns:

the portObject

setPortObject

public void setPortObject(int portObject)

Parameters:

portObject - the portObject to set

getNucleusFamily

public static java.util.Collection getNucleusFamily()

get the location belongs to nucleus. WARNING: this is hard coded and should be synchronized with database later. Right now there are 8 locations belonging to nucleus family.

Returns:

the location belongs to nucleus

getMitochondrionFamily

public static java.util.Collection getMitochondrionFamily()

get the location belongs to mitochondrion. WARNING: this is hard coded and should be synchronized with database later. Right now there are 6 locations belonging to mitochondrion family.

Returns:

the location belongs to mitochondrion

getPlastidFamily

public static java.util.Collection getPlastidFamily()

get the location belongs to plastid. WARNING: this is hard coded and should be synchronized with database later. Right now there are 25 locations belonging to plastid family.

Returns:

the location belongs to plastid

validateGraph

public GraphValidity validateGraph(org.jgraph.JGraph jGraph)

we shoudl check the graph at the model level rather than from the user interface level which is hard to infer the graph structure

Parameters:

jGraph - the user interface level graph

Returns:

the graph validity result

getCurrentValidity

public GraphValidity getCurrentValidity()

Returns:

the currentValidity

setCurrentValidity

public void setCurrentValidity(GraphValidity currentValidity)

Parameters:

currentValidity - the currentValidity to set