jp.ac.keio.bio.fun.xitosbml.visual

Class DomainStruct

java.lang.Object

jp.ac.keio.bio.fun.xitosbml.visual.DomainStruct

public class DomainStruct
extends Object

The class DomainStruct, which defines the structure of domains, and visualize the graph with JGraphX. The graph used in XitoSBML is an inclusion relationship of domains. Date Created: Feb 21, 2017

Author:

Kaito Ii <ii@fun.bio.keio.ac.jp>, Akira Funahashi <funa@bio.keio.ac.jp>

Constructor Summary

Constructors

Constructor and Description
DomainStruct()

Method Summary

Modifier and Type	Method and Description
void	addEdge(org.sbml.jsbml.ListOf<org.sbml.jsbml.ext.spatial.AdjacentDomains> load) Add edges to the graph structure of an inclusion relationship of domains.
void	addVertex(org.sbml.jsbml.ListOf<org.sbml.jsbml.ext.spatial.Domain> lod) Add vertices to the graph structure of an inclusion relationship of domains.
org.sbml.jsbml.ext.spatial.DomainType	getDomainType(String spId) Get domain type by given SpatialId.
GraphStruct	getGraphStruct() Gets the graph structure.
static void	main(String[] args) Example main() method which will launch a GUI and draw an inclusion relationship of domains as a graph.
void	setGraphStruct(GraphStruct graphStruct) Sets the graph structure.
void	show(org.sbml.jsbml.ext.spatial.Geometry geometry) Visualize the graph structure of an inclusion relationship of domains.

Methods inherited from class java.lang.Object

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

Constructor Detail

DomainStruct

public DomainStruct()

Method Detail

show

public void show(org.sbml.jsbml.ext.spatial.Geometry geometry)

Visualize the graph structure of an inclusion relationship of domains. Currently it supports the domain order of SampledFieldGeometry and AnalyticGeometry.

Parameters:

geometry - the geometry obtained from SBML model

addEdge

public void addEdge(org.sbml.jsbml.ListOf<org.sbml.jsbml.ext.spatial.AdjacentDomains> load)

Add edges to the graph structure of an inclusion relationship of domains. TODO change to a better algorithm since this assumes the order of list of AdjacentDomains to be specified

Parameters:

load - the list of AdjacentDomains

addVertex

public void addVertex(org.sbml.jsbml.ListOf<org.sbml.jsbml.ext.spatial.Domain> lod)

Add vertices to the graph structure of an inclusion relationship of domains.

Parameters:

lod - the list of Domains

getDomainType

public org.sbml.jsbml.ext.spatial.DomainType getDomainType(String spId)

Get domain type by given SpatialId.

Parameters:

spId - the SpatialId of domain type as String

Returns:

DomainType object if found, otherwise null

getGraphStruct

public GraphStruct getGraphStruct()

Gets the graph structure.

Returns:

the graph structure

setGraphStruct

public void setGraphStruct(GraphStruct graphStruct)

Sets the graph structure.

Parameters:

graphStruct - the new graph structure

main

public static void main(String[] args)

Example main() method which will launch a GUI and draw an inclusion relationship of domains as a graph. This example requires a specific SBML model "analytic_3d.xml" located under the "sample/" directory.

Parameters:

args - an array of command-line arguments for the application