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

Class MainModelEdit

java.lang.Object

jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSBaseSpatial

jp.ac.keio.bio.fun.xitosbml.xitosbml.MainModelEdit

All Implemented Interfaces:

ij.plugin.PlugIn

public class MainModelEdit
extends MainSBaseSpatial

The class MainModelEdit, which implements "run Model Editor" function. Date Created: Aug 28, 2015

Author:

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

Field Summary

Fields inherited from class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

document, hashSampledValue, imgexp, model, spatialplugin, spImg, viewer

Constructor Summary

Constructors

Constructor and Description
MainModelEdit()

Method Summary

Modifier and Type	Method and Description
void	run(String arg) Overrides ij.plugin.PlugIn#run(java.lang.String).

Methods inherited from class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSBaseSpatial

checkExtension, checkLevelAndVersion, checkSBMLDocument, getDocument, main, visualize

Methods inherited from class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

addSBases, computeImg, gui, print, showDomainStructure, showStep, visualize

Methods inherited from class java.lang.Object

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

Constructor Detail

MainModelEdit

public MainModelEdit()

Method Detail

run

public void run(String arg)

Overrides ij.plugin.PlugIn#run(java.lang.String). A dialog for editing the model will be displayed. Users can add, modify following SBML elements and save the model through the dialog.

• Species
• Parameter
• Advection coefficient
• Diffusion coefficient
• Boundary condition
• Reaction

Once the model is saved as SBML, XitoSBML will visualize the model in 3D space, and execute a syntax validation for both SBML core and spatial extension by using SBML online validator. With this plugin, users can create a reaction-diffusion model in spatial SBML format.

Specified by:

run in interface ij.plugin.PlugIn

Specified by:

run in class MainSBaseSpatial

Parameters:

arg - name of the method defined in plugins.config

See Also:

PlugIn.run(java.lang.String)