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

Class GeometryDatas

java.lang.Object

jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

public class GeometryDatas
extends Object

The class GeometryDatas, which contains following objects which are related to geometry.

• SBML model Model
• Geometry Geometry
• coordinates of boundary
• dimension
• list of domains(String)
• list of SpatialImages

This class is used in MainSBaseSpatial, to visualize a model in 3D space. Date Created: Jun 25, 2015

Author:

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

Field Summary

Fields

Modifier and Type	Field and Description
protected int	dimension The dimension of the geometry.
protected math3d.Point3d	dispCoord The displacement from original coordinates to modified coordinate.
protected ArrayList<String>	domList The list of domains.
protected org.sbml.jsbml.ext.spatial.Geometry	geometry The Geometry object.
protected math3d.Point3d	maxCoord The maximum value of the coordinate axis (boundary).
protected math3d.Point3d	minCoord The minimum value of the coordinate axis (boundary).
protected org.sbml.jsbml.Model	model The SBML model.
protected org.sbml.jsbml.ext.spatial.SpatialModelPlugin	spatialplugin The spatialplugin.

Constructor Summary

Constructors

Constructor and Description
GeometryDatas(org.sbml.jsbml.Model model) Instantiates a new GeometryDatas object with given SBML model.

Method Summary

Modifier and Type	Method and Description
protected void	adjustAxis() Adjust axis to 0 origin.
protected void	createspImgList() Create the list of SpatialImage, which is a class for handling spatial image in XitoSBML.
protected void	getCoordinates() Gets the minimum and maximum values of the coordinate axis (boundary) from the geometry, and then adjust the axis (reset to 0 origin).
protected void	getDomainTypes() Gets the domain types from the geometry object, and then add them to the list of domains.
protected SpatialImage	getSpImgFromGeo(org.sbml.jsbml.ext.spatial.GeometryDefinition gd) Gets the SpatialImage object from given GeometryDefinition.
ArrayList<SpatialImage>	getSpImgList() Gets the list of SpatialImage.

Methods inherited from class java.lang.Object

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

Field Detail

model

protected org.sbml.jsbml.Model model

The SBML model.

spatialplugin

protected org.sbml.jsbml.ext.spatial.SpatialModelPlugin spatialplugin

The spatialplugin.

geometry

protected org.sbml.jsbml.ext.spatial.Geometry geometry

The Geometry object. Geometry might be a SampledFieldGeometry or AnalyticGeometry

minCoord

protected math3d.Point3d minCoord

The minimum value of the coordinate axis (boundary).

maxCoord

protected math3d.Point3d maxCoord

The maximum value of the coordinate axis (boundary).

dispCoord

protected math3d.Point3d dispCoord

The displacement from original coordinates to modified coordinate.

dimension

protected int dimension

The dimension of the geometry.

domList

protected ArrayList<String> domList

The list of domains.

Constructor Detail

GeometryDatas

public GeometryDatas(org.sbml.jsbml.Model model)

Instantiates a new GeometryDatas object with given SBML model. The geometry, minimum values of the coordinate * axis (boundary), domain types which are stored in the model will be set to this object.

Parameters:

model - the model

Method Detail

createspImgList

protected void createspImgList()

Create the list of SpatialImage, which is a class for handling spatial image in XitoSBML.

getSpImgFromGeo

protected SpatialImage getSpImgFromGeo(org.sbml.jsbml.ext.spatial.GeometryDefinition gd)

Gets the SpatialImage object from given GeometryDefinition. Currently, this method supports AnalyticGeometry and SampledFieldGeometry.

Parameters:

gd - the JSBML GeometryDefinition object

Returns:

the SpatialImage object

getCoordinates

protected void getCoordinates()

Gets the minimum and maximum values of the coordinate axis (boundary) from the geometry, and then adjust the axis (reset to 0 origin).

adjustAxis

protected void adjustAxis()

Adjust axis to 0 origin. This adjustment is required to properly visualized on ImageJ 3D Viewer.

getDomainTypes

protected void getDomainTypes()

Gets the domain types from the geometry object, and then add them to the list of domains.

getSpImgList

public ArrayList<SpatialImage> getSpImgList()

Gets the list of SpatialImage.

Returns:

the list of SpatialImage.