A B C D F G H I J L M O P R S T U V

A

AbstractData - Class in jp.ac.keio.bio.fun.xitosbml.geometry

The class AbstractData, which is an abstract class and be used to create data objects for geometry objects (AnalyticGeometryData, SampledFieldGeometryData and ParametricGeometryData).

actionPerformed(ActionEvent) - Method in class jp.ac.keio.bio.fun.xitosbml.gui.MenuColumn

Not used in this class

actionPerformed(ActionEvent) - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageExplorer

The listener interface for receiving action events.

actionPerformed(ActionEvent) - Method in class jp.ac.keio.bio.fun.xitosbml.pane.TabTables

Invoked when an action occurs.

addAdjacentDomains() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Adds the adjacent domains.

addCellDesignerAnnotationTag(String) - Static method in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

Generate CellDesigner annotation with given annotation string.

addCoordinates() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Adds the coordinates to the Geometry object.

addCoordinates(HashMap<String, Point3d>) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Adds the coordinates to the Geometry object.

addCoordParameter() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Adds the global Parameter to each CoordinateComponent.

addDomains() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Adds domains to corresponding domaintypes.

addDomainTypes() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Adds the domain types to the Geometry object.

addEdge(ListOf<AdjacentDomains>) - Method in class jp.ac.keio.bio.fun.xitosbml.visual.DomainStruct

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

addEdge(String, String) - Method in class jp.ac.keio.bio.fun.xitosbml.visual.GraphStruct

Adds an edge from vertex1 to vertex2 to the graph.

addGeometryDefinitions() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Adds the geometry definitions.

AddingColumn - Class in jp.ac.keio.bio.fun.xitosbml.gui

The class AddingColumn, which creates an adding column for JTable used in ImageTable.

AddingColumn(JTable, int) - Constructor for class jp.ac.keio.bio.fun.xitosbml.gui.AddingColumn

Instantiates a new adding column.

addMembrane() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageEdit

Adds a membrane between two different domains.

addParaGeoDefinitions(HashMap<String, List<Point3d>>, HashMap<String, Point3d>) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Adds the parametric geometry definitions.

addSBases() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

Create a tabbed table which allows users to add the SBases to the model through GUI.

addUniqueVertices(SpatialPoints, ArrayList<Point3d>) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Adds the unique vertices to the SpatialPoints object.

addUnits() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Adds the units (length, area and volume) to the model.

addVertex(ListOf<Domain>) - Method in class jp.ac.keio.bio.fun.xitosbml.visual.DomainStruct

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

addVertex(String) - Method in class jp.ac.keio.bio.fun.xitosbml.visual.GraphStruct

Adds a vertex to the graph.

adjustAxis() - Method in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

Adjust axis to 0 origin.

AdvectionDialog - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class AdvectionDialog, which generates a GUI for creating / editing Advection Coefficient.

AdvectionDialog(Model) - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.AdvectionDialog

Instantiates a new advection dialog.

AdvectionTable - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class AdvectionTable, which inherits SBaseTable and implements add() and edit() method for adding and editing advection coefficient.

AnalyticGeometryData - Class in jp.ac.keio.bio.fun.xitosbml.geometry

The class AnalyticGeometryData, which inherits ImageGeometryData and implements getSampledValues() and createImage() methods.

ArrowColumn - Class in jp.ac.keio.bio.fun.xitosbml.gui

The class ArrowColumn, which creates an arrow column for JTable used in ImageTable.

ArrowColumn(JTable, int, int) - Constructor for class jp.ac.keio.bio.fun.xitosbml.gui.ArrowColumn

Instantiates a new arrow column.

B

BoundaryConditionDialog - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class BoundaryConditionDialog, which generates a GUI for creating / editing Boundary Condition.

BoundaryConditionDialog(Model) - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.BoundaryConditionDialog

Instantiates a new boundary condition dialog.

BoundaryConditionTable - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class BoundaryConditionTable, which inherits SBaseTable and implements add() and edit() method for adding and editing boundary condition.

bounds - Static variable in class jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

The Constant bounds.

boundType - Static variable in class jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

The Constant boundType.

ButtonColumn - Class in jp.ac.keio.bio.fun.xitosbml.gui

The class ButtonColumn, which creates a button column for JTable used in ImageTable.

ButtonColumn(JTable, int) - Constructor for class jp.ac.keio.bio.fun.xitosbml.gui.ButtonColumn

Instantiates a new button column.

byteArrayToIntArray(byte[]) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Convert byte array to int array.

C

CDNAMESPACE - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

The Constant CDNAMESPACE.

checkAdjacentsLabel(int, int, int, int) - Method in class jp.ac.keio.bio.fun.xitosbml.image.Filler

Check adjacent pixels whether it contains the given label (labelNum).

checkExtension() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSBaseSpatial

Check whether the model contains spatial extension.

checkHole() - Method in class jp.ac.keio.bio.fun.xitosbml.image.Filler

Check whether a hole exists in the hashmap of pixels (HashMap<label number, pixel value>).

checkLevelAndVersion() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSBaseSpatial

Check whether SBML level and version matches with Level 3 Version 1.

checkSBMLDocument(SBMLDocument) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSBaseSpatial

Check SBML document.

ComboBoxRenderer - Class in jp.ac.keio.bio.fun.xitosbml.gui

The class ComboBoxRenderer, which renders a combobox.

ComboBoxRenderer(String) - Constructor for class jp.ac.keio.bio.fun.xitosbml.gui.ComboBoxRenderer

Instantiates a new combo box renderer.

compressRawData(byte[]) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Compress raw data of spatial image in 1D array.

computeImg() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

Following process is performed to an image: Interpolate an image if it is a Z-stack image (3D image) and the voxel size of each axis (x, y and z) is not equal Fill holes (blank pixels) in the image by morphology operation if exists Add a membrane between two different domains if exists The converted image will be generated as SpatialImage, which is a base class for representing spatial image in XitoSBML.

copyAdvectionCoefficientContents(Parameter, Parameter) - Static method in class jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

Copy contents of AdvectionCoefficient from src to dst and returns dst object.

copyBoundaryConditionContents(Parameter, Parameter) - Static method in class jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

Copy contents of BoundaryCondition from src to dst and returns dst object.

copyDiffusionCoefficientContents(Parameter, Parameter) - Static method in class jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

Copy contents of DiffusionCoefficient from src to dst and returns dst object.

copyMat(ImagePlus) - Static method in class jp.ac.keio.bio.fun.xitosbml.image.ImgProcessUtil

Converts given image object (ImagePlus) to a raw data (1D byte array).

copyParameterContents(Parameter, Parameter) - Static method in class jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

Copy contents of Parameter from src to dst and returns dst object.

copyReactionContents(Reaction, Reaction) - Static method in class jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

Copy contents of Reaction from src to dst and returns dst object.

copySpeciesContents(Species, Species) - Static method in class jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

Copy contents of Species from src to dst and returns dst object.

countDomain() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageEdit

Count number of domains in each domain types and store the number to the hashmap (hashDomainNum<String domain type, Integer count number>).

createGeometryElements() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Creates the geometry elements.

createHashDomainTypes() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Creates the hashmap of domain types of spatial image.

createImage() - Method in class jp.ac.keio.bio.fun.xitosbml.geometry.SampledFieldGeometryData

Create a stacked image from spatial image (3D).

CreateImage - Class in jp.ac.keio.bio.fun.xitosbml.image

The class CreateImage, which creates composite image.

CreateImage(HashMap<String, ImagePlus>, HashMap<String, Integer>) - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.CreateImage

Instantiates a new CreateImage object with given hashmap of domain images and hashmap of sampled value of spatial image.

createMembrane() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageEdit

Creates the membrane.

createParametric(HashMap<String, List<Point3d>>, HashMap<String, Point3d>) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Creates the ParametricGeometry.

createspImgList() - Method in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

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

D

diffType - Static variable in class jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

The Constant diffType.

DiffusionDialog - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class DiffusionDialog, which generates a GUI for creating / editing Diffusion Coefficient.

DiffusionDialog(Model) - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.DiffusionDialog

Instantiates a new diffusion dialog.

DiffusionTable - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class DiffusionTable, which inherits SBaseTable and implements add() and edit() method for adding and editing diffusion coefficient.

dimension - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

The dimension of the geometry.

dispCoord - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.AnalyticGeometryData

The coordinate of displacement.

dispCoord - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

The displacement from original coordinates to modified coordinate.

document - Variable in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

The SBML document.

DomainStruct - Class in jp.ac.keio.bio.fun.xitosbml.visual

The class DomainStruct, which defines the structure of domains, and visualize the graph with JGraphX.

DomainStruct() - Constructor for class jp.ac.keio.bio.fun.xitosbml.visual.DomainStruct

domList - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

The list of domains.

domtype(HashMap<Integer, Integer>) - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageEdit

Create hashmap of count number of labels and set the value with given hashmap of pixels.

F

fill(ImagePlus) - Method in class jp.ac.keio.bio.fun.xitosbml.image.Filler

Fill a hole in the given image (ImagePlus object) by morphology operation, and returns the filled image.

fill(SpatialImage) - Method in class jp.ac.keio.bio.fun.xitosbml.image.Filler

Fill a hole in the given image (SpatialImage object) by morphology operation, and returns the filled image as ImageJ image object.

fill(int) - Method in class jp.ac.keio.bio.fun.xitosbml.image.Filler

Fill a hole in the hashmap of pixels (HashMap<label number, pixel value> by morphology operation.

Filler - Class in jp.ac.keio.bio.fun.xitosbml.image

The class Filler, which provides several morphological operations for filling holes in the image.

Filler() - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.Filler

fillHole() - Method in class jp.ac.keio.bio.fun.xitosbml.image.Filler

Fill a hole in the hashmap of pixels (HashMap<label number, pixel value> by morphology operation.

findPoints() - Method in class jp.ac.keio.bio.fun.xitosbml.visual.Viewer

Find points in the 3D universe.

fromFile() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageDialog

Handle importing an image from file.

G

g - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.ImageGeometryData

The Geometry object.

geometry - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

The Geometry object.

GeometryDatas - Class in jp.ac.keio.bio.fun.xitosbml.geometry

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

GeometryDatas(Model) - Constructor for class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

Instantiates a new GeometryDatas object with given SBML model.

getAdjacentsList() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Gets the list of adjacent of spatial image.

getAdjacentToTargetList() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SplitDomains

Gets the hashset of target of adjacent pixels.

getCellEditorValue() - Method in class jp.ac.keio.bio.fun.xitosbml.gui.ButtonColumn

Overrides javax.swing.CellEditor#getCellEditorValue()

getCellEditorValue() - Method in class jp.ac.keio.bio.fun.xitosbml.gui.MenuColumn

Overrides javax.swing.CellEditor#getCellEditorValue()

getColumnClass(int) - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageTable.MyTableModel

Get the class of selected cell.

getCompoImg() - Method in class jp.ac.keio.bio.fun.xitosbml.image.CreateImage

Gets the composite image.

getCoordinates() - Method in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

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

getDelta() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Gets the delta of spatial image.

getDepth() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Gets the depth of spatial image.

getDocument() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSBaseSpatial

Returns an SBML document from given file path.

getDocument() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Gets the SBML document.

getDomainType(String) - Method in class jp.ac.keio.bio.fun.xitosbml.visual.DomainStruct

Get domain type by given SpatialId.

getDomainTypes() - Method in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

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

getDomainTypes() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageExplorer

Sets the datatable(hashmap of domain file) to the hashmap of domain types and returns the hashmap of domain types.

getDomFile() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageExplorer

Gets the hashmap of domain file.

getFileInfo() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageExplorer

Gets the file information of composite image.

getFileInfo() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageTable

Gets the file information of composite image.

getFromSpatialList(ListOf<?>, String) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Returns SpatialNamedSBase object which has SpatialId "id" from given list of Objects.

getGraphStruct() - Method in class jp.ac.keio.bio.fun.xitosbml.visual.DomainStruct

Gets the graph structure.

gethashBound() - Method in class jp.ac.keio.bio.fun.xitosbml.visual.Viewer

Gets the hashmap of boundary.

getHashDomainNum() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Gets the hashmap of the count number of domains in each domain types.

getHashDomainTypes() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Gets the hashmap of domain types of spatial image.

getHashDomFile() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageTable

Gets the hashmap of domain file.

getHashDomInteriorPt() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Gets the hashmap of domain InteriorPoint of spatial image.

getHashSampledValue() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Gets the hash sampled value of spatial image.

gethashVertices() - Method in class jp.ac.keio.bio.fun.xitosbml.visual.Viewer

Gets the hashmap of vertices.

getHeight() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Gets the height of spatial image.

getImage() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Gets the ImageJ image object.

getImgNum() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageTable

Gets the number of images, that is, the size of the hashmap of domain file.

getInterpolatedImage() - Method in class jp.ac.keio.bio.fun.xitosbml.image.Interpolator

Gets the interpolated image object.

getlabelMat(ImagePlus) - Static method in class jp.ac.keio.bio.fun.xitosbml.image.ImgProcessUtil

Gets the label matrix.

getListCellRendererComponent(JList<?>, Object, int, boolean, boolean) - Method in class jp.ac.keio.bio.fun.xitosbml.gui.ComboBoxRenderer

Overrides ListCellRenderer.getListCellRendererComponent(javax.swing.JList, java.lang.Object, int, boolean, boolean)

getModel() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Gets the SBML model.

getName() - Method in class jp.ac.keio.bio.fun.xitosbml.util.ModelSaver

Gets the filename of the SBML file.

getPath() - Method in class jp.ac.keio.bio.fun.xitosbml.util.ModelSaver

Gets the path to the directory where SBML file is located.

getRaw(ImagePlus) - Static method in class jp.ac.keio.bio.fun.xitosbml.image.ImgProcessUtil

Converts given image object (ImagePlus) to a raw data (1D byte array).

getRaw() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Gets the raw data of spatial image in 1D array.

getSampledValues() - Method in class jp.ac.keio.bio.fun.xitosbml.geometry.SampledFieldGeometryData

Get sampled value from Geometry (SampledFieldGeometry) and sets its value to the hashSampledValue (hashmap of sampled value).

getSampledValues(ImageTable) - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageExplorer

Sets the hashmap of sampled values and returns the hashmap of sampled values.

getSpatialImage() - Method in class jp.ac.keio.bio.fun.xitosbml.geometry.AnalyticGeometryData

Create and return a new spatial image.

getSpatialImage() - Method in class jp.ac.keio.bio.fun.xitosbml.geometry.ImageGeometryData

Create and return a new spatial image.

getSpatialImage() - Method in class jp.ac.keio.bio.fun.xitosbml.geometry.SampledFieldGeometryData

Create and return a new spatial image.

getSpImgFromGeo(GeometryDefinition) - Method in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

Gets the SpatialImage object from given GeometryDefinition.

getSpImgList() - Method in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

Gets the list of SpatialImage.

getStackImage() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageBorder

Gets the stack of images.

getStackImage() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SplitDomains

Gets the stack of split images.

getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class jp.ac.keio.bio.fun.xitosbml.gui.ButtonColumn

Sets an initial value for the editor.

getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class jp.ac.keio.bio.fun.xitosbml.gui.MenuColumn

Sets an initial value for the editor.

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class jp.ac.keio.bio.fun.xitosbml.gui.ButtonColumn

Returns the component used for drawing the cell.

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class jp.ac.keio.bio.fun.xitosbml.gui.MenuColumn

Returns the component used for drawing the cell.

getUnit() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Gets the unit of a CoordinateComponent.

getWidth() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Gets the width of spatial image.

GraphStruct - Class in jp.ac.keio.bio.fun.xitosbml.visual

The class GraphStruct, which defines the structure of a graph, and visualize the graph with JGraphX.

gray - Variable in class jp.ac.keio.bio.fun.xitosbml.pane.SBaseTable

The gray color.

gui() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

Create a GUI which allows users to specify the correspondence between each image and the region in the cell.

H

hashSampledValue - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.ImageGeometryData

The hashmap of sampled value of spatial image.

hashSampledValue - Variable in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

The hashmap of sampled value of spatial image.

I

ImageBorder - Class in jp.ac.keio.bio.fun.xitosbml.image

The class ImageBorder, which provides several image processing functions to handle X-Y and Z border.

ImageBorder(SpatialImage) - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.ImageBorder

Instantiates a new ImageBorder object.

ImageDialog - Class in jp.ac.keio.bio.fun.xitosbml.image

The class ImageDialog, which generates a GUI for importing an image from ImageJ or a file.

ImageDialog() - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.ImageDialog

ImageEdit - Class in jp.ac.keio.bio.fun.xitosbml.image

The class ImageEdit, which provides several image processing filters to add a membrane between two different domains if exists.

ImageEdit(SpatialImage) - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.ImageEdit

Instantiates a new image edit with given spatial image object.

ImageExplorer - Class in jp.ac.keio.bio.fun.xitosbml.image

The class ImageExplorer, which inherits JFrame and implements table component of XitoSBML.

ImageExplorer() - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.ImageExplorer

Instantiates a new image explorer.

ImageExplorer(HashMap<String, Integer>, HashMap<String, Integer>) - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.ImageExplorer

Instantiates a new image explorer with given hashmap of domain types and hashmap of sampled values.

ImageGeometryData - Class in jp.ac.keio.bio.fun.xitosbml.geometry

The class ImageGeometryData, which is an abstract class and be used to create data objects for geometry objects (AnalyticGeometryData, SampledFieldGeometryData and ParametricGeometryData).

ImageTable - Class in jp.ac.keio.bio.fun.xitosbml.image

The class ImageTable, which inherits JTable and implements mousePressed() method for adding images to the spatial model.

ImageTable() - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.ImageTable

Instantiates a new image table.

ImageTable.MyTableModel - Class in jp.ac.keio.bio.fun.xitosbml.image

The class MyTableModel, which inherits DefaultTableModel and implements isCellEditable() and getColumnClass() methods.

img - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.ImageGeometryData

The ImageJ image object.

imgexp - Variable in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

The ImageExplorer.

ImgProcessUtil - Class in jp.ac.keio.bio.fun.xitosbml.image

The class ImgProcessUtil, which contains several useful static methods which wll convert ImageJ image object (ImagePlus) to raw data (1D byte array).

ImgProcessUtil() - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.ImgProcessUtil

importFile(int, ImagePlus) - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageTable

Import a file to the selected row.

interpolate(ImagePlus) - Method in class jp.ac.keio.bio.fun.xitosbml.image.Interpolator

Interpolate given image object and return the interpolated image object.

interpolate(SpatialImage) - Method in class jp.ac.keio.bio.fun.xitosbml.image.Interpolator

Interpolate given spatial image object and return the interpolated spatial image object.

interpolate(HashMap<String, ImagePlus>) - Method in class jp.ac.keio.bio.fun.xitosbml.image.Interpolator

Interpolate given set of ImageJ image objects (as hashmap of domain files, HashMap<String, ImagePlus>).

Interpolator - Class in jp.ac.keio.bio.fun.xitosbml.image

The class Interpolator, which provides interpolation operations for Z-stack images.

Interpolator() - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.Interpolator

Instantiates a new interpolator.

Interpolator(SpatialImage) - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.Interpolator

Instantiates a new interpolator with given spatial image.

isCellEditable(int, int) - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageTable.MyTableModel

The cells in column 1 is not editable.

isCellEditable(int, int) - Method in class jp.ac.keio.bio.fun.xitosbml.pane.SBaseTable.MyTableModel

Returns false regardless of parameter values.

isRunning() - Method in class jp.ac.keio.bio.fun.xitosbml.pane.TabTables

Checks if is running.

itemStateChanged(ItemEvent) - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageDialog

Invoked when an item has been selected or deselected by the user.

J

jp.ac.keio.bio.fun.xitosbml - package jp.ac.keio.bio.fun.xitosbml

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

jp.ac.keio.bio.fun.xitosbml.gui - package jp.ac.keio.bio.fun.xitosbml.gui

jp.ac.keio.bio.fun.xitosbml.image - package jp.ac.keio.bio.fun.xitosbml.image

jp.ac.keio.bio.fun.xitosbml.pane - package jp.ac.keio.bio.fun.xitosbml.pane

jp.ac.keio.bio.fun.xitosbml.util - package jp.ac.keio.bio.fun.xitosbml.util

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

jp.ac.keio.bio.fun.xitosbml.xitosbml - package jp.ac.keio.bio.fun.xitosbml.xitosbml

L

label() - Method in class jp.ac.keio.bio.fun.xitosbml.image.Filler

Assign a label (label number) to each pixel.

label() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageEdit

Set the label of each pixel to the 1D array of labels (matrix).

lcoord - Static variable in class jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

The Constant lcoord.

list - Variable in class jp.ac.keio.bio.fun.xitosbml.pane.SBaseTable

The list of Object.

listIdToStringArray(ListOf<?>) - Static method in class jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

Converts list of SBase to a String.

LOWERSBMLLEVEL - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

The Constant LOWERSBMLLEVEL.

LOWERSBMLLEVEL - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginInfo

The Constant LOWERSBMLLEVEL.

LOWERSBMLVERSION - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

The Constant LOWERSBMLVERSION.

LOWERSBMLVERSION - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginInfo

The Constant LOWERSBMLVERSION.

M

main(String[]) - Static method in class jp.ac.keio.bio.fun.xitosbml.image.ImageExplorer

Example main() method which will launch a GUI and show this JFrame object.

main(String[]) - Static method in class jp.ac.keio.bio.fun.xitosbml.image.ImageTable

Example main() method which will launch a GUI and show this JTable object.

main(String[]) - Static method in class jp.ac.keio.bio.fun.xitosbml.pane.TabTables

Example main() method which will read an SBML file and create a GUI for editing SBML model.

main(String[]) - Static method in class jp.ac.keio.bio.fun.xitosbml.Spatial_Img_SBML

Example main() method which will launch ImageJ and call "run Spatial Image SBML plugin".

main(String[]) - Static method in class jp.ac.keio.bio.fun.xitosbml.util.ModelValidator

Example main() method which will read an SBML file and execute a validation.

main(String[]) - Static method in class jp.ac.keio.bio.fun.xitosbml.visual.DomainStruct

Example main() method which will launch a GUI and draw an inclusion relationship of domains as a graph.

main(String[]) - Static method in class jp.ac.keio.bio.fun.xitosbml.visual.GraphStruct

Example main() method which will launch a GUI and draw an inclusion relationship of domains as a graph.

main(String[]) - Static method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSBaseSpatial

Example main() method which will launch ImageJ and call "run Spatial Image SBML plugin".

MainImgSpatial - Class in jp.ac.keio.bio.fun.xitosbml.xitosbml

The class MainImgSpatial, which implements "run Spatial Image SBML plugin" function.

MainImgSpatial() - Constructor for class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainImgSpatial

MainModelEdit - Class in jp.ac.keio.bio.fun.xitosbml.xitosbml

The class MainModelEdit, which implements "run Model Editor" function.

MainModelEdit() - Constructor for class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainModelEdit

MainModelValidator - Class in jp.ac.keio.bio.fun.xitosbml.xitosbml

The class MainModelValidator, which implements "run Model Validation" function.

MainModelValidator() - Constructor for class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainModelValidator

MainParametricSpatial - Class in jp.ac.keio.bio.fun.xitosbml.xitosbml

The class MainParametricSpatial, which implements "run Spatial Parametric SBML plugin" function.

MainParametricSpatial() - Constructor for class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainParametricSpatial

MainSBaseSpatial - Class in jp.ac.keio.bio.fun.xitosbml.xitosbml

The class MainSBaseSpatial.

MainSBaseSpatial() - Constructor for class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSBaseSpatial

MainSpatial - Class in jp.ac.keio.bio.fun.xitosbml.xitosbml

The class MainSpatial, which creates a GUI for XitoSBML.

MainSpatial() - Constructor for class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

maxCoord - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.AnalyticGeometryData

The maximum value of the coordinate axis (boundary).

maxCoord - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

The maximum value of the coordinate axis (boundary).

memberList - Variable in class jp.ac.keio.bio.fun.xitosbml.pane.SBaseTable

The member list of SBML Level 3 Version 1 SBase objects.

MenuColumn - Class in jp.ac.keio.bio.fun.xitosbml.gui

The class MenuColumn, which generates a GUI for XitoSBML.

MenuColumn(JTable, int) - Constructor for class jp.ac.keio.bio.fun.xitosbml.gui.MenuColumn

Instantiates a new menu column.

minCoord - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.AnalyticGeometryData

The minimum value of the coordinate axis (boundary).

minCoord - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

The minimum value of the coordinate axis (boundary).

model - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

The SBML model.

model - Variable in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

The SBML model.

ModelSaver - Class in jp.ac.keio.bio.fun.xitosbml.util

The class ModelSaver, which is an utility class to save SBML document to a file.

ModelSaver(SBMLDocument) - Constructor for class jp.ac.keio.bio.fun.xitosbml.util.ModelSaver

Instantiates a new model saver.

ModelValidator - Class in jp.ac.keio.bio.fun.xitosbml.util

The class ModelValidator, which is an utility class to validate SBML document.

ModelValidator(SBMLDocument) - Constructor for class jp.ac.keio.bio.fun.xitosbml.util.ModelValidator

Instantiates a new model validator.

mouseClicked(MouseEvent) - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageTable

mouseEntered(MouseEvent) - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageTable

mouseExited(MouseEvent) - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageTable

mousePressed(MouseEvent) - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageTable

Invoked when a mouse button has been pressed on a component.

mouseReleased(MouseEvent) - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageTable

MyTableModel(Object[][], String[]) - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.ImageTable.MyTableModel

Instantiates a new my table model.

MyTableModel(Object[][], String[]) - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.SBaseTable.MyTableModel

Instantiates a new my table model with data and header.

MyTableModel(int, int) - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.SBaseTable.MyTableModel

Instantiates a new my table model with row count and column count.

O

OUTSIDE - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

The Constant OUTSIDE.

P

pane - Variable in class jp.ac.keio.bio.fun.xitosbml.pane.SBaseTable

The JScrollPane object.

panel - Variable in class jp.ac.keio.bio.fun.xitosbml.pane.SBaseTable

The JPanel object.

ParameterDialog - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class ParameterDialog, which generates a GUI for creating / editing a Parameter.

ParameterDialog(Model) - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.ParameterDialog

Instantiates a new parameter dialog.

ParameterTable - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class ParameterTable, which inherits SBaseTable and implements add() and edit() method for adding and editing parameters.

ParametricGeometryData - Class in jp.ac.keio.bio.fun.xitosbml.geometry

The class ParametricGeometryData, which inherits ImageGeometryData.

PluginConstants - Class in jp.ac.keio.bio.fun.xitosbml.util

The class PluginConstants, which contains constant values used in XitoSBML.

PluginConstants() - Constructor for class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

PluginInfo - Class in jp.ac.keio.bio.fun.xitosbml.util

The class PluginInfo, which contains constant values used in XitoSBML.

PluginInfo() - Constructor for class jp.ac.keio.bio.fun.xitosbml.util.PluginInfo

print() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

Prints the SBML document to stdout.

R

raw - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.ImageGeometryData

The raw data of spatial image in 1D array.

ReactionDialog - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class ReactionDialog, which generates a GUI for creating / editing a Reaction.

ReactionDialog(Model) - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.ReactionDialog

Instantiates a new reaction dialog.

ReactionTable - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class ReactionTable, which inherits SBaseTable and implements add() and edit() method for adding and editing reaction.

run(String) - Method in class jp.ac.keio.bio.fun.xitosbml.Spatial_Img_SBML

Launch XitoSBML as ImageJ plugin.

run(String) - Method in class jp.ac.keio.bio.fun.xitosbml.Spatial_Model_Edit

Launch XitoSBML as ImageJ plugin.

run(String) - Method in class jp.ac.keio.bio.fun.xitosbml.Spatial_Model_Validator

Launch XitoSBML as ImageJ plugin.

run(String) - Method in class jp.ac.keio.bio.fun.xitosbml.Spatial_Parametric_SBML

Launch XitoSBML as ImageJ plugin.

run(String) - Method in class jp.ac.keio.bio.fun.xitosbml.Spatial_SBML

Launch XitoSBML as ImageJ plugin.

run(String) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainImgSpatial

Overrides ij.plugin.PlugIn#run(java.lang.String).

run(String) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainModelEdit

Overrides ij.plugin.PlugIn#run(java.lang.String).

run(String) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainModelValidator

Overrides ij.plugin.PlugIn#run(java.lang.String).

run(String) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainParametricSpatial

Overrides ij.plugin.PlugIn#run(java.lang.String).

run(String) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSBaseSpatial

Not used in this class.

S

SampledFieldGeometryData - Class in jp.ac.keio.bio.fun.xitosbml.geometry

The class SampledFieldGeometryData, which inherits ImageGeometryData and implements getSampledValues() and createImage() methods.

SampledFieldGeometryData(GeometryDefinition, Geometry) - Constructor for class jp.ac.keio.bio.fun.xitosbml.geometry.SampledFieldGeometryData

Instantiates a new sampled field geometry data with given GeometryDefinition and Geometry.

save() - Method in class jp.ac.keio.bio.fun.xitosbml.util.ModelSaver

Save an SBML document to a file.

saveAsImage(String, String) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Save image as TIFF file.

SBaseTable - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class SBaseTable, which is an abstract class and be used to create tables for SBase objects (Species, Reaction, Parameter, etc.).

SBaseTable() - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.SBaseTable

SBaseTable.MyTableModel - Class in jp.ac.keio.bio.fun.xitosbml.pane

The Class MyTableModel.

SBMLLEVEL - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

The Constant SBMLLEVEL.

SBMLLEVEL - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginInfo

The Constant SBMLLEVEL.

SBMLProcessUtil - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class SBMLProcessUtil, which contains several useful static methods to manipulate SBML objects.

SBMLProcessUtil() - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

SBMLVERSION - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

The Constant SBMLVERSION.

SBMLVERSION - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginInfo

The Constant SBMLVERSION.

setAdjacentsList(ArrayList<ArrayList<String>>) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Sets the list of adjacent of spatial image.

setButtons(JButton, JButton) - Method in class jp.ac.keio.bio.fun.xitosbml.gui.ButtonColumn

Sets the buttons.

setCompoImg(ImagePlus) - Method in class jp.ac.keio.bio.fun.xitosbml.image.CreateImage

Sets the composite image.

setCoordinateBoundary(CoordinateComponent, String, double, double, double) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Sets the minimum and maximum values of the coordinate axis (boundary) to a CoordinateComponent object which explicitly defines a coordinate component of the coordinate axes.

setDelta(Point3d) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Sets the delta of spatial image.

setDepth(int) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Sets the depth of spatial image with given depth value.

setGraphStruct(GraphStruct) - Method in class jp.ac.keio.bio.fun.xitosbml.visual.DomainStruct

Sets the graph structure.

setHashDomainNum(HashMap<String, Integer>) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Sets the hashmap of the count number of domains in each domain types with given HashMap<String, Integer>

setHashDomainTypes(HashMap<String, Integer>) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Sets the hashmap of domain types.

setHashDomInteriorpt(HashMap<String, Point3d>) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Sets the hashmap of domain InteriorPoint of spatial image.

setHashSampledValue(HashMap<String, Integer>) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Sets the hashmap of sampled value of spatial image.

setHeight(int) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Sets the height of spatial image with given height value.

setImage(ImagePlus) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Sets the image object and create 1D array of the image and sets to raw object.

setPointIndex(ParametricObject, List<Point3d>, ArrayList<Point3d>) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Sets the index of unique vertices to the SpatialPoints object.

setRaw(byte[]) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Sets the raw data of spatial image in 1D array.

setUnit() - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Sets the unit of a CoordinateComponent.

setWidth(int) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Sets the width of spatial image with given width value.

show(Geometry) - Method in class jp.ac.keio.bio.fun.xitosbml.visual.DomainStruct

Visualize the graph structure of an inclusion relationship of domains.

showAbout() - Method in class jp.ac.keio.bio.fun.xitosbml.Spatial_Img_SBML

Display "About" message

showDialog() - Method in class jp.ac.keio.bio.fun.xitosbml.image.ImageDialog

Show dialog.

showDialog() - Method in class jp.ac.keio.bio.fun.xitosbml.pane.AdvectionDialog

Create and show a dialog for adding Advection Coefficient.

showDialog(Parameter) - Method in class jp.ac.keio.bio.fun.xitosbml.pane.AdvectionDialog

Create and show a dialog for adding Advection Coefficient with given JSBML Parameter object.

showDialog() - Method in class jp.ac.keio.bio.fun.xitosbml.pane.BoundaryConditionDialog

Create and show a dialog for adding Boundary Condition.

showDialog(Parameter) - Method in class jp.ac.keio.bio.fun.xitosbml.pane.BoundaryConditionDialog

Create and show a dialog for adding Boundary Condition with given JSBML Parameter object.

showDialog() - Method in class jp.ac.keio.bio.fun.xitosbml.pane.DiffusionDialog

Create and show a dialog for adding Diffusion Coefficient.

showDialog(Parameter) - Method in class jp.ac.keio.bio.fun.xitosbml.pane.DiffusionDialog

Create and show a dialog for adding Diffusion Coefficient with given JSBML Parameter object.

showDialog() - Method in class jp.ac.keio.bio.fun.xitosbml.pane.ParameterDialog

Create and show a dialog for adding Parameter.

showDialog(Parameter) - Method in class jp.ac.keio.bio.fun.xitosbml.pane.ParameterDialog

Create and show a dialog for adding Parameter with given JSBML Parameter object.

showDialog() - Method in class jp.ac.keio.bio.fun.xitosbml.pane.ReactionDialog

Create and show a dialog for adding Reaction.

showDialog(Reaction) - Method in class jp.ac.keio.bio.fun.xitosbml.pane.ReactionDialog

Create and show a dialog for adding Reaction with given JSBML Reaction object.

showDialog() - Method in class jp.ac.keio.bio.fun.xitosbml.pane.SpeciesDialog

Create and show a dialog for adding Species.

showDialog(Species) - Method in class jp.ac.keio.bio.fun.xitosbml.pane.SpeciesDialog

Create and show a dialog for adding Species with given JSBML Species object.

showDomainStructure() - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

Show inclusion relationship of domains as a graph.

showStep(SpatialImage) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

Visualize SpatialImage.

Spatial_Img_SBML - Class in jp.ac.keio.bio.fun.xitosbml

The class Spatial_Img_SBML.

Spatial_Img_SBML() - Constructor for class jp.ac.keio.bio.fun.xitosbml.Spatial_Img_SBML

Spatial_Model_Edit - Class in jp.ac.keio.bio.fun.xitosbml

The class Spatial_Model_Edit.

Spatial_Model_Edit() - Constructor for class jp.ac.keio.bio.fun.xitosbml.Spatial_Model_Edit

Spatial_Model_Validator - Class in jp.ac.keio.bio.fun.xitosbml

The class Spatial_Model_Validator.

Spatial_Model_Validator() - Constructor for class jp.ac.keio.bio.fun.xitosbml.Spatial_Model_Validator

Spatial_Parametric_SBML - Class in jp.ac.keio.bio.fun.xitosbml

The class Spatial_Parametric_SBML.

Spatial_Parametric_SBML() - Constructor for class jp.ac.keio.bio.fun.xitosbml.Spatial_Parametric_SBML

Spatial_SBML - Class in jp.ac.keio.bio.fun.xitosbml

The base class of this plugin (XitoSBML).

Spatial_SBML() - Constructor for class jp.ac.keio.bio.fun.xitosbml.Spatial_SBML

SpatialImage - Class in jp.ac.keio.bio.fun.xitosbml.image

The class SpatialImage, which is a class for handling spatial image in XitoSBML.

SpatialImage(HashMap<String, Integer>, HashMap<String, Integer>, ImagePlus) - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Instantiates a new spatial image with given image object.

SpatialImage(HashMap<String, Integer>, ImagePlus) - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Instantiates a new spatial image given image object.

spatialplugin - Variable in class jp.ac.keio.bio.fun.xitosbml.geometry.GeometryDatas

The spatialplugin.

spatialplugin - Variable in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

The SBML spatialplugin.

SpatialSBMLExporter - Class in jp.ac.keio.bio.fun.xitosbml.xitosbml

The class SpatialSBMLExporter, which converts a spatial model generated from microscopic images to an SBML model.

SpatialSBMLExporter() - Constructor for class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Instantiates a new spatial SBML exporter.

SpatialSBMLExporter(SpatialImage) - Constructor for class jp.ac.keio.bio.fun.xitosbml.xitosbml.SpatialSBMLExporter

Instantiates a new spatial SBML exporter with given SpatialImage.

SpeciesDialog - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class SpeciesDialog, which generates a GUI for creating / editing Species.

SpeciesDialog(Model) - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.SpeciesDialog

Instantiates a new species dialog.

SpeciesTable - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class SpeciesTable, which inherits SBaseTable and implements add() and edit() method for adding and editing species.

spImg - Variable in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

The SpatialImage, which is a class for handling spatial image in XitoSBML.

SplitDomains - Class in jp.ac.keio.bio.fun.xitosbml.image

The class SplitDomain, which provides several image processing filters to split domains with given pixel value (sampled value).

SplitDomains(SpatialImage, String) - Constructor for class jp.ac.keio.bio.fun.xitosbml.image.SplitDomains

Instantiates a new split domains with given SpatialImage.

T

TabTables - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class TabTables, which inherits JFrame and implements main component of XitoSBML.

TabTables() - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.TabTables

Instantiates a new tab tables.

TabTables(Model) - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.TabTables

Instantiates a new tab tables with given SBML model.

TAG_CELLDESIGNER_EXTENSIONTOPLEVEL - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

TAG_CELLDESIGNER_PREFIX - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

The Constant CDURI.

TAG_END_ANNOTATION - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

The Constant TAG_END_ANNOTATION.

TAG_END_CELLDESIGNER - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

The Constant TAG_END_CELLDESIGNER.

TAG_START_ANNOTATION - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

The Constant TAG_START_ANNOTATION.

TAG_START_CELLDESIGNER - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

The Constant TAG_START_CELLDESIGNER.

title - Variable in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

The title of the image.

U

UnitDefinitionDialog - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class UnitDefinitionDialog, which generates a GUI for creating / editing UnitDefinition.

UnitDefinitionDialog() - Constructor for class jp.ac.keio.bio.fun.xitosbml.pane.UnitDefinitionDialog

UnitDefinitionTable - Class in jp.ac.keio.bio.fun.xitosbml.pane

The class UnitDefinitionTable, which inherits SBaseTable and implements add() and edit() method for adding and editing unit definition.

updateImage(ImageStack) - Method in class jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

Update image with given stack of images.

updateRow(int, Vector<Object>) - Method in class jp.ac.keio.bio.fun.xitosbml.pane.SBaseTable.MyTableModel

Update row.

V

validate() - Method in class jp.ac.keio.bio.fun.xitosbml.util.ModelValidator

Validate the SBML document.

view(SpatialImage) - Method in class jp.ac.keio.bio.fun.xitosbml.visual.Viewer

Visualize SpatialImage object on ImageJ 3D Viewer

Viewer - Class in jp.ac.keio.bio.fun.xitosbml.visual

The class Viewer, which visualizes a SpatialImage object on ImageJ 3D Viewer.

Viewer() - Constructor for class jp.ac.keio.bio.fun.xitosbml.visual.Viewer

viewer - Variable in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

The viewer.

VIEWERVERSION - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginConstants

The Constant VIEWERVERSION.

VIEWERVERSION - Static variable in class jp.ac.keio.bio.fun.xitosbml.util.PluginInfo

The Constant VIEWERVERSION.

visualize() - Method in class jp.ac.keio.bio.fun.xitosbml.visual.GraphStruct

Visualize the Graph.

visualize(ArrayList<SpatialImage>) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSBaseSpatial

Visualize the model in 3D space (even a model is 2D model).

visualize(SpatialImage) - Method in class jp.ac.keio.bio.fun.xitosbml.xitosbml.MainSpatial

Visualize the spatial model with ImageJ 3D Viewer.

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