public abstract class MainSBaseSpatial extends MainSpatial implements ij.plugin.PlugIn
document, hashSampledValue, imgexp, model, spatialplugin, spImg, viewer
Constructor and Description |
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MainSBaseSpatial() |
Modifier and Type | Method and Description |
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protected void |
checkExtension()
Check whether the model contains spatial extension.
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protected void |
checkLevelAndVersion()
Check whether SBML level and version matches with Level 3 Version 1.
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void |
checkSBMLDocument(org.sbml.jsbml.SBMLDocument document)
Check SBML document.
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protected org.sbml.jsbml.SBMLDocument |
getDocument()
Returns an SBML document from given file path.
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static void |
main(String[] args)
Example main() method which will launch ImageJ and call "run Spatial Image SBML plugin".
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abstract void |
run(String arg)
Not used in this class.
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protected void |
visualize(ArrayList<SpatialImage> spImgList)
Visualize the model in 3D space (even a model is 2D model).
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addSBases, computeImg, gui, print, showDomainStructure, showStep, visualize
public abstract void run(String arg)
run
in interface ij.plugin.PlugIn
PlugIn.run(java.lang.String)
protected void visualize(ArrayList<SpatialImage> spImgList)
spImgList
- list of SpatialImage
,
which is a class for storing an image in XitoSBMLprotected org.sbml.jsbml.SBMLDocument getDocument() throws NullPointerException, XMLStreamException, IOException
NullPointerException
- the null pointer exceptionXMLStreamException
- the XML stream exceptionIOException
- the IOException exceptionpublic void checkSBMLDocument(org.sbml.jsbml.SBMLDocument document)
document
- SBML documentprotected void checkLevelAndVersion()
protected void checkExtension()
public static void main(String[] args)
args
- an array of command-line arguments for the applicationCopyright © 2017–2019 Funahashi Lab.. All rights reserved.