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

import ij.IJ;
import ij.ImageJ;
import jp.ac.keio.bio.fun.xitosbml.xitosbml.MainImgSpatial;

// TODO: Auto-generated Javadoc
/**
 * The Class Spatial_Img_SBML.
 */
public class Spatial_Img_SBML extends Spatial_SBML {

	/* (non-Javadoc)
	 * @see sbmlplugin.Spatial_SBML#run(java.lang.String)
	 */
	public void run(String args) {   
	  if (args.equals("about")) {
	    showAbout();
	    return;
	  } else {
			new MainImgSpatial().run(args);	
	  }
	}
	
	public void showAbout() {
    IJ.showMessage("XitoSBML",
        "XitoSBML " + this.version + ": Spatial SBML Plugin for ImageJ\n"
        + "Copyright (C) 2014-2017 Funahashi Lab. Keio University.\n \n"
        + "XitoSBML is an ImageJ plugin which creates Spatial SBML model\n"
        + "from segmented images. XitoSBML is not just a converter,\n"
        + "but also a spatial model editor so that users can add\n"
        + "molecules(species), reactions and advection/diffusion coefficients\n"
        + "to the converted Spatial SBML model.\n"
        + "More information is available at\n \n"
        + "    "+"https://github.com/spatialsimulator/XitoSBML"
        );
  }

	public static void main(String[] args) {
		// set the plugins.dir property to make the plugin appear in the Plugins menu
		Class<?> clazz = Spatial_Img_SBML.class;
		String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
		String pluginsDir = url.substring("file:".length(), url.length() - clazz.getName().length() - ".class".length());
		System.setProperty("plugins.dir", pluginsDir);

		// start ImageJ
		new ImageJ();
		// run the plugin
		IJ.runPlugIn(clazz.getName(), "");
	}
}
@@ -128,40 +128,8 @@
 l;%0A%0A
-// TODO: Auto-generated Javadoc%0A
 /**%0A
@@ -165,138 +165,410 @@
 .%0A *
-/%0Apublic class Spatial_Img_SBML extends Spatial_SBML %7B%0A%0A%09/* (non-Javadoc)%0A%09 * @see sbmlplugin.Spatial_SBML#run(java.lang.String)%0A%09
+ This class has several methods which will be able to launch from * 'Plugins' -%3E 'XitoSBML'.%0A * List of ImageJ plugins which XitoSBML provieds is described in src/main/resources/plugins.config.%0A */%0Apublic class Spatial_Img_SBML extends Spatial_SBML %7B%0A%0A  /**%0A   * Launch XitoSBML as ImageJ plugin.%0A   * List of ImageJ plugins which XitoSBML provieds is described in src/main/resources/plugins.config.%0A  
  */%0A
@@ -722,16 +722,54 @@
  %7D%0A%09%7D%0A%09%0A
+%09/**%0A%09 * Display %22About%22 message%0A%09 */%0A
 %09public 
@@ -929,9 +929,9 @@
 -201
-7
+9
  Fun
@@ -1442,16 +1442,112 @@
 );%0A  %7D%0A%0A
+%09/**%0A%09 * Example main() method which will launch ImageJ and call XitoSBML.%0A%09 * @param args%0A%09 */%0A
 %09public 

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