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import org.sbml.libsbml.ConversionProperties;
import org.sbml.libsbml.LayoutModelPlugin;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.SBMLNamespaces;
import org.sbml.libsbml.SBasePlugin;
import org.sbml.libsbml.libsbml;
/**
* This Class converts a document (including layout) from L3 to L2 or from L2 to
* L3V1
*
* @author Frank Bergmann
*
*/
public class SimpleLayoutConverter
{
public static void main(String args[])
{
// check arguments
if (args.length != 2)
{
System.err.println("usage: SimpleLayoutConverter <input file> <output file>");
System.exit(1);
}
// load native library
System.loadLibrary("sbmlj");
// read document
SBMLDocument doc = libsbml.readSBMLFromFile(args[0]);
// bail on error
if (doc.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0)
{
doc.checkConsistency();
System.err.println("The document contains errors that need to be corrected first:");
System.err.println(doc.getErrorLog().toString());
System.exit(1);
}
// check for layout
if (doc.getPlugin("layout") == null)
{
System.err.println("This document contains no layout, conversion skipped.");
System.exit(0);
}
// perform the conversion
if (doc.getLevel() == 3)
convertToL2(doc);
else
convertToL3(doc);
// write document to file
libsbml.writeSBMLToFile(doc, args[1]);
}
/**
* This function converts the given document to L3v1, converting also layout
* and render elements
*
* @param doc
* the document to convert
*/
private static void convertToL3(SBMLDocument doc)
{
if (doc == null || doc.getModel() == null) return;
String layoutNsUri = "http://www.sbml.org/sbml/level3/version1/layout/version1";
String renderNsUri = "http://www.sbml.org/sbml/level3/version1/render/version1";
LayoutModelPlugin plugin = (LayoutModelPlugin) doc.getModel()
.getPlugin("layout");
// bail if we don't have layout
if (plugin == null) return;
// convert document
ConversionProperties prop = new ConversionProperties(
new SBMLNamespaces(
3,
1));
prop.addOption("strict", false);
prop.addOption("setLevelAndVersion", true);
prop.addOption("ignorePackages", true);
if (doc.convert(prop) != libsbml.LIBSBML_OPERATION_SUCCESS)
{
System.err.println("Conversion failed!");
doc.printErrors();
System.exit(2);
}
// add new layout namespace and set required flag
SBasePlugin docPlugin = doc.getPlugin("layout");
// if we don't have layout there isnothing to do
if (docPlugin == null) return;
docPlugin.setElementNamespace(layoutNsUri);
doc.getSBMLNamespaces().addPackageNamespace("layout", 1);
doc.setPackageRequired("layout", false);
// add enable render if needed
SBasePlugin rdocPlugin = doc.getPlugin("render");
if (rdocPlugin != null)
{
doc.getSBMLNamespaces().addPackageNamespace("render", 1);
}
else
{
doc.enablePackage(renderNsUri, "render", true);
}
doc.setPackageRequired("render", false);
}
/**
* This function converts a SBML L3 document to an L2 document, moving the
* layout package into the annotation
*
* @param doc
* the document to convert
*/
private static void convertToL2(SBMLDocument doc)
{
if (doc == null || doc.getModel() == null) return;
String layoutNsUri = "http://projects.eml.org/bcb/sbml/level2";
String renderNsUri = "http://projects.eml.org/bcb/sbml/render/level2";
LayoutModelPlugin plugin = (LayoutModelPlugin) doc.getModel()
.getPlugin("layout");
// bail if we don't have layout
if (plugin == null) return;
// perform the conversion
ConversionProperties prop = new ConversionProperties(
new SBMLNamespaces(
2,
4));
prop.addOption("strict", false);
prop.addOption("setLevelAndVersion", true);
prop.addOption("ignorePackages", true);
if (doc.convert(prop) != libsbml.LIBSBML_OPERATION_SUCCESS)
{
System.err.println("Conversion failed!");
doc.printErrors();
System.exit(2);
}
SBasePlugin docPlugin = doc.getPlugin("layout");
// if we don't have layout, there is nothing to do
if (docPlugin == null) return;
docPlugin.setElementNamespace(layoutNsUri);
doc.getSBMLNamespaces().removePackageNamespace(3, 1, "layout", 1);
doc.getSBMLNamespaces().addPackageNamespace("layout", 1);
SBasePlugin rdocPlugin = doc.getPlugin("render");
if (rdocPlugin != null)
{
rdocPlugin.setElementNamespace(renderNsUri);
doc.getSBMLNamespaces().removePackageNamespace(3, 1, "render", 1);
doc.getSBMLNamespaces().addPackageNamespace("render", 1);
}
}
}
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