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/**
* @file getAllElementsWithNotes.java
* @brief Utility program, demontrating how to use the element filter
* class to search the model for elements with specific attributes
* in this example, we look for elements with notes
*
* @author Frank T. Bergmann
*
* <!--------------------------------------------------------------------------
* This sample program is distributed under a different license than the rest
* of libSBML. This program uses the open-source MIT license, as follows:
*
* Copyright (c) 2013-2016 by the California Institute of Technology
* (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
* and the University of Heidelberg (Germany), with support from the National
* Institutes of Health (USA) under grant R01GM070923. All rights reserved.
*
* Permission is hereby granted, free of charge, to any person obtaining a
* copy of this software and associated documentation files (the "Software"),
* to deal in the Software without restriction, including without limitation
* the rights to use, copy, modify, merge, publish, distribute, sublicense,
* and/or sell copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
* THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
* DEALINGS IN THE SOFTWARE.
*
* Neither the name of the California Institute of Technology (Caltech), nor
* of the European Bioinformatics Institute (EMBL-EBI), nor of the University
* of Heidelberg, nor the names of any contributors, may be used to endorse
* or promote products derived from this software without specific prior
* written permission.
* ------------------------------------------------------------------------ -->
*/
import java.util.Vector;
import org.sbml.libsbml.ElementFilter;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.SBase;
import org.sbml.libsbml.SBaseList;
import org.sbml.libsbml.libsbml;
public class getAllElementsWithNotes
extends ElementFilter
{
/**
* @param args
*/
public static void main(String[] args)
{
System.loadLibrary("sbmlj");
System.out.println("Using libSBML : "
+ libsbml.getLibSBMLDottedVersion());
if (args.length != 1)
{
System.out.format("\nUsage: getAllElementsWithNotes filename\n\n");
System.exit(1);
}
String filename = args[0];
// read the document
long start = System.currentTimeMillis();
SBMLDocument document = libsbml.readSBMLFromFile(filename);
long stop = System.currentTimeMillis();
System.out.println();
System.out.format(" filename: %s\n", filename);
System.out.format(" read time (ms): %d\n", (stop - start));
// stop in case of serious errors
long errors = document.getNumErrors(libsbml.LIBSBML_SEV_ERROR);
if (errors > 0)
{
System.out.format(" error(s): %d\n", errors);
document.printErrors();
System.exit((int) errors);
}
// create the filter to use
getAllElementsWithNotes filter = new getAllElementsWithNotes();
// get a list of all elements, as we will need to know all identifiers
// so that we don't create duplicates.
start = System.currentTimeMillis();
System.out.println(" searching ......:");
SBaseList allElements = document.getListOfAllElements(filter);
stop = System.currentTimeMillis();
System.out.format(" seaching took (ms): %d\n", (stop - start));
System.out.format(" elements with notes: %d\n", (allElements.getSize()));
// if we got here all went well ...
}
// <summary>
// Constructor initializing this element filter
// </summary>
public getAllElementsWithNotes()
{
}
@Override
public boolean filter(SBase element)
{
// return in case we don't have a valid element
if (element == null
|| !element.isSetNotes())
return false;
// otherwise we have notes set and want to keep the element
if (element.isSetId())
System.out.println(" found : " + element.getId() );
else
System.out.println(" found element without id");
return true;
}
}
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