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/**
* @file appendAnnotation.java
* @brief Adds annotation to a model and a species
* @author Akira Funahashi (translated from libSBML C++ examples (using other Java examples provided by Nicolas Rodriguez))
* @author Akiya Jouraku
*
* <!--------------------------------------------------------------------------
* 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 org.sbml.libsbml.libsbmlConstants;
import org.sbml.libsbml.CVTerm;
import org.sbml.libsbml.Date;
import org.sbml.libsbml.ModelCreator;
import org.sbml.libsbml.ModelHistory;
import org.sbml.libsbml.SBMLWriter;
import org.sbml.libsbml.Species;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.SBMLReader;
public class appendAnnotation
{
public static void main (String[] args)
{
if (args.length != 2)
{
println("\n usage: java appendAnnotation <input-filename> <output-filename>\n");
System.exit(2);
}
SBMLDocument d;
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
d = reader.readSBML(args[0]);
long errors = d.getNumErrors();
if (errors > 0)
{
println("Read Error(s):");
d.printErrors();
println("Correct the above and re-run.");
}
else
{
String model_history_annotation =
"<annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
" <rdf:Description rdf:about=\"#\">\n" +
" <dc:creator rdf:parseType=\"Resource\">\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:parseType=\"Resource\">\n" +
" <vCard:N rdf:parseType=\"Resource\">\n" +
" <vCard:Family>Keating</vCard:Family>\n" +
" <vCard:Given>Sarah</vCard:Given>\n" +
" </vCard:N>\n" +
" <vCard:EMAIL>sbml-team@caltech.edu</vCard:EMAIL>\n" +
" <vCard:ORG>\n" +
" <vCard:Orgname>University of Hertfordshire</vCard:Orgname>\n" +
" </vCard:ORG>\n" +
" </rdf:li>\n" +
" </rdf:Bag>\n" +
" </dc:creator>\n" +
" <dcterms:created rdf:parseType=\"Resource\">\n" +
" <dcterms:W3CDTF>1999-11-13T06:54:32Z</dcterms:W3CDTF>\n" +
" </dcterms:created>\n" +
" <dcterms:modified rdf:parseType=\"Resource\">\n" +
" <dcterms:W3CDTF>2007-11-31T06:54:00-02:00</dcterms:W3CDTF>\n" +
" </dcterms:modified>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
"</annotation>\n";
d.getModel().appendAnnotation(model_history_annotation);
/*
* The above code can be replaced by the following code.
*
ModelHistory h = new ModelHistory();
ModelCreator c = new ModelCreator();
c.setFamilyName("Keating");
c.setGivenName("Sarah");
c.setEmail("sbml-team@caltech.edu");
c.setOrganisation("University of Hertfordshire");
h.addCreator(c);
Date date = new Date("1999-11-13T06:54:32");
Date date2 = new Date("2007-11-31T06:54:00-02:00");
h.setCreatedDate(date);
h.setModifiedDate(date2);
d.getModel().setModelHistory(h);
*
*/
long n = d.getModel().getNumSpecies();
if (n > 0)
{
Species s = d.getModel().getSpecies(0);
String cvterms_annotation =
"<annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
" <rdf:Description rdf:about=\"#\">\n" +
" <bqbiol:isVersionOf>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005892\"/>\n" +
" <rdf:li rdf:resource=\"http://www.ebi.ac.uk/interpro/#IPR002394\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:isVersionOf>\n" +
" <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005895\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:is>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
"</annotation>\n";
s.appendAnnotation(cvterms_annotation);
/*
* The above code can be replaced by the following code.
*
CVTerm cv = new CVTerm();
cv.setQualifierType(libsbmlConstants.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(libsbmlConstants.BQB_IS_VERSION_OF);
cv.addResource("http://www.geneontology.org/#GO:0005892");
CVTerm cv2 = new CVTerm();
cv2.setQualifierType(libsbmlConstants.BIOLOGICAL_QUALIFIER);
cv2.setBiologicalQualifierType(libsbmlConstants.BQB_IS);
cv2.addResource("http://www.geneontology.org/#GO:0005895");
CVTerm cv1 = new CVTerm();
cv1.setQualifierType(libsbmlConstants.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbmlConstants.BQB_IS_VERSION_OF);
cv1.addResource("http://www.ebi.ac.uk/interpro/#IPR002394");
s.addCVTerm(cv);
s.addCVTerm(cv2);
s.addCVTerm(cv1);
*
*/
}
}
writer.writeSBML(d, args[1]);
}
static void println (String msg)
{
System.out.println(msg);
}
/**
* Loads the SWIG-generated libSBML Java module when this class is
* loaded, or reports a sensible diagnostic message about why it failed.
*/
static
{
try
{
System.loadLibrary("sbmlj");
// For extra safety, check that the jar file is in the classpath.
Class.forName("org.sbml.libsbml.libsbml");
}
catch (UnsatisfiedLinkError e)
{
System.err.println("Error encountered while attempting to load libSBML:");
System.err.println("Please check the value of your "
+ (System.getProperty("os.name").startsWith("Mac OS")
? "DYLD_LIBRARY_PATH" : "LD_LIBRARY_PATH") +
" environment variable and/or your" +
" 'java.library.path' system property (depending on" +
" which one you are using) to make sure it list the" +
" directories needed to find the " +
System.mapLibraryName("sbmlj") + " library file and" +
" libraries it depends upon (e.g., the XML parser).");
System.exit(1);
}
catch (ClassNotFoundException e)
{
System.err.println("Error: unable to load the file 'libsbmlj.jar'." +
" It is likely that your -classpath command line " +
" setting or your CLASSPATH environment variable " +
" do not include the file 'libsbmlj.jar'.");
e.printStackTrace();
System.exit(1);
}
catch (SecurityException e)
{
System.err.println("Error encountered while attempting to load libSBML:");
e.printStackTrace();
System.err.println("Could not load the libSBML library files due to a"+
" security exception.\n");
System.exit(1);
}
}
}
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