example1-L3.cs

A version of example1.cs for SBML Level 3.

/// 
/// \file    example1-L3.cs
/// \brief   SBML Layout example
/// \author  Ralph Gauges
/// \author  Akiya Jouraku
/// \author  Frank Bergmann (translated to C# and adapted to use libsbml-5 package version)
/// 

using System;
using libsbmlcs;

class Example1
{
    public static void Main (string[] args)
    {
        
        //
        // Creates an SBMLNamespaces object with the given SBML level, version
        // package name, package version.
        //
        // (NOTE) By defualt, the name of package (i.e. "layout") will be used
        // if the arugment for the prefix is missing or empty. Thus the argument
        // for the prefix can be added as follows:
        //
        //    SBMLNamespaces sbmlns(3,1,"layout",1,"LAYOUT");
        //
        
        SBMLNamespaces sbmlns = new SBMLNamespaces (3, 1, "layout", 1);
        
        //
        // (NOTES) The above code creating an SBMLNamespaces object can be replaced 
        //         with one of the following other styles.
        //
        // (1) Creates an SBMLNamespace object with a SBML core namespace and then
        //     adds a layout package namespace to the object. 
        //
        //         SBMLNamespaces sbmlns(3,1);
        //         sbmlns.addPkgNamespace("layout",1);
        //
        //           OR
        //
        //         SBMLNamespaces sbmlns(3,1);
        //         sbmlns.addNamespace(LayoutExtension::XmlnsL3V1V1,"layout");
        //
        // (2) Creates a LayoutPkgNamespaces object (SBMLNamespace derived class for
        //     layout package. The class is basically used for createing an SBase derived
        //     objects belonging to the layout package) with the given SBML level, version, 
        //     and package version
        //
        //        LayoutPkgNamespaces sbmlns(3,1,1);
        //     
        
        // create the document
        
        SBMLDocument document = new SBMLDocument (sbmlns);
        
        // set the "required" attribute of layout package  to "true"
        document.setPkgRequired ("layout", true);
        
        // create the Model
        
        Model model = document.createModel ();
        model.setId ("TestModel");
        document.setModel (model);
        
        
        // create the Compartment
        
        Compartment compartment = model.createCompartment ();
        compartment.setId ("Compartment_1");
        compartment.setConstant (true);
        
        // create the Species
        
        Species species1 = model.createSpecies ();
        species1.setId ("Species_1");
        species1.setCompartment (compartment.getId ());
        species1.setHasOnlySubstanceUnits (false);
        species1.setBoundaryCondition (false);
        species1.setConstant (false);
        
        Species species2 = model.createSpecies ();
        species2.setId ("Species_2");
        species2.setCompartment (compartment.getId ());
        species2.setHasOnlySubstanceUnits (false);
        species2.setBoundaryCondition (false);
        species2.setConstant (false);
        
        // create the Reactions
        
        Reaction reaction1 = model.createReaction ();
        reaction1.setId ("Reaction_1");
        reaction1.setReversible (false);
        reaction1.setFast (false);
        
        SpeciesReference reference1 = reaction1.createReactant ();
        reference1.setSpecies (species1.getId ());
        reference1.setId ("SpeciesReference_1");
        reference1.setConstant (false);
        
        
        SpeciesReference reference2 = reaction1.createProduct ();
        reference2.setSpecies (species2.getId ());
        reference2.setId ("SpeciesReference_2");
        reference2.setConstant (false);
        
        Reaction reaction2 = model.createReaction ();
        reaction2.setId ("Reaction_2");
        reaction2.setReversible (false);
        reaction2.setFast (false);
        
        SpeciesReference reference3 = reaction2.createReactant ();
        reference3.setSpecies (species2.getId ());
        reference3.setId ("SpeciesReference_3");
        reference3.setConstant (false);
        
        SpeciesReference reference4 = reaction2.createProduct ();
        reference4.setSpecies (species1.getId ());
        reference4.setId ("SpeciesReference_4");
        reference4.setConstant (false);
        
        
        // create the Layout
        
        //
        // set the LayoutPkgNamespaces for Level 3 Version1 Layout Version 1
        //
        LayoutPkgNamespaces layoutns = new LayoutPkgNamespaces (3, 1, 1);
        
        //
        // Get a LayoutModelPlugin object plugged in the model object.
        //
        // The type of the returned value of SBase::getPlugin() function is SBasePlugin, and
        // thus the value needs to be casted for the corresponding derived class.
        //
        
        LayoutModelPlugin mplugin = (LayoutModelPlugin)(model.getPlugin ("layout"));
        
        if (mplugin == null) {
            Console.Error.WriteLine ("[Fatal Error] Layout Extension Level " + layoutns.getLevel () + " Version " + layoutns.getVersion () + " package version " + layoutns.getPackageVersion () + " is not registered.");
            Environment.Exit (1);
        }
        
        //
        // Creates a Layout object via LayoutModelPlugin object.
        //
        Layout layout = mplugin.createLayout ();
        
        layout.setId ("Layout_1");
        Dimensions dim = new Dimensions (layoutns, 400.0, 220.0);
        layout.setDimensions (dim);
        
        
        // create the CompartmentGlyph
        
        CompartmentGlyph compartmentGlyph = layout.createCompartmentGlyph ();
        compartmentGlyph.setId ("CompartmentGlyph_1");
        compartmentGlyph.setCompartmentId (compartment.getId ());
        BoundingBox bb = new BoundingBox (layoutns, "bb1", 5, 5, 390, 210);
        compartmentGlyph.setBoundingBox (bb);
        
        
        // create the SpeciesGlyphs
        
        SpeciesGlyph speciesGlyph1 = layout.createSpeciesGlyph ();
        speciesGlyph1.setId ("SpeciesGlyph_1");
        speciesGlyph1.setSpeciesId (species1.getId ());
        bb = new BoundingBox (layoutns, "bb2", 80, 26, 240, 24);
        speciesGlyph1.setBoundingBox (bb);
        
        TextGlyph textGlyph1 = layout.createTextGlyph ();
        textGlyph1.setId ("TextGlyph_01");
        bb = new BoundingBox (layoutns, "bbA", 92, 26, 228, 24);
        textGlyph1.setBoundingBox (bb);
        textGlyph1.setOriginOfTextId (speciesGlyph1.getId ());
        textGlyph1.setGraphicalObjectId (speciesGlyph1.getId ());
        
        SpeciesGlyph speciesGlyph2 = layout.createSpeciesGlyph ();
        speciesGlyph2.setId ("SpeciesGlyph_2");
        speciesGlyph2.setSpeciesId (species2.getId ());
        bb = new BoundingBox (layoutns, "bb3", 80, 170, 240, 24);
        speciesGlyph2.setBoundingBox (bb);
        
        TextGlyph textGlyph2 = layout.createTextGlyph ();
        textGlyph2.setId ("TextGlyph_02");
        bb = new BoundingBox (layoutns, "bbB", 92, 170, 228, 24);
        textGlyph2.setBoundingBox (bb);
        textGlyph2.setOriginOfTextId (speciesGlyph2.getId ());
        textGlyph2.setGraphicalObjectId (speciesGlyph2.getId ());
        
        // create the ReactionGlyphs
        
        ReactionGlyph reactionGlyph1 = layout.createReactionGlyph ();
        reactionGlyph1.setId ("ReactionGlyph_1");
        reactionGlyph1.setReactionId (reaction1.getId ());
        
        Curve reactionCurve1 = reactionGlyph1.getCurve ();
        LineSegment ls = reactionCurve1.createLineSegment ();
        Point p = new Point (layoutns, 165, 105);
        ls.setStart (p);
        p = new Point (layoutns, 165, 115);
        ls.setEnd (p);
        
        ReactionGlyph reactionGlyph2 = layout.createReactionGlyph ();
        reactionGlyph2.setId ("ReactionGlyph_1");
        reactionGlyph2.setReactionId (reaction2.getId ());
        
        Curve reactionCurve2 = reactionGlyph2.getCurve ();
        ls = reactionCurve2.createLineSegment ();
        p = new Point (layoutns, 235, 105);
        ls.setStart (p);
        p = new Point (layoutns, 235, 115);
        ls.setEnd (p);
        
        // add the SpeciesReferenceGlyphs
        
        SpeciesReferenceGlyph speciesReferenceGlyph1 = reactionGlyph1.createSpeciesReferenceGlyph ();
        speciesReferenceGlyph1.setId ("SpeciesReferenceGlyph_1");
        speciesReferenceGlyph1.setSpeciesGlyphId (speciesGlyph1.getId ());
        speciesReferenceGlyph1.setSpeciesReferenceId (reference1.getId ());
        speciesReferenceGlyph1.setRole (libsbml.SPECIES_ROLE_SUBSTRATE);
        
        Curve speciesReferenceCurve1 = speciesReferenceGlyph1.getCurve ();
        CubicBezier cb = speciesReferenceCurve1.createCubicBezier ();
        p = new Point (layoutns, 165, 105);
        cb.setStart (p);
        p = new Point (layoutns, 165, 90);
        cb.setBasePoint1 (p);
        p = new Point (layoutns, 165, 90);
        cb.setBasePoint2 (p);
        p = new Point (layoutns, 195, 60);
        cb.setEnd (p);
        
        SpeciesReferenceGlyph speciesReferenceGlyph2 = reactionGlyph1.createSpeciesReferenceGlyph ();
        speciesReferenceGlyph2.setId ("SpeciesReferenceGlyph_2");
        speciesReferenceGlyph2.setSpeciesGlyphId (speciesGlyph2.getId ());
        speciesReferenceGlyph2.setSpeciesReferenceId (reference2.getId ());
        speciesReferenceGlyph2.setRole (libsbml.SPECIES_ROLE_PRODUCT);
        
        Curve speciesReferenceCurve2 = speciesReferenceGlyph2.getCurve ();
        cb = speciesReferenceCurve2.createCubicBezier ();
        p = new Point (layoutns, 165, 115);
        cb.setStart (p);
        p = new Point (layoutns, 165, 130);
        cb.setBasePoint1 (p);
        p = new Point (layoutns, 165, 130);
        cb.setBasePoint2 (p);
        p = new Point (layoutns, 195, 160);
        cb.setEnd (p);
        
        
        SpeciesReferenceGlyph speciesReferenceGlyph3 = reactionGlyph2.createSpeciesReferenceGlyph ();
        speciesReferenceGlyph3.setId ("SpeciesReferenceGlyph_3");
        speciesReferenceGlyph3.setSpeciesGlyphId (speciesGlyph2.getId ());
        speciesReferenceGlyph3.setSpeciesReferenceId (reference3.getId ());
        speciesReferenceGlyph3.setRole (libsbml.SPECIES_ROLE_SUBSTRATE);
        
        Curve speciesReferenceCurve3 = speciesReferenceGlyph3.getCurve ();
        cb = speciesReferenceCurve3.createCubicBezier ();
        p = new Point (layoutns, 235, 115);
        cb.setStart (p);
        p = new Point (layoutns, 235, 130);
        cb.setBasePoint1 (p);
        p = new Point (layoutns, 235, 130);
        cb.setBasePoint2 (p);
        p = new Point (layoutns, 205, 160);
        cb.setEnd (p);
        
        SpeciesReferenceGlyph speciesReferenceGlyph4 = reactionGlyph2.createSpeciesReferenceGlyph ();
        speciesReferenceGlyph4.setId ("SpeciesReferenceGlyph_4");
        speciesReferenceGlyph4.setSpeciesGlyphId (speciesGlyph1.getId ());
        speciesReferenceGlyph4.setSpeciesReferenceId (reference4.getId ());
        speciesReferenceGlyph4.setRole (libsbml.SPECIES_ROLE_PRODUCT);
        
        Curve speciesReferenceCurve4 = speciesReferenceGlyph4.getCurve ();
        cb = speciesReferenceCurve4.createCubicBezier ();
        p = new Point (layoutns, 235, 105);
        cb.setStart (p);
        p = new Point (layoutns, 235, 90);
        cb.setBasePoint1 (p);
        p = new Point (layoutns, 235, 90);
        cb.setBasePoint2 (p);
        p = new Point (layoutns, 205, 60);
        cb.setEnd (p);
        
        libsbml.writeSBML (document, "layout_example1_L3-cs.xml");          
        Console.WriteLine("all done ...");
    }
}