public static int Main(string[] args)
{
int retval = 0;
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// create the Model
Model model = document.createModel();
// create a replacement parameter
Parameter parameter = model.createParameter();
parameter.setId("x");
parameter.setConstant(true);
// create a parameter to be a conversion factor
Parameter param2 = model.createParameter();
param2.setId("x_conv");
param2.setMetaId("_110013");
param2.setConstant(true);
// create a parameter to be a conversion factor
Parameter param3 = model.createParameter();
param3.setId("lcf");
param3.setConstant(true);
// Convert parameter to the plugin version so we can add the new attributes and replacements to it.
CompSBasePlugin splugin = (CompSBasePlugin) (parameter.getPlugin("comp"));
// Add a replaced element.
ReplacedElement rep1 = splugin.createReplacedElement();
int rv = rep1.setSubmodelRef("submod1");
rv = rep1.setConversionFactor("x_conv");
rv = rep1.setIdRef("param1");
// Add a second replaced element in a different way.
ReplacedElement rep2 = new ReplacedElement();
rv = rep2.setSubmodelRef("submod2");
rv = rep2.setDeletion("del1");
rv = splugin.addReplacedElement(rep2);
//Now create a replaced element that points into a submodel.
rep2.unsetDeletion();
rep2.setIdRef("submod2");
SBaseRef sbr5 = rep2.createSBaseRef();
sbr5.setIdRef("submodelG");
SBaseRef sbr6 = sbr5.createSBaseRef();
sbr6.setIdRef("buriedElement");
splugin.addReplacedElement(rep2);
// Create a submodel
CompModelPlugin mplugin = (CompModelPlugin) (model.getPlugin("comp"));
CompSBMLDocumentPlugin compdoc = (CompSBMLDocumentPlugin) (document.getPlugin("comp"));
compdoc.setRequired(true);
ModelDefinition moddef1 = compdoc.createModelDefinition();
moddef1.setId("Mod1");
Parameter m1param1 = moddef1.createParameter();
m1param1.setId("param1");
m1param1.setConstant(true);
Parameter m1param2 = moddef1.createParameter();
m1param2.setId("param2");
m1param2.setConstant(false);
m1param2.setValue(3.2);
ModelDefinition moddef2 = new ModelDefinition();
moddef2.setId("Mod2");
Parameter subparam2 = moddef2.createParameter();
subparam2.setId("subparam2");
subparam2.setConstant(false);
compdoc.addModelDefinition(moddef2);
ExternalModelDefinition extmod1 = compdoc.createExternalModelDefinition();
extmod1.setId("ExtMod1");
extmod1.setSource("urn:miriam:biomodels.db:BIOMD0000000127");
ExternalModelDefinition extmod2 = new ExternalModelDefinition();
extmod2.setId("ExtMod2");
extmod2.setSource("otherfile.xml");
extmod2.setModelRef("modelnamethere");
extmod2.setMd5("406022s908ge74sklj");
compdoc.addExternalModelDefinition(extmod2);
Submodel submod1 = mplugin.createSubmodel();
submod1.setId("submod1");
submod1.setModelRef("Mod1");
Deletion del1 = submod1.createDeletion();
del1.setId("deletionA");
del1.setIdRef("param2");
Submodel submod2 = new Submodel();
submod2.setId("submod2");
submod2.setModelRef("ExtMod1");
submod2.setSubstanceConversionFactor("subcf");
submod2.setTimeConversionFactor("tcf");
submod2.setExtentConversionFactor("xtf");
Deletion del2 = new Deletion();
del2.setId("deletionB");
del2.setMetaIdRef("_0010110");
rv = submod2.addDeletion(del2);
del2.setId("deletionC");
del2.unsetMetaIdRef();
del2.setPortRef("port2");
rv = submod2.addDeletion(del2);
del2.unsetId();
del2.unsetPortRef();
del2.setUnitRef("mph");
rv = submod2.addDeletion(del2);
del2.unsetUnitRef();
del2.setIdRef("submodG");
SBaseRef sbr = del2.createSBaseRef();
sbr.setIdRef("element5");
rv = submod2.addDeletion(del2);
Deletion del3 = new Deletion();
del3.setIdRef("submodG");
SBaseRef sbr2 = new SBaseRef();
sbr2.setIdRef("subsubmodQ");
SBaseRef subsbr = sbr2.createSBaseRef();
subsbr.setPortRef("toBdel");
del3.setSBaseRef(sbr2);
submod2.addDeletion(del3);
mplugin.addSubmodel(submod2);
Port port1 = mplugin.createPort();
port1.setId("port1");
port1.setMetaIdRef("_110013");
Port port2 = new Port();
port2.setId("port2");
port2.setIdRef("x");
mplugin.addPort(port2);
port2.setId("port3");
port2.setIdRef("submod2");
port2.setSBaseRef(sbr2);
mplugin.addPort(port2);
libsbml.writeSBMLToFile(document, "comp_example1.xml");
document = libsbml.readSBMLFromFile("comp_example1.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
OStringStream stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "comp_example1_rt.xml");
}
return retval;
}
public static int Main(string[] args)
{
int retval = 0;
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// create the Model
Model model = document.createModel();
// create a replacement parameter
Parameter parameter = model.createParameter();
parameter.setId("x");
parameter.setConstant(true);
// create a parameter to be a conversion factor
Parameter param2 = model.createParameter();
param2.setId("x_conv");
param2.setMetaId("_110013");
param2.setConstant(true);
// create a parameter to be a conversion factor
Parameter param3 = model.createParameter();
param3.setId("lcf");
param3.setConstant(true);
// Convert parameter to the plugin version so we can add the new attributes and replacements to it.
CompSBasePlugin splugin = (CompSBasePlugin)(parameter.getPlugin("comp"));
// Add a replaced element.
ReplacedElement rep1 = splugin.createReplacedElement();
int rv = rep1.setSubmodelRef("submod1");
rv = rep1.setConversionFactor("x_conv");
rv = rep1.setIdRef("param1");
// Add a second replaced element in a different way.
ReplacedElement rep2 = new ReplacedElement();
rv = rep2.setSubmodelRef("submod2");
rv = rep2.setDeletion("del1");
rv = splugin.addReplacedElement(rep2);
//Now create a replaced element that points into a submodel.
rep2.unsetDeletion();
rep2.setIdRef("submod2");
SBaseRef sbr5 = rep2.createSBaseRef();
sbr5.setIdRef("submodelG");
SBaseRef sbr6 = sbr5.createSBaseRef();
sbr6.setIdRef("buriedElement");
splugin.addReplacedElement(rep2);
// Create a submodel
CompModelPlugin mplugin = (CompModelPlugin)(model.getPlugin("comp"));
CompSBMLDocumentPlugin compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
compdoc.setRequired(true);
ModelDefinition moddef1 = compdoc.createModelDefinition();
moddef1.setId("Mod1");
Parameter m1param1 = moddef1.createParameter();
m1param1.setId("param1");
m1param1.setConstant(true);
Parameter m1param2 = moddef1.createParameter();
m1param2.setId("param2");
m1param2.setConstant(false);
m1param2.setValue(3.2);
ModelDefinition moddef2 = new ModelDefinition();
moddef2.setId("Mod2");
Parameter subparam2 = moddef2.createParameter();
subparam2.setId("subparam2");
subparam2.setConstant(false);
compdoc.addModelDefinition(moddef2);
ExternalModelDefinition extmod1 = compdoc.createExternalModelDefinition();
extmod1.setId("ExtMod1");
extmod1.setSource("urn:miriam:biomodels.db:BIOMD0000000127");
ExternalModelDefinition extmod2 = new ExternalModelDefinition();
extmod2.setId("ExtMod2");
extmod2.setSource("otherfile.xml");
extmod2.setModelRef("modelnamethere");
extmod2.setMd5("406022s908ge74sklj");
compdoc.addExternalModelDefinition(extmod2);
Submodel submod1 = mplugin.createSubmodel();
submod1.setId("submod1");
submod1.setModelRef("Mod1");
Deletion del1 = submod1.createDeletion();
del1.setId("deletionA");
del1.setIdRef("param2");
Submodel submod2 = new Submodel();
submod2.setId("submod2");
submod2.setModelRef("ExtMod1");
submod2.setSubstanceConversionFactor("subcf");
submod2.setTimeConversionFactor("tcf");
submod2.setExtentConversionFactor("xtf");
Deletion del2 = new Deletion();
del2.setId("deletionB");
del2.setMetaIdRef("_0010110");
rv = submod2.addDeletion(del2);
del2.setId("deletionC");
del2.unsetMetaIdRef();
del2.setPortRef("port2");
rv = submod2.addDeletion(del2);
del2.unsetId();
del2.unsetPortRef();
del2.setUnitRef("mph");
rv = submod2.addDeletion(del2);
del2.unsetUnitRef();
del2.setIdRef("submodG");
SBaseRef sbr = del2.createSBaseRef();
sbr.setIdRef("element5");
rv = submod2.addDeletion(del2);
Deletion del3 = new Deletion();
del3.setIdRef("submodG");
SBaseRef sbr2 = new SBaseRef();
sbr2.setIdRef("subsubmodQ");
SBaseRef subsbr = sbr2.createSBaseRef();
subsbr.setPortRef("toBdel");
del3.setSBaseRef(sbr2);
submod2.addDeletion(del3);
mplugin.addSubmodel(submod2);
Port port1 = mplugin.createPort();
port1.setId("port1");
port1.setMetaIdRef("_110013");
Port port2 = new Port();
port2.setId("port2");
port2.setIdRef("x");
mplugin.addPort(port2);
port2.setId("port3");
port2.setIdRef("submod2");
port2.setSBaseRef(sbr2);
mplugin.addPort(port2);
libsbml.writeSBMLToFile(document, "comp_example1.xml");
document = libsbml.readSBMLFromFile("comp_example1.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
OStringStream stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "comp_example1_rt.xml");
}
return(retval);
}
public ChartSheetContentSequence(IStreamReader reader)
: base(reader)
{
// reset id counter for chart groups
ChartFormatIdGenerator.Instance.StartNewChartsheetSubstream();
ChartAxisIdGenerator.Instance.StartNewChartsheetSubstream();
// CHARTSHEETCONTENT = [WriteProtect] [SheetExt] [WebPub] *HFPicture PAGESETUP PrintSize [HeaderFooter] [BACKGROUND] *Fbi *Fbi2 [ClrtClient] [PROTECTION]
// [Palette] [SXViewLink] [PivotChartBits] [SBaseRef] [MsoDrawingGroup] OBJECTS Units CHARTFOMATS SERIESDATA *WINDOW *CUSTOMVIEW [CodeName] [CRTMLFRT] EOF
// [WriteProtect]
if (BiffRecord.GetNextRecordType(reader) == RecordType.WriteProtect)
{
this.WriteProtect = (WriteProtect)BiffRecord.ReadRecord(reader);
}
// [SheetExt]
if (BiffRecord.GetNextRecordType(reader) == RecordType.SheetExt)
{
this.SheetExt = (SheetExt)BiffRecord.ReadRecord(reader);
}
// [WebPub]
if (BiffRecord.GetNextRecordType(reader) == RecordType.WebPub)
{
this.WebPub = (WebPub)BiffRecord.ReadRecord(reader);
}
// *HFPicture
while (BiffRecord.GetNextRecordType(reader) == RecordType.HFPicture)
{
this.HFPictures.Add((HFPicture)BiffRecord.ReadRecord(reader));
}
// PAGESETUP
this.PageSetupSequence = new PageSetupSequence(reader);
// PrintSize
if (BiffRecord.GetNextRecordType(reader) == RecordType.PrintSize)
{
this.PrintSize = (PrintSize)BiffRecord.ReadRecord(reader);
}
// [HeaderFooter]
if (BiffRecord.GetNextRecordType(reader) == RecordType.HeaderFooter)
{
this.HeaderFooter = (HeaderFooter)BiffRecord.ReadRecord(reader);
}
// [BACKGROUND]
if (BiffRecord.GetNextRecordType(reader) == RecordType.BkHim)
{
this.BackgroundSequence = new BackgroundSequence(reader);
}
// *Fbi
this.Fbis = new List <Fbi>();
while (BiffRecord.GetNextRecordType(reader) == RecordType.Fbi)
{
this.Fbis.Add((Fbi)BiffRecord.ReadRecord(reader));
}
// *Fbi2
this.Fbi2s = new List <Fbi2>();
while (BiffRecord.GetNextRecordType(reader) == RecordType.Fbi2)
{
this.Fbi2s.Add((Fbi2)BiffRecord.ReadRecord(reader));
}
// [ClrtClient]
if (BiffRecord.GetNextRecordType(reader) == RecordType.ClrtClient)
{
this.ClrtClient = (ClrtClient)BiffRecord.ReadRecord(reader);
}
// [PROTECTION]
this.ProtectionSequence = new ProtectionSequence(reader);
// [Palette]
if (BiffRecord.GetNextRecordType(reader) == RecordType.Palette)
{
this.Palette = (Palette)BiffRecord.ReadRecord(reader);
}
// [SXViewLink]
if (BiffRecord.GetNextRecordType(reader) == RecordType.SXViewLink)
{
this.SXViewLink = (SXViewLink)BiffRecord.ReadRecord(reader);
}
// [PivotChartBits]
if (BiffRecord.GetNextRecordType(reader) == RecordType.PivotChartBits)
{
this.PivotChartBits = (PivotChartBits)BiffRecord.ReadRecord(reader);
}
// [SBaseRef]
if (BiffRecord.GetNextRecordType(reader) == RecordType.SBaseRef)
{
this.SBaseRef = (SBaseRef)BiffRecord.ReadRecord(reader);
}
// [MsoDrawingGroup]
if (BiffRecord.GetNextRecordType(reader) == RecordType.MsoDrawingGroup)
{
this.MsoDrawingGroup = (MsoDrawingGroup)BiffRecord.ReadRecord(reader);
}
// OBJECTS
this.ObjectsSequence = new ObjectsSequence(reader);
// Units
this.Units = (Units)BiffRecord.ReadRecord(reader);
// CHARTFOMATS
this.ChartFormatsSequence = new ChartFormatsSequence(reader);
// SERIESDATA
this.SeriesDataSequence = new SeriesDataSequence(reader);
// *WINDOW
this.WindowSequences = new List <WindowSequence>();
while (BiffRecord.GetNextRecordType(reader) == RecordType.Window2)
{
this.WindowSequences.Add(new WindowSequence(reader));
}
// *CUSTOMVIEW
this.CustomViewSequences = new List <CustomViewSequence>();
// CUSTOMVIEW seems to be totally optional,
// so check for the existence of the next sequences
while (BiffRecord.GetNextRecordType(reader) != RecordType.CodeName &&
BiffRecord.GetNextRecordType(reader) != RecordType.CrtMlFrt &&
BiffRecord.GetNextRecordType(reader) != RecordType.EOF)
{
this.CustomViewSequences.Add(new CustomViewSequence(reader));
}
//this.CustomViewSequences = new List<CustomViewSequence>();
//while (BiffRecord.GetNextRecordType(reader) == RecordType.UserSViewBegin)
//{
// this.CustomViewSequences.Add(new CustomViewSequence(reader));
//}
// [CodeName]
if (BiffRecord.GetNextRecordType(reader) == RecordType.CodeName)
{
this.CodeName = (CodeName)BiffRecord.ReadRecord(reader);
}
// [CRTMLFRT]
if (BiffRecord.GetNextRecordType(reader) == RecordType.CrtMlFrt)
{
this.CrtMlfrtSequence = new CrtMlfrtSequence(reader);
}
// EOF
this.EOF = (EOF)BiffRecord.ReadRecord(reader);
}