本文整理汇总了C#中libsbmlcs.ConversionProperties.addOption方法的典型用法代码示例。如果您正苦于以下问题：C# ConversionProperties.addOption方法的具体用法？C# ConversionProperties.addOption怎么用？C# ConversionProperties.addOption使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类libsbmlcs.ConversionProperties的用法示例。
在下文中一共展示了ConversionProperties.addOption方法的8个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C#代码示例。
示例1: Main
public static void Main(String[] args)
{
if (args.Length < 2 || args.Length > 3)
{
Console.WriteLine("Usage: FlattenModel [-p] input-filename output-filename");
Console.WriteLine(" -p : list unused ports");
Environment.Exit(2);
}
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
bool leavePorts = false;
SBMLDocument doc;
if (args.Length == 2)
{
doc = reader.readSBML(args[0]);
}
else
{
doc = reader.readSBML(args[1]);
leavePorts = true;
}
if (doc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
{
doc.printErrors();
}
else
{
/* create a new conversion properties structure */
ConversionProperties props = new ConversionProperties();
/* add an option that we want to flatten */
props.addOption("flatten comp", true, "flatten comp");
/* add an option to leave ports if the user has requested this */
props.addOption("leavePorts", leavePorts, "unused ports should be listed in the flattened model");
/* perform the conversion */
int result = doc.convert(props);
if (result != libsbml.LIBSBML_OPERATION_SUCCESS)
{
Console.WriteLine("conversion failed ... ({0})", result);
doc.printErrors();
Environment.Exit(3);
}
if (args.Length == 2)
{
writer.writeSBML(doc, args[1]);
}
else
{
writer.writeSBML(doc, args[2]);
}
}
}示例2: Main
public static void Main(string[] args)
{
if (args.Length != 3)
{
string myname = Path.GetFileName(Environment.GetCommandLineArgs()[0]);
Console.WriteLine("Usage: {0} input-filename package-to-strip output-filename", myname);
Environment.Exit(1);
}
string inputFile = args[0];
string packageToStrip = args[1];
string outputFile = args[2];
if ( ! File.Exists(inputFile) )
{
Console.WriteLine("[Error] {0} : No such file.", inputFile);
Environment.Exit(1);
}
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument sbmlDoc = reader.readSBML(inputFile);
if ( sbmlDoc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
{
sbmlDoc.printErrors();
Console.WriteLine("[Error] Cannot read {0}", inputFile);
Environment.Exit(1);
}
/* create a new conversion properties structure */
ConversionProperties props = new ConversionProperties();
/* add an option that we want to strip a given package */
props.addOption("stripPackage", true, "Strip SBML Level 3 package constructs from the model");
/* add an option with the package we want to remove */
props.addOption("package", packageToStrip, "Name of the SBML Level 3 package to be stripped");
/* perform the conversion */
if (sbmlDoc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS)
{
Console.WriteLine ("conversion failed ... ");
Environment.Exit(3);
}
writer.writeSBML(sbmlDoc, outputFile);
Console.WriteLine("[OK] Stripped package '{0}' from {1} and wrote to {2}", packageToStrip, inputFile, outputFile);
}示例3: Main
public static void Main(string[] args)
{
if (args.Length != 2)
{
string myname = Path.GetFileName(Environment.GetCommandLineArgs()[0]);
Console.WriteLine("Usage: {0} input-filename output-filename", myname);
Environment.Exit(1);
}
string inputFile = args[0];
string outputFile = args[1];
if ( ! File.Exists(inputFile) )
{
Console.WriteLine("[Error] {0} : No such file.", inputFile);
Environment.Exit(1);
}
var now = DateTime.Now.Ticks;
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument sbmlDoc = reader.readSBML(inputFile);
if ( sbmlDoc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
{
sbmlDoc.printErrors();
Console.WriteLine("[Error] Cannot read {0}", inputFile);
Environment.Exit(1);
}
Console.WriteLine("Read {0} in {1}", inputFile, new TimeSpan(DateTime.Now.Ticks - now).TotalMilliseconds);
/* create a new conversion properties structure */
ConversionProperties props = new ConversionProperties();
/* add an option that we want to convert a model with
L3 FBC to L2 with COBRA annotation */
props.addOption("convert fbc to cobra", true, "Convert FBC model to Cobra model");
now = DateTime.Now.Ticks;
/* perform the conversion */
int result = sbmlDoc.convert(props);
if (result != libsbml.LIBSBML_OPERATION_SUCCESS)
{
Console.WriteLine ("conversion failed ... ");
Environment.Exit(3);
}
writer.writeSBML(sbmlDoc, outputFile);
Console.WriteLine("[OK] converted to FBC from {0} and wrote to {1} (in {2} msec)", inputFile, outputFile, new TimeSpan(DateTime.Now.Ticks - now).TotalMilliseconds);
}示例4: Main
public static void Main(string[] args)
{
if (args.Length != 2)
{
string myname = Path.GetFileName(Environment.GetCommandLineArgs()[0]);
Console.WriteLine("Usage: {0} input-filenameoutput-filename", myname);
Environment.Exit(1);
}
string inputFile = args[0];
string outputFile = args[1];
if ( ! File.Exists(inputFile) )
{
Console.WriteLine("[Error] {0} : No such file.", inputFile);
Environment.Exit(1);
}
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument sbmlDoc = reader.readSBML(inputFile);
if ( sbmlDoc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
{
sbmlDoc.printErrors();
Console.WriteLine("[Error] Cannot read {0}", inputFile);
Environment.Exit(1);
}
/* create a new conversion properties structure */
ConversionProperties props = new ConversionProperties();
/* add an option that we want to promote parameters */
props.addOption("promoteLocalParameters", true, "Promotes all Local Parameters to Global ones");
/* perform the conversion */
if (sbmlDoc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS)
{
Console.WriteLine ("conversion failed ... ");
Environment.Exit(3);
}
writer.writeSBML(sbmlDoc, outputFile);
Console.WriteLine("[OK] promoted paramters from {0} and wrote to {1}", inputFile, outputFile);
}示例5: WriteUsingFBC
private string WriteUsingFBC(int version = 1)
{
var doc = libsbml.readSBMLFromString(SBML);
var model = doc.getModel();
if (doc.getLevel() < 3)
{
var properties = new ConversionProperties(new SBMLNamespaces(3, 1));
properties.addOption("strict", false);
properties.addOption("setLevelAndVersion", true);
properties.addOption("ignorePackages", true);
doc.convert(properties);
}
if (version == 1)
{
doc.enablePackage(FbcExtension.getXmlnsL3V1V2(), "fbc", false);
doc.enablePackage(FbcExtension.getXmlnsL3V1V1(), "fbc", true);
}
else if (version == 2)
{
doc.enablePackage(FbcExtension.getXmlnsL3V1V1(), "fbc", false);
doc.enablePackage(FbcExtension.getXmlnsL3V1V2(), "fbc", true);
}
doc.setPackageRequired("fbc", false);
var plugin = (FbcModelPlugin)model.getPlugin("fbc");
if (plugin == null)
{
throw new Exception("Could not save using Fbc. Please check that your model contains no errors!");
}
plugin.getListOfFluxBounds().clear();
plugin.getListOfGeneAssociations().clear();
plugin.getListOfObjectives().clear();
plugin.getListOfGeneProducts().clear();
if (version == 1)
{
plugin.unsetStrict();
foreach (var constraint in Constraints)
{
var bound = plugin.createFluxBound();
bound.setReaction(constraint.Id);
bound.setOperation(ToFbcString(constraint.Operator));
bound.setValue(constraint.Value);
}
}
else
{
plugin.setStrict(false);
foreach (var constraint in Constraints)
{
var reaction = model.getReaction(constraint.Id);
if (reaction == null) continue;
var rplug = (FbcReactionPlugin)reaction.getPlugin("fbc");
if (rplug == null) continue;
switch (constraint.Operator)
{
case lpsolve_constr_types.LE:
{
var param = model.createParameter();
param.setId(string.Format("fb_{0}_ub", reaction.getId()));
param.setConstant(true);
param.setValue(constraint.Value);
rplug.setUpperFluxBound(param.getId());
}
break;
case lpsolve_constr_types.EQ:
{
var param = model.createParameter();
param.setId(string.Format("fb_{0}_ub", reaction.getId()));
param.setConstant(true);
param.setValue(constraint.Value);
rplug.setUpperFluxBound(param.getId());
param = model.createParameter();
param.setId(string.Format("fb_{0}_lb", reaction.getId()));
param.setConstant(true);
param.setValue(constraint.Value);
rplug.setLowerFluxBound(param.getId());
}
break;
case lpsolve_constr_types.GE:
{
var param = model.createParameter();
param.setId(string.Format("fb_{0}_lb", reaction.getId()));
param.setConstant(true);
param.setValue(constraint.Value);
rplug.setLowerFluxBound(param.getId());
}
break;
default:
break;
}
}
//.........这里部分代码省略.........
示例6: InitializeFromCobraAnnotation
private void InitializeFromCobraAnnotation(string sbmlContent)
{
try
{
var doc = libsbml.readSBMLFromString(sbmlContent);
var props = new ConversionProperties();
props.addOption("convert cobra", true, "");
if (doc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS)
return;
InitializeFromSBMLDocument(doc);
}
catch
{
}
}示例7: WriteAsCobraAnnotation
public string WriteAsCobraAnnotation()
{
var doc = libsbml.readSBMLFromString(SBML);
var model = doc.getModel();
if (doc.getLevel() < 3)
{
var properties = new ConversionProperties(new SBMLNamespaces(3, 1));
properties.addOption("strict", false);
properties.addOption("setLevelAndVersion", true);
properties.addOption("ignorePackages", true);
doc.convert(properties);
}
doc.enablePackage(FbcExtension.getXmlnsL3V1V1(), "fbc", true);
var plugin = (FbcModelPlugin)model.getPlugin("fbc");
if (plugin == null)
{
throw new Exception("Could not save using Fbc. Please check that your model contains no errors!");
}
plugin.getListOfFluxBounds().clear();
plugin.getListOfGeneAssociations().clear();
plugin.getListOfObjectives().clear();
foreach (var constraint in Constraints)
{
var bound = plugin.createFluxBound();
bound.setReaction(constraint.Id);
bound.setOperation(ToFbcString(constraint.Operator));
bound.setValue(constraint.Value);
}
var active = plugin.createObjective();
active.setId("objective1");
active.setType(Mode == FBA_Mode.maximize ? "maximize" : "minimize");
foreach (var objective in Objectives)
{
var current = active.createFluxObjective();
current.setReaction(objective.Id);
current.setCoefficient(objective.Value);
}
plugin.setActiveObjectiveId("objective1");
// convert to COBRA
var props = new ConversionProperties();
props.addOption("convert fbc to cobra", true, "Convert FBC model to Cobra model");
if (doc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS)
{
throw new Exception(doc.getErrorLog().toString());
}
model = doc.getModel();
plugin = (FbcModelPlugin)model.getPlugin("fbc");
if (plugin != null)
{
plugin.getListOfGeneProducts().clear();
plugin.getListOfGeneAssociations().clear();
plugin.getListOfFluxBounds().clear();
plugin.getListOfObjectives().clear();
}
return libsbml.writeSBMLToString(doc);
}示例8: ConvertToL2
public static string ConvertToL2(string model)
{
try
{
var doc = libsbml.readSBMLFromString(model);
if (doc.isPackageEnabled("fbc"))
doc.enablePackageInternal(doc.getNamespaces().getURI("fbc"), "fbc", false);
var properties = new ConversionProperties(new SBMLNamespaces(2, 4));
properties.addOption("strict", false);
properties.addOption("setLevelAndVersion", true);
properties.addOption("ignorePackages", true);
doc.convert(properties);
return libsbml.writeSBMLToString(doc);
}
catch// (Exception)
{
return model;
}
}