public void test_SBMLConvertStrict_convertToL1()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
(m).setMetaId("_m");
Compartment c = m.createCompartment();
c.setId("c");
(c).setSBOTerm(240);
Species s = m.createSpecies();
s.setId("s");
s.setCompartment("c");
assertTrue(d.setLevelAndVersion(1, 2, true) == true);
assertTrue(d.getLevel() == 1);
assertTrue(d.getVersion() == 2);
Model m1 = d.getModel();
assertTrue((m1).getMetaId() == "");
Compartment c1 = m1.getCompartment(0);
assertTrue((c1).getSBOTerm() == -1);
Species s1 = m1.getSpecies(0);
assertTrue(s1.getHasOnlySubstanceUnits() == false);
d = null;
}
public void test_SBMLConvertStrict_convertNonStrictSBO()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
c.setConstant(false);
(c).setSBOTerm(64);
assertTrue(d.setLevelAndVersion(2, 3, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 2, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 1, true) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
Compartment c1 = d.getModel().getCompartment(0);
assertTrue((c1).getSBOTerm() == -1);
assertTrue(d.setLevelAndVersion(1, 2, true) == true);
assertTrue(d.getLevel() == 1);
assertTrue(d.getVersion() == 2);
Compartment c2 = d.getModel().getCompartment(0);
assertTrue((c2).getSBOTerm() == -1);
d = null;
}
public void test_SBMLConvertStrict_convertNonStrictUnits()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
c.setConstant(false);
Parameter p = m.createParameter();
p.setId("p");
p.setUnits("mole");
ASTNode math = libsbml.parseFormula("p");
Rule ar = m.createAssignmentRule();
ar.setVariable("c");
ar.setMath(math);
assertTrue(d.setLevelAndVersion(2, 1, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 2, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 3, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(1, 2, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
d = null;
}
protected internal CurrentModelSelection GetCurrentSelectedPersistentType()
{
CurrentModelSelection result = new CurrentModelSelection();
result.DocData = Owner.GetModelingDocData();
result.DiagramDocView = Owner.GetDiagramDocView();
result.CurrentSelection = Owner.CurrentSelection;
result.IsPersistentTypeSelected = Owner.CurrentSelection.OfType <PersistentShape>().Count() == 1;
result.IsCompartmentSelected = Owner.CurrentSelection.OfType <Compartment>().Count() == 1;
if (result.IsPersistentTypeSelected || result.IsCompartmentSelected)
{
if (result.IsPersistentTypeSelected)
{
result.CurrentPersistentType =
Owner.CurrentSelection.OfType <PersistentShape>().Select(shape => shape.ModelElement).OfType
<PersistentType>().Single();
}
else
{
Compartment compartment = Owner.CurrentSelection.OfType <Compartment>().Single();
result.CompartmentName = compartment.Name;
result.CurrentPersistentType = (PersistentType)compartment.ParentShape.ModelElement;
}
}
return(result);
}
public void test_SBMLConvertStrict_convertL1ParamRule()
{
SBMLDocument d = new SBMLDocument(1, 2);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Parameter p = m.createParameter();
p.setId("p");
Parameter p1 = m.createParameter();
p1.setId("p1");
ASTNode math = libsbml.parseFormula("p");
Rule ar = m.createAssignmentRule();
ar.setVariable("p1");
ar.setMath(math);
ar.setUnits("mole");
assertTrue(d.setLevelAndVersion(2, 1, true) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
Rule r1 = d.getModel().getRule(0);
assertTrue(r1.getUnits() == "");
d = null;
}
Compartment remove(long n)
{
IntPtr cPtr = libsbmlPINVOKE.ListOfCompartments_remove__SWIG_0(swigCPtr, n);
Compartment ret = (cPtr == IntPtr.Zero) ? null : new Compartment(cPtr, true);
return(ret);
}
public void test_Compartment()
{
Compartment c = new Compartment(2, 4);
assertEquals(true, c.hasRequiredElements());
c = null;
}
public void Graph(Compartment AxisX, Compartment AxisY)
{
List <string> arguments = new List <string>()
{
"x"
};
Function function = new Function(this.function_expression, arguments);
this.chart.Series[0].Points.Clear();
this.chart.ChartAreas[0].AxisX.Maximum = AxisX.Max;
this.chart.ChartAreas[0].AxisX.Minimum = AxisX.Min;
this.chart.ChartAreas[0].AxisY.Maximum = AxisY.Max;
this.chart.ChartAreas[0].AxisY.Minimum = AxisY.Min;
this.chart.Series[0].BorderWidth = 3;
this.chart.ChartAreas[0].AxisX.Crossing = 0; // <--- These two lines
chart.ChartAreas[0].AxisY.Crossing = 0;
this.chart.ChartAreas[0].CursorX.IsUserEnabled = true;
this.chart.ChartAreas[0].CursorX.IsUserSelectionEnabled = true;
this.chart.ChartAreas[0].AxisX.ScaleView.Zoomable = true;
for (int i = (int)AxisX.Min; i <= (int)AxisX.Max; i++)
{
double functionValue = function.Evaluate(new List <double>()
{
i
});
this.chart.Series[0].Points.AddXY(i, functionValue);
this.chart.Series[0].ChartType = SeriesChartType.Line;
}
}
public void Graph(Compartment AxisX)
{
this.chart.Series[0].Points.Clear();
this.chart.ChartAreas[0].AxisX.Maximum = AxisX.Max + 1;
this.chart.ChartAreas[0].AxisX.Minimum = AxisX.Min - 1;
this.chart.ChartAreas[0].AxisY.Maximum = 0;
this.chart.ChartAreas[0].AxisY.Minimum = 0;
this.chart.Series[0].BorderWidth = 5;
this.chart.Legends[0].Name = this.function_expression;
for (double i = this.chart.ChartAreas[0].AxisX.Minimum; i <= this.chart.ChartAreas[0].AxisX.Maximum; i += 0.2)
{
double functionValue = function.Evaluate(new List <double>()
{
i
});
if (functionValue > chart.ChartAreas[0].AxisY.Maximum)
{
this.chart.ChartAreas[0].AxisY.Maximum = functionValue;
}
if (functionValue < chart.ChartAreas[0].AxisY.Minimum)
{
this.chart.ChartAreas[0].AxisY.Minimum = functionValue;
}
this.chart.Series[0].Points.AddXY(i, functionValue);
}
}
//[ValidateAntiForgeryToken]
public ActionResult Create([Bind(Include = "CompartmentID,CompartmentCode,Capactiy,TrailerID,Description,ModifiedDate,CreatedDate")] Compartment compartment)
{
if (ModelState.IsValid)
{
if (compartment.CompartmentID.Equals(0))
{
db.Compartments.Add(compartment);
db.SaveChanges();
return(RedirectToAction("Index", new
{
ID = compartment.TrailerID
}));
}
else
{
db.Entry(compartment).State = EntityState.Modified;
db.SaveChanges();
return(RedirectToAction("Index", new
{
ID = compartment.TrailerID
}));
}
}
else
{
var errors = ModelState.Values.SelectMany(v => v.Errors);
}
ViewBag.TrailerID = new SelectList(db.Trailers, "TrailerID", "TrailerCode", compartment.TrailerID);
return(View(compartment));
}
public static Compartment CompartmentFromJson(dynamic json)
{
Compartment Compartment = new Compartment()
{
name = json.Name
};
// Compartments have name of form "Slotnn_Sizenn"
Match matches = Regex.Match((string)json.Name, @"Size([0-9]+)");
if (matches.Success)
{
Compartment.size = Int32.Parse(matches.Groups[1].Value);
if (json.Value is JObject)
{
JToken value;
if (json.Value.TryGetValue("module", out value))
{
Compartment.module = ModuleFromJson((string)json.Name, json.Value);
}
}
}
return(Compartment);
}
internal ThawBuffer(Compartment setting, ObjectRegistry reg, SerUnit unit, byte[] data)
{
this.data = data;
this.setting = setting;
this.reg = reg;
this.unit = unit;
}
protected override void Context()
{
base.Context();
_simulation.RemoveAllBuildingBlockOfType(PKSimBuildingBlockType.Individual);
_parameters = new List <IParameter>();
var kidney = new Organ().WithName(CoreConstants.Organ.KIDNEY);
var kidney_cell = new Compartment().WithName(CoreConstants.Compartment.INTRACELLULAR).WithParentContainer(kidney);
var kid_cell_trans = new Container().WithName(_transporter.Name).WithParentContainer(kidney_cell);
var relExp2Param = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP)
.WithParentContainer(kid_cell_trans);
relExp2Param.Origin.SimulationId = "Sim";
var liver = new Organ().WithName(CoreConstants.Organ.LIVER);
var liver_cell = new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithParentContainer(liver);
var liver_enz = new Container().WithName(_enzyme.Name).WithParentContainer(liver_cell);
var relExp1Param = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP)
.WithParentContainer(liver_enz);
relExp1Param.Origin.SimulationId = "Sim";
_referenceConcentrationParam = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REFERENCE_CONCENTRATION);
_halfLifeLiverParameter = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.HALF_LIFE_LIVER);
_halfLifeLiverIntestineParameter = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.HALF_LIFE_INTESTINE);
_parameters.AddRange(new[]
{ _halfLifeLiverParameter, _halfLifeLiverIntestineParameter, _referenceConcentrationParam, relExp1Param, relExp2Param });
}
protected override void Context()
{
base.Context();
_parameters = new List <IParameter>();
var brain = new Organ().WithName(CoreConstants.Organ.BRAIN);
var brain_pls = new Compartment().WithName(CoreConstants.Compartment.PLASMA).WithParentContainer(brain);
var brain_pls_trans = new Container().WithName(_transporter.Name).WithParentContainer(brain_pls);
var relExp2Param = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP)
.WithParentContainer(brain_pls_trans);
relExp2Param.Origin.SimulationId = "Sim";
var liver = new Organ().WithName(CoreConstants.Organ.LIVER);
var liver_cell = new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithParentContainer(liver);
var liver_enz = new Container().WithName(_enzyme.Name).WithParentContainer(liver_cell);
var relExp1Param = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP)
.WithParentContainer(liver_enz);
relExp1Param.Origin.SimulationId = "Sim";
_referenceConcentrationParam = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REFERENCE_CONCENTRATION);
_halfLifeLiverParameter = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.HALF_LIFE_LIVER);
_halfLifeLiverIntestineParameter = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.HALF_LIFE_INTESTINE);
_parameters.AddRange(new[]
{ _halfLifeLiverParameter, _halfLifeLiverIntestineParameter, _referenceConcentrationParam, relExp1Param, relExp2Param });
}
protected override void Because()
{
var model = new Model(3, 1);
model.setName("TestModel");
model.setNotes("TestNotes");
model.setMetaId("TestMetaId");
sut.CreateEventsTopContainer();
sut.CreateTopContainer(model);
var compartment = new Compartment(3, 1);
compartment.setName("Compartment");
compartment.setId("c1");
compartment.setSpatialDimensions(1);
compartment.setSize(5);
var compartment2 = new Compartment(3, 1);
compartment2.setName("Compartment");
compartment2.setId("c2");
compartment2.setSpatialDimensions(2);
compartment2.setSize(5);
var compartment3 = new Compartment(3, 1);
compartment3.setName("Compartment");
compartment3.setId("c3");
compartment3.setSpatialDimensions(3);
compartment3.setSize(5);
_container = sut.CreateContainerFromCompartment(compartment);
_container2 = sut.CreateContainerFromCompartment(compartment2);
_container3 = sut.CreateContainerFromCompartment(compartment3);
sut.CreateSpatialStructureFromModel(sut._topContainer, model);
}
public void test_SBMLConvert_convertToL1_Species_Concentration()
{
SBMLDocument d = new SBMLDocument(2, 1);
Model m = d.createModel();
string sid = "C";
Compartment c = new Compartment(2, 1);
Species s = new Species(2, 1);
c.setId(sid);
c.setSize(1.2);
m.addCompartment(c);
s.setId("s");
s.setCompartment(sid);
s.setInitialConcentration(2.34);
m.addSpecies(s);
assertTrue(d.setLevelAndVersion(1, 2, true) == true);
Species s1 = m.getSpecies(0);
assertTrue(s1 != null);
assertTrue(("C" == s1.getCompartment()));
assertTrue(m.getCompartment("C").getSize() == 1.2);
assertTrue(s1.getInitialConcentration() == 2.34);
assertTrue(s1.isSetInitialConcentration() == true);
d = null;
}
Compartment remove(string sid)
{
IntPtr cPtr = libsbmlPINVOKE.ListOfCompartments_remove__SWIG_1(swigCPtr, sid);
Compartment ret = (cPtr == IntPtr.Zero) ? null : new Compartment(cPtr, true);
return(ret);
}
public void test_SBMLConvert_convertToL3_localParameters()
{
SBMLDocument d = new SBMLDocument(1, 2);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Species s = m.createSpecies();
s.setId("s");
s.setCompartment("c");
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
sr.setSpecies("s");
KineticLaw kl = r.createKineticLaw();
kl.setFormula("s*k");
Parameter p = kl.createParameter();
p.setId("k");
assertTrue(kl.getNumLocalParameters() == 0);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
m = d.getModel();
r = m.getReaction(0);
kl = r.getKineticLaw();
assertTrue(kl.getNumLocalParameters() == 1);
LocalParameter lp = kl.getLocalParameter(0);
d = null;
}
private static async Task DisplayAudit(
AuditClientAsync client, IdentityClient identityClinet,
Compartment compartment, string startDate, string endDate,
string requestId = "", string pageId = "")
{
// get Audit Events
var listEventsRequest = new ListEventsRequest()
{
CompartmentId = compartment.Id,
StartTime = startDate,
EndTime = endDate,
Page = pageId
};
var events = await client.ListEvents(listEventsRequest);
if (!string.IsNullOrEmpty(events.OpcNextPage))
{
await DisplayAudit(client, identityClinet, compartment, startDate, endDate, events.OpcRequestId, events.OpcNextPage);
}
if (events.Items.Count > 0)
{
Count += events.Items.Count;
Console.WriteLine($"enventset: com={compartment.Name}, start={startDate}, end={endDate}, events.Items:{events.Items.Count}");
}
}
public void test_SBMLConvert_convertToL3_stoichiometryMath()
{
SBMLDocument d = new SBMLDocument(2, 1);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Species s = m.createSpecies();
s.setId("s");
s.setCompartment("c");
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
sr.setSpecies("s");
StoichiometryMath sm = sr.createStoichiometryMath();
ASTNode ast = libsbml.parseFormula("c*2");
sm.setMath(ast);
assertTrue(m.getNumRules() == 0);
assertTrue(sr.isSetId() == false);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
m = d.getModel();
r = m.getReaction(0);
sr = r.getReactant(0);
assertTrue(m.getNumRules() == 1);
assertTrue(sr.isSetId() == true);
Rule rule = m.getRule(0);
assertTrue((rule.getVariable() == sr.getId()));
d = null;
}
/// <summary>
/// Gets called whenever a shape is inserted into the diagram.
/// This is a good time to setup visuals, because all shapes,
/// decorators, compartments, shapefields, etc. have been created.
/// </summary>
public override void OnShapeInserted()
{
base.OnShapeInserted();
// Define the font change to make.
// In this case, make all decorators show bold, italic,
// and bigger sized text.
FontSettings fs = new FontSettings();
foreach (ShapeDecorator decorator in this.Decorators)
{
// Only do this for all of the text decorators in this shape.
TextShapeDecorator shapeDec = decorator as TextShapeDecorator;
if (shapeDec != null)
{
shapeDec.StyleSet.OverrideFont(DiagramFonts.ShapeText, fs);
}
}
// make the compartment item text bold.
FontSettings fsBold = new FontSettings();
foreach (ShapeElement shape in this.NestedChildShapes)
{
// Only do this for all of the compartments in this shape.
Compartment compartment = shape as Compartment;
if (compartment != null)
{
compartment.StyleSet.OverrideFont(DiagramFonts.ShapeTitle, fsBold);
}
}
}
public async Task <IActionResult> Edit(int id, [Bind("Id,Name")] Compartment compartment)
{
if (id != compartment.Id)
{
return(NotFound());
}
if (ModelState.IsValid)
{
try
{
_context.Update(compartment);
await _context.SaveChangesAsync();
}
catch (DbUpdateConcurrencyException)
{
if (!CompartmentExists(compartment.Id))
{
return(NotFound());
}
else
{
throw;
}
}
return(RedirectToAction(nameof(Index)));
}
return(View(compartment));
}
/// <summary>
/// Sélection des propriétes dans la compartiment list
/// </summary>
/// <param name="view">The view.</param>
/// <param name="association">The association.</param>
/// <param name="entity">The entity.</param>
/// <param name="properties">The properties.</param>
private static void SelectProperties(DiagramClientView view, Association association, Entity entity,
IList <Property> properties)
{
IList <PresentationElement> presentations = PresentationViewsSubject.GetPresentation(entity);
Debug.Assert(presentations.Count > 0);
Compartment compartment = ((CompartmentShape)presentations[0]).FindCompartment("Properties");
Debug.Assert(compartment != null);
foreach (ShapeField field in compartment.ShapeFields)
{
if (field is ListField)
{
foreach (Property property in properties)
{
if (property != null)
{
int index = entity.Properties.IndexOf(property);
DiagramItem item = new DiagramItem(compartment, field, new ListItemSubField(index));
if (!view.Selection.Contains(item))
{
view.Selection.Add(item);
}
}
}
break;
}
}
}
public void test_L3_Compartment_initDefaults()
{
Compartment c = new Compartment(3, 1);
c.setId("A");
assertEquals(true, c.isSetId());
assertEquals(false, c.isSetName());
assertEquals(false, c.isSetSize());
assertEquals(false, c.isSetVolume());
assertEquals(false, c.isSetUnits());
assertEquals(false, c.isSetConstant());
assertEquals(false, c.isSetSpatialDimensions());
c.initDefaults();
assertTrue(("A" == c.getId()));
assertTrue(c.getName() == "");
assertTrue(("litre" == c.getUnits()));
assertTrue(c.getSpatialDimensions() == 3);
assertTrue(c.getSize() == 1);
assertTrue(c.getConstant() == true);
assertEquals(true, c.isSetId());
assertEquals(false, c.isSetName());
assertEquals(false, c.isSetSize());
assertEquals(false, c.isSetVolume());
assertEquals(true, c.isSetUnits());
assertEquals(true, c.isSetConstant());
assertEquals(true, c.isSetSpatialDimensions());
c = null;
}
public void test_L3_Compartment_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1);
sbmlns.addNamespaces(xmlns);
Compartment c = new Compartment(sbmlns);
assertTrue(c.getTypeCode() == libsbml.SBML_COMPARTMENT);
assertTrue(c.getMetaId() == "");
assertTrue(c.getNotes() == null);
assertTrue(c.getAnnotation() == null);
assertTrue(c.getLevel() == 3);
assertTrue(c.getVersion() == 1);
assertTrue(c.getNamespaces() != null);
assertTrue(c.getNamespaces().getLength() == 2);
assertTrue(c.getId() == "");
assertTrue(c.getName() == "");
assertTrue(c.getUnits() == "");
assertTrue(c.getOutside() == "");
assertEquals(true, isnan(c.getSpatialDimensionsAsDouble()));
assertEquals(true, isnan(c.getVolume()));
assertTrue(c.getConstant() == true);
assertEquals(false, c.isSetId());
assertEquals(false, c.isSetSpatialDimensions());
assertEquals(false, c.isSetName());
assertEquals(false, c.isSetSize());
assertEquals(false, c.isSetVolume());
assertEquals(false, c.isSetUnits());
assertEquals(false, c.isSetOutside());
assertEquals(false, c.isSetConstant());
c = null;
}
Compartment get(long n)
{
IntPtr cPtr = libsbmlPINVOKE.ListOfCompartments_get__SWIG_0(swigCPtr, n);
Compartment ret = (cPtr == IntPtr.Zero) ? null : new Compartment(cPtr, false);
return(ret);
}
/// <summary>
/// Gets the compartment status with Json web token credentials.
/// Json web token credentials contains enable or disable, if enable then need to provide jwt secret and token.
/// </summary>
/// <returns>
/// List of compartment status with object detection and LED status based requested compartment id's.
/// </returns>
public CompartmentStatusDto CompartmentStatus(Compartment model)
{
var compartment = new Compartment(model.TransactionId, model.LockerId, model.CompartmentIds, model.JwtCredentials.IsEnabled, model.JwtCredentials.Secret, model.JwtCredentials.Token);
var result = LockerManager.CompartmentStatus(compartment);
return(result);
}
Compartment get(string sid)
{
IntPtr cPtr = libsbmlPINVOKE.ListOfCompartments_get__SWIG_2(swigCPtr, sid);
Compartment ret = (cPtr == IntPtr.Zero) ? null : new Compartment(cPtr, false);
return(ret);
}
public Compartment ()
{
aabb = new AABBi(new Vec2i(0,0), new Vec2i(0,0));
color = new Color(UnityEngine.Random.value, UnityEngine.Random.value, UnityEngine.Random.value);
isPtr = false;
ptrValue = null;
}
/// <summary>
/// Remember which item the mouse was dragged from.
/// We don't create an Action immediately, as this would inhibit the
/// inline text editing feature. Instead, we just remember the details
/// and will create an Action when/if the mouse moves off this list item.
/// </summary>
private void Compartment_MouseDown(object sender, DiagramMouseEventArgs e)
{
Compartment compartment = (Compartment)sender;
var compartmentElementToDrag = GetCompartmentElementToDrag(compartment, e.HitDiagramItem.RepresentedElements);
dragStartElement = compartmentElementToDrag;
compartmentBounds = e.HitDiagramItem.Shape.AbsoluteBoundingBox;
}
public void setUp()
{
string filename = "../../sbml/annotation/test/test-data/annotationL3.xml";
d = libsbml.readSBML(filename);
m = d.getModel();
c = m.getCompartment(0);
}
internal GState(Compartment setting, string orig, P6any actions) {
this.setting = setting;
this.actions = (actions == setting.AnyP) ? null : actions;
orig_s = orig;
orig_a = orig.ToCharArray();
highwater = (orig_a.Length < 100 || !Cursor.HwTrace) ?
int.MaxValue : 0;
}
public void Combine(Compartment other)
{
if (other != this) {
isPtr = true;
ptrValue = other.Instance;
other.aabb.FitAABB(ref aabb);
}
}
internal static Variable DCResult(Compartment s, object r) {
if (r == null) return s.AnyMO.typeObj;
else if (r is string) return s.MakeStr((string)r);
else if (r is int) return s.MakeInt((int)r);
else if (r is bool) return ((bool)r) ? s.TrueV : s.FalseV;
else if (r is Exception) throw new NieczaException(((Exception)r).Message);
else if (r is object[]) {
object[] ra = (object[])r;
Variable[] ba = new Variable[ra.Length];
for (int i = 0; i < ba.Length; i++) ba[i] = DCResult(s,ra[i]);
return s.MakeParcel(ba);
}
else {
string t = (string)RawDowncall("gettype", r);
P6any pr = (t == "type") ? TypeP :
(t == "sub") ? StaticSubP :
(t == "param") ? ParamP :
(t == "value") ? ValueP :
(t == "unit") ? UnitP : s.AnyMO.typeObj;
return Kernel.BoxAnyMO(r, pr.mo);
}
}
internal Cursor(Compartment setting, P6any proto, string text, P6any actions)
: this(new GState(setting, text, actions), proto.mo, null, null, null, 0, null) { }
public static P6any MakeDispatcher(Compartment s, string name, P6any proto, P6any[] cands) {
if (proto != null) {
SubInfo si = new SubInfo(Kernel.GetInfo(proto));
si.param = new object[] { cands, null };
return Kernel.MakeSub(si, Kernel.GetOuter(proto));
} else {
SubInfo si = new SubInfo(s, name, StandardProtoC);
si.param = new object[] { cands, null };
si.ltm = new LADDispatcher();
return Kernel.MakeSub(si, null);
}
}
public void CompartmentElement(Hashtable attrs)
{
Compartment compartment = new Compartment(this.model, attrs);
CompartmentType compartmentType = null;
int spatialDimensions = 3;
double size = 1;
String units = null; // unit enum or user-defined unit
Compartment outside = null;
Boolean constant = true;
if (attrs.Contains("constant"))
constant = Boolean.Parse((String)attrs["units"]);
if (attrs.Contains("spatialdimensions"))
spatialDimensions = (int)(Int32.Parse((String)attrs["spatialdimensions"]));
if (attrs.Contains("size"))
size = (double)(Double.Parse((String)attrs["size"]));
else if (attrs.Contains("volume")) // from SBML Level 1
size = (double)(Double.Parse((String)attrs["volume"]));
if (attrs.Contains("units") && this.model.IsUnits((String)attrs["units"]))
units = (String)attrs["units"];
else
{
switch (spatialDimensions)
{
case 1:
units = "length";
break;
case 2:
units = "area";
break;
case 3:
units = "volume";
break;
}
}
if (attrs.Contains("compartmenttype"))
{
String cTypeId = (String)attrs["compartmenttype"];
compartmentType = (CompartmentType)this.model.findObject(cTypeId);
}
if (attrs.Contains("outside"))
{
String cId = (String)attrs["outside"];
outside = (Compartment)this.model.findObject(cId);
}
compartment.AddProperties(compartmentType, spatialDimensions, size,
units, outside, constant);
this.model.listOfCompartments.Add(compartment);
}
private List<SectionElement> GetSectionElementsVisibleInSketch(Section section, Compartment compartment)
{
try
{
List<SectionElement> sectionElements = new List<SectionElement>();
Vector3D xAxis = new Vector3D(1, 0, 0);
Plane minPlane = new Plane(xAxis, compartment.BoundingBox.MinPoint);
Plane maxPlane = new Plane(xAxis, compartment.BoundingBox.MaxPoint);
SectionElementsSet sectionElementsSet = section.GetPermanentSectionElementsSet("Plate");
foreach (Plate plate in sectionElementsSet.Elements.Values)
{
Point3D point = plate.Design.Geometry.Primitive(0).Centroid;
if (minPlane.Signal(point) == 1 && maxPlane.Signal(point) == -1)
{
sectionElements.Add(plate);
}
}
return sectionElements;
}
catch (Exception ex)
{
throw new ApplicationException("Section elements visible in skectch cannot be get!", ex);
}
}
private static void FillTile(AdjacentTiles t)
{
if ((t.tile.flags & (uint)VesselTile.FLAGS.SOLID_BLOCK) > 0) {
t.tile.c0 = null;
t.tile.c1 = null;
}
//take the compartments from left or bottom no matter what in these cases
if ((t.bTile != null && t.bTile.Contains(WallTypeMask.OneByTwo)) || (t.brTile != null && t.brTile.Contains(WallTypeMask.OneByTwoFlipped))) {
t.tile.c0 = t.bTile.c0.Instance;
t.tile.c1 = t.bTile.c1.Instance;
return;
}
if ((t.lTile != null && t.lTile.Contains(WallTypeMask.TwoByOne)) || (t.rTile != null && t.rTile.Contains(WallTypeMask.TwoByOneFlipped))) {
t.tile.c0 = t.lTile.c0.Instance;
t.tile.c1 = t.lTile.c1.Instance;
return;
}
//
//try take from bottom
Compartment b = null;
if (t.bTile != null) {
if ((t.bTile.flags & (uint)VesselTile.FLAGS.SOLID_BLOCK) > 0)
b = null;
else if (!t.tile.Contains(WallTypeMask.OneByZero)) {
//set the appropriate compartment field depending on how "bTile" is cut
if (
(t.blTile != null && t.blTile.Contains(WallTypeMask.TwoByOne)) ||
(t.bTile.Contains(WallTypeMask.OneByOne)) ||
(t.b2Tile != null && t.b2Tile.Contains(WallTypeMask.OneByTwo))) {
b = t.bTile.c1.Instance;
//} else if (
// (t.b2rTile != null && t.b2rTile.Contains(WallTypeMask.OneByTwoFlipped)) ||
// (t.brTile != null && t.brTile.Contains(WallTypeMask.OneByOneFlipped)) ||
// (t.br2Tile != null && t.br2Tile.Contains(WallTypeMask.TwoByOneFlipped))){
// b = t.bTile.c0.Instance;
} else {
b = t.bTile.c0.Instance;
}
}
}
Compartment l = null;
if (t.lTile != null) {
if ((t.lTile.flags & (uint)VesselTile.FLAGS.SOLID_BLOCK) > 0)
l = null;
else if (!t.tile.Contains(WallTypeMask.ZeroByOne)) {
l = t.lTile.c0.Instance;
}
}
if (
(t.r2Tile != null && t.r2Tile.Contains(WallTypeMask.TwoByOneFlipped)) ||
(t.rTile != null && t.rTile.Contains(WallTypeMask.OneByOneFlipped | WallTypeMask.OneByTwoFlipped))) {
if (l != null && b != null) {
l.Combine(b);
}
if (b != null) {
t.tile.c1 = b;
} else if (l != null) {
t.tile.c1 = l;
}
t.tile.c0 = new Compartment();
return;
} else if (t.tile.Contains(WallTypeMask.TwoByOne | WallTypeMask.OneByOne | WallTypeMask.OneByTwo)) {
if (b == null) {
b = new Compartment();
}
t.tile.c0 = b;
if (l == null) {
l = new Compartment();
}
t.tile.c1 = l;
return;
} else {
if (l != null && b != null) {
l.Combine(b);
}
l = (l == null) ? b : l;
if (l == null) {
l = new Compartment();
}
t.tile.c0 = l.Instance;
}
}
public void SetCompartmentFloor(FloorType type, Compartment c)
{
Vec2i start = ChunkIToTileI(aabb.bl);
Vec2i end = ChunkIToTileI(aabb.tr);
for (int i = start.y; i < end.y; i++) {
for (int j = start.x; j < end.x; j++) {
Vec2i tileI = new Vec2i(j, i);
VesselTile tile;
if ((tile = TryGetTile(tileI)) != null) {
bool modified = false;
if (tile.c0 != null && tile.c0.Instance == c) {
tile.floor0 = type;
modified = true;
}
if (tile.c1 != null && tile.c1.Instance == c) {
tile.floor1 = type;
modified |= true;
}
if (modified) {
AddModifiedChunk((ServerVC)chunks.Get(TileToChunkI(tileI)));
}
}
}
}
}
internal static int numcompare_core(Compartment s, Variable a1, P6any o1,
Variable a2, P6any o2, bool complex_ok)
{
int r1, r2;
P6any n1 = GetNumber(a1, o1, out r1);
P6any n2 = GetNumber(a2, o2, out r2);
if (r1 == NR_COMPLEX || r2 == NR_COMPLEX) {
if (!complex_ok)
throw new NieczaException("Complex numbers are not arithmetically ordered; use cmp if you want an arbitrary order");
Complex v1 = PromoteToComplex(r1, n1);
Complex v2 = PromoteToComplex(r2, n2);
if (double.IsNaN(v1.re) || double.IsNaN(v1.im) ||
double.IsNaN(v2.re) || double.IsNaN(v2.im))
return O_IS_UNORD;
else if (v1.re != v2.re)
return v1.re > v2.re ? O_IS_GREATER : O_IS_LESS;
else
return v1.im > v2.im ? O_IS_GREATER : v1.im < v2.im ? O_IS_LESS : O_IS_EQUAL;
}
else if (r1 == NR_FLOAT || r2 == NR_FLOAT) {
double d1 = PromoteToFloat(r1, n1);
double d2 = PromoteToFloat(r2, n2);
if (double.IsNaN(d1) || double.IsNaN(d2)) return O_IS_UNORD;
else return d1 > d2 ? O_IS_GREATER : d1 < d2 ? O_IS_LESS : O_IS_EQUAL;
}
else if (r1 == NR_FATRAT || r2 == NR_FATRAT) {
FatRat v1 = PromoteToFatRat(r1, n1);
FatRat v2 = PromoteToFatRat(r2, n2);
r1 = BigInteger.Compare(v1.num*v2.den, v2.num*v1.den);
}
else if (r1 == NR_FIXRAT || r2 == NR_FIXRAT) {
Rat v1 = PromoteToFixRat(r1, n1);
Rat v2 = PromoteToFixRat(r2, n2);
r1 = BigInteger.Compare(v1.num*v2.den, v2.num*v1.den);
}
else if (r1 == NR_BIGINT || r2 == NR_BIGINT) {
r1 = BigInteger.Compare(PromoteToBigInt(r1, n1),
PromoteToBigInt(r2, n2));
}
else
r1 = PromoteToFixInt(r1, n1).CompareTo(PromoteToFixInt(r2, n2));
return (r1 > 0) ? O_IS_GREATER : (r1 < 0) ? O_IS_LESS : O_IS_EQUAL;
}
// This function implements the actual looping part of autothreading
internal static Variable AutoThread(Compartment c, P6any j,
Func<Variable,Variable> dgt)
{
P6opaque j_ = (P6opaque)j;
P6any listObj = (P6any) j_.slots[1];
Variable[] list = Kernel.UnboxAny<Variable[]>(listObj);
Variable[] nlist = new Variable[list.Length];
for (int i = 0; i < list.Length; i++) {
nlist[i] = dgt(list[i]);
}
P6any newList = Kernel.BoxRaw(nlist, c.ParcelMO);
P6opaque newJunc = new P6opaque(c.JunctionMO);
newJunc.slots[0] = j_.slots[0];
newJunc.slots[1] = newList;
return newJunc;
}
internal static object UpCall(Compartment c, params object[] args)
{
return c.upcall_receiver[args];
}
// Type-check val against any, tracking state appropriately for
// junctions.
static void CheckSpecialArg(Compartment s, int ix, ref int pivot,
ref uint rank, P6any val)
{
if (val.mo.is_any) {
// fine as is
} else if (val.mo.HasType(s.JunctionMO)) {
int jtype = Kernel.UnboxAny<int>((P6any)(val as P6opaque).slots[0]) / 2;
if ((uint)jtype < rank) {
rank = (uint)jtype;
pivot = ix;
}
} else {
throw new NieczaException("Nominal type check failed for #" + ix +
" needed Any got " + val.mo.name);
}
}
// Unifies the MakeFixRat logic and tries to avoid a huge computation
// that will just be rounded away.
// Invariant: pow >= 0
static Variable RatPow(Compartment s, BigInteger num, BigInteger den, BigInteger pow)
{
if (den == -BigInteger.One) { den = BigInteger.One; num = -num; }
if (den == BigInteger.One) {
// den won't be getting any bigger
return s.MakeFixRat(big_pow(num, pow), 1);
}
// den >= 2
if (pow >= 64) {
// Overflow is inevitable.
return s.MakeFloat(Math.Pow(RatToFloat(num, den), (double)pow));
}
// we might consider detecting smaller overflows, but the penalty
// of $int ** 63 is not _that_ huge.
return s.MakeFixRat(big_pow(num, pow), big_pow(den, pow));
}
private static int substr_len(Compartment s, Variable v1, int pos, Variable v3)
{
P6any o1 = v1.Fetch(), o3 = v3.Fetch();
int r3;
if (o3.Does(s.CodeMO)) {
string s1 = o1.mo.mro_raw_Str.Get(v1);
Variable no3 = InvokeSub(o3, s.MakeInt(s1.Length));
r3 = (int)no3.Fetch().mo.mro_raw_Numeric.Get(no3) - pos;
} else {
r3 = (int)o3.mo.mro_raw_Numeric.Get(v3);
}
return r3;
}
private static int substr_pos(Compartment s, Variable v1, Variable v2)
{
P6any o1 = v1.Fetch(), o2 = v2.Fetch();
int r2;
if (o2.Does(s.CodeMO)) {
string s1 = o1.mo.mro_raw_Str.Get(v1);
Variable no2 = InvokeSub(o2, s.MakeInt(s1.Length));
r2 = (int)no2.Fetch().mo.mro_raw_Numeric.Get(no2);
} else {
r2 = (int)o2.mo.mro_raw_Numeric.Get(v2);
}
return r2;
}
