public void PrintSubDataType(int indnt, StreamWriter writer, IBoolean s)
{
if (s != null)
{
indent(indnt, writer); writer.Write("<IBoolean/>\n");
}
}
public sdwSSA(ModelInfo modelinfo, double duration, int repeats, int samples)
: base(modelinfo, duration, repeats, samples)
{
Configuration config = Configuration.CurrentConfiguration;
_reactions = new StateDependentReactionSet(model.Reactions, _gammaSize);
_trajectoryCounter = 0;
_runningMean = 0.0;
_runningVariance = 0.0;
_crossEntropyRuns = config.GetParameterWithDefault("sdwSSA.crossEntropyRuns", 100000);
_crossEntropyThreshold = config.GetParameterWithDefault("sdwSSA.crossEntropyThreshold", 0.01);
_crossEntropyMinDataSize = config.GetParameterWithDefault("sdwSSA.crossEntropyMinDataSize", 200);
_reExpressionName = config.GetParameterWithDefault("sdwSSA.reExpressionName", "reExpression");
_reValName = config.GetParameterWithDefault("sdwSSA.reValName", "reVal");
_gammaSize = config.GetParameterWithDefault("sdwSSA.gammaSize", 15);
_binCountThreshold = config.GetParameterWithDefault("sdwSSA.binCount", 20);
_reExpression = model.Expressions.FirstOrDefault(e => e.Name == _reExpressionName);
_rareEventValue = 0.0;
_rareEventTest = new EqualTo(_reExpression, new ConstantValue(_rareEventValue));
_gamma = new List <double[]>();
_propensityCutoff = new List <double[]>();
_gammaIndex = new int[_reactions.NumReactions];
_binIndex = new int[_reactions.NumReactions];
_biasingParametersFileName = config.GetParameterWithDefault("sdwSSA.biasingParametersFileName", modelinfo.Name + "_biasingParameters.json");
_biasingParametersFlag = (String.CompareOrdinal(_biasingParametersFileName, modelinfo.Name + "_biasingParameters.json") == 0);
_biasingParameters = _biasingParametersFlag ? new BiasingParameters() : BiasingParametersDeserializer.ReadParametersFromJsonFile(_biasingParametersFileName);
_outputFileName = config.GetParameterWithDefault("sdwSSA.outputFileName", modelInfo.Name + "_sdwSSA_1e" + Math.Log(SamplingParams.RealizationCount, 10) + ".txt");
}
protected BinaryBooleanOp(IBooleanOperator firstArgument, IBooleanOperator secondArgument)
{
_operatorA = firstArgument;
_operatorB = secondArgument;
ArgumentA = null;
ArgumentB = null;
}
public IBoolean ResolveReferences(IDictionary <string, IBoolean> bmap, IDictionary <string, IValue> nmap)
{
if (Argument == null)
{
Argument = _argument.ResolveReferences(bmap, nmap);
}
return(GetValue());
}
public void GreaterThanTest()
{
IBoolean greaterThanTrue = (new GreaterThanOperator(_twentyTwo, _twenty)).ResolveReferences(null, null);
IBoolean greaterThanFalse = (new GreaterThanOperator(_twenty, _twentyTwo)).ResolveReferences(null, null);
Console.WriteLine("Testing GreaterThan() expressions...");
Console.WriteLine();
Expect(greaterThanTrue.Value);
Expect(!greaterThanFalse.Value);
}
public BooleanStatementBuilder Or(IBoolean statement)
{
if (Component == null)
{
Component = statement;
}
else
{
Component = new OrStatement(Component, statement.Wrap());
}
return(this);
}
public void NotEqualToTest()
{
IBoolean notEqualTo1 = (new NotEqualToOperator(_twenty, _twenty)).ResolveReferences(null, null);
IBoolean notEqualTo2 = (new NotEqualToOperator(_twenty, _twentyTwo)).ResolveReferences(null, null);
IBoolean notEqualTo3 = (new NotEqualToOperator(_twentyTwo, _twenty)).ResolveReferences(null, null);
Console.WriteLine("Testing NotEqualTo() expressions...");
Console.WriteLine();
Expect(!notEqualTo1.Value);
Expect(notEqualTo2.Value);
Expect(notEqualTo3.Value);
}
public void GreaterThanOrEqualTest()
{
IBoolean greaterThanOrEqual1 = (new GreaterThanOrEqualOperator(_twenty, _twenty)).ResolveReferences(null, null);
IBoolean greaterThanOrEqual2 = (new GreaterThanOrEqualOperator(_twenty, _twentyTwo)).ResolveReferences(null, null);
IBoolean greaterThanOrEqual3 = (new GreaterThanOrEqualOperator(_twentyTwo, _twenty)).ResolveReferences(null, null);
Console.WriteLine("Testing GreaterThanOrEqual() expressions...");
Console.WriteLine();
Expect(greaterThanOrEqual1.Value);
Expect(!greaterThanOrEqual2.Value);
Expect(greaterThanOrEqual3.Value);
}
public void Initialize()
{
CheckParameters();
_rareEventValue = model.Parameters.First(p => p.Name == _reValName).Value;
_rareEventTest = new EqualTo(_reExpression, new ConstantValue(_rareEventValue));
SetRareEventType();
if (!Configuration.CurrentConfiguration.HasParameter("dwSSA.gamma"))
{
Console.WriteLine("Biasing parameters not found. Starting multilevel cross entropy simulation with " + _crossEntropyRuns + " realizations...");
RunCrossEntropy();
}
}
public IBoolean ResolveReferences(IDictionary <string, IBoolean> bmap, IDictionary <string, IValue> nmap)
{
if (_value == null)
{
_value = _rootOperator.ResolveReferences(bmap, nmap);
if (_name != null)
{
bmap.Add(_name, _value);
}
}
return(_value);
}
public IBoolean[] Provide()
{
IBoolean[] booleans = new IBoolean[this._booleans.Length + this._conditions.Length];
int a = 0;
this._booleans.CopyTo(booleans, a);
a += this._booleans.Length;
this._conditions.CopyTo(booleans, a);
a += this._conditions.Length;
return(booleans);
}
public IBoolean ResolveReferences(IDictionary <string, IBoolean> bmap, IDictionary <string, IValue> nmap)
{
if (ArgumentA == null)
{
ArgumentA = _operatorA.ResolveReferences(bmap, nmap);
}
if (ArgumentB == null)
{
ArgumentB = _operatorB.ResolveReferences(bmap, nmap);
}
return(GetValue());
}
protected virtual string Boolean(IBoolean boolean)
{
if (boolean is True)
{
return("1");
}
else if (boolean is False)
{
return("0");
}
else
{
throw new Exception("不可识别的bool类型。");
}
}
public void TestBooleanAnd()
{
IBoolean andTrueTrue = (new And(new BooleanTrue(), new BooleanTrue()));
IBoolean andTrueFalse = (new And(new BooleanTrue(), new BooleanFalse()));
IBoolean andFalseTrue = (new And(new BooleanFalse(), new BooleanTrue()));
IBoolean andFalseFalse = (new And(new BooleanFalse(), new BooleanFalse()));
Console.WriteLine("Testing And() expressions...");
Console.WriteLine();
Expect(andTrueTrue.Value);
Expect(!andTrueFalse.Value);
Expect(!andFalseTrue.Value);
Expect(!andFalseFalse.Value);
}
public void Initialize()
{
CheckParameters();
_rareEventValue = model.Parameters.First(p => p.Name == _reValName).Value;
_rareEventTest = new EqualTo(_reExpression, new ConstantValue(_rareEventValue));
SetRareEventType();
if (_biasingParametersFlag)
{
for (int i = 0; i < _reactions.NumReactions; i++)
{
_gamma.Add(new double[_gammaSize]);
_propensityCutoff.Add(new double[_gammaSize - 1]);
}
_biasingParameters.RareEvent.ExpressionLocale = "global";
_biasingParameters.RareEvent.ExpressionName = _reExpressionName;
foreach (var locale in modelInfo.Locales)
{
var newLocaleInfo = new BiasingParameters.LocaleInfo {
Name = locale.Name
};
var newReactionInfo = newLocaleInfo.Reactions;
LocaleInfo testLocale = locale;
var reactions = modelInfo.Reactions.Where(r => r.Locale == testLocale);
newReactionInfo.AddRange(reactions.Select(reaction => new BiasingParameters.ReactionInfo {
Name = reaction.Name
}));
_biasingParameters.Locales.Add(newLocaleInfo);
}
}
else
{
for (int i = 0; i < _reactions.NumReactions; i++)
{
var localeIndex = LocaleIndex(_reactions.Reactions[i]);
var reactionIndex = ReactionIndex(_reactions.Reactions[i], localeIndex);
var tempRareEvent = _biasingParameters.Locales[localeIndex].Reactions[reactionIndex].RareEvents[_biasingParameters.RareEvent.IntermediateRareEventCount - 1];
_gamma.Add(tempRareEvent.Gammas);
_propensityCutoff.Add(tempRareEvent.Thresholds);
}
}
}
public void BooleanExpressionTreeTest()
{
const string name = "bit";
IBooleanOperator expression = new GreaterThanOperator(Three, Two);
var bet = new BooleanExpressionTree(name, expression);
Console.Write("Created new BooleanExpressionTree: ");
Console.WriteLine(bet);
Console.WriteLine("BooleanExpressionTreeTest: test Name property...");
Expect(bet.Name == name);
Console.WriteLine("BooleanExpressionTreeTest: test expression and ResolveReferences()...");
IDictionary <string, IBoolean> bmap = new Dictionary <string, IBoolean>();
IBoolean predicate = bet.ResolveReferences(bmap, null);
Expect(predicate.Value == true);
Console.WriteLine("BooleanExpressionTreeTest: testing map size (1)...");
Expect(bmap.Count == 1);
Console.WriteLine("BooleanExpressionTreeTest: testing map contents...");
Expect(bmap[name] == predicate);
}
public dwSSA(ModelInfo modelInfo, float duration, int repeats, int samples)
: base(modelInfo, duration, repeats, samples)
{
Configuration config = Configuration.CurrentConfiguration;
_reactions = new ReactionSet(model.Reactions);
_trajectoryCounter = 0;
_runningMean = 0.0;
_runningVariance = 0.0;
_crossEntropyRuns = config.GetParameterWithDefault("dwSSA.crossEntropyRuns", 100000);
_crossEntropyThreshold = config.GetParameterWithDefault("dwSSA.crossEntropyThreshold", 0.01f);
_crossEntropyMinDataSize = config.GetParameterWithDefault("dwSSA.crossEntropyMinDataSize", 200);
_reExpressionName = config.GetParameterWithDefault("dwSSA.reExpressionName", "reExpression");
_reValName = config.GetParameterWithDefault("dwSSA.reValName", "reVal");
_reExpression = model.Expressions.FirstOrDefault(e => e.Name == _reExpressionName);
_rareEventValue = 0.0f;
_rareEventTest = new EqualTo(_reExpression, new ConstantValue(_rareEventValue));
_gamma = config.GetParameterWithDefault("dwSSA.gamma", new double[_reactions.NumReactions]);
_outputFileName = config.GetParameterWithDefault("dwSSA.outputFileName", modelInfo.Name + "_dwSSA_1e" + Math.Log(SamplingParams.RealizationCount, 10) + ".txt");
}
public void SetValueFromDialog(ValueUI valueUI, IValue value)
{
SetValueDialog setDialog = Instantiate(_resourceProvider.SetValueDialog, _dialogLayer);
string inputValue = "0";
bool isNumber = true;
INumber number = value as INumber;
if (number != null)
{
inputValue = number.Value.ToString();
}
IBoolean boolean = value as IBoolean;
if (boolean != null)
{
inputValue = boolean.IsTrue ? "1" : "0";
isNumber = false;
}
setDialog.Init("Set Constant", inputValue);
setDialog.OnOk.AddListener(
(valueString) =>
{
if (isNumber)
{
if (float.TryParse(valueString, out float floatValue))
{
FloatConstant constant = number as FloatConstant;
if (constant != null)
{
number.Value = floatValue;
}
else
{
constant = new FloatConstant();
constant.Value = floatValue;
_cursorTool.SetLabelTarget.Value = constant;
if (_cursorTool.SetLabelTarget.Value.Parent == null)
{
_cursorTool.SetLabelValueUi.Value = _cursorTool.SetLabelTarget.Value;
}
}
}
}
else
{
if (float.TryParse(valueString, out float floatValue))
{
BoolConstant constant = boolean as BoolConstant;
if (constant != null)
{
boolean.IsTrue = floatValue != 0;
}
else
{
constant = new BoolConstant();
constant.IsTrue = floatValue != 0;
_cursorTool.SetLabelTarget.Value = constant;
if (_cursorTool.SetLabelTarget.Value.Parent == null)
{
_cursorTool.SetLabelValueUi.Value = _cursorTool.SetLabelTarget.Value;
}
}
}
}
valueUI.RebuildAnValue();
});
}
public Join(TabularDataSource source, IBoolean expression)
{
this.joinType = JoinType.Inner;
this.source = source;
this.expression = expression;
}
public OrStatement(IBoolean lStatement, IBoolean rStatement)
: base(lStatement, rStatement, Keywords.Or)
{
}
public Predicate(BooleanExpressionTree expressionTree, IDictionary <string, IBoolean> bmap, IDictionary <string, IValue> nmap)
{
_tree = expressionTree;
_expression = expressionTree.ResolveReferences(bmap, nmap);
}
public BooleanExpression(IBoolean a = null, IBoolean b = null, Operator op = Operator.Or)
{
A = a;
B = b;
OP = op;
}
public AndStatement(IBoolean lStatement, IBoolean rStatement)
: base(lStatement, rStatement, Keywords.And)
{
}
public Constraint(ConstraintInfo info, IDictionary <string, IBoolean> bmap, IDictionary <string, IValue> nmap)
{
_info = info;
_predicate = info.Predicate.ResolveReferences(bmap, nmap);
}
public TriggeredEvent(TriggeredEventInfo eventInfo, IDictionary <string, IBoolean> bmap, IDictionary <string, IValue> nmap, IDictionary <string, IUpdateable> umap) :
base(eventInfo, nmap, umap)
{
_predicate = eventInfo.Predicate.ResolveReferences(bmap, nmap);
Repeats = eventInfo.Repeats;
}
public Join(JoinType joinType, TabularDataSource source, IBoolean expression)
{
this.joinType = joinType;
this.source = source;
this.expression = expression;
}
public JoinBuilder(Table mainTable, IBoolean onStatement)
{
MainTable = mainTable;
_statement = onStatement;
}
protected BinaryBooleanOperation(IBoolean argA, IBoolean argB)
{
ArgumentA = argA;
ArgumentB = argB;
}
public And(IBoolean argA, IBoolean argB) : base(argA, argB)
{
}
public Xor(IBoolean argA, IBoolean argB) : base(argA, argB)
{
}
