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main(String[]) - Static method in class org.simulator.About

main(String[]) - Static method in class org.simulator.sbml.ConstraintTest

main(String[]) - Static method in class org.simulator.SBMLTestSuiteRunner

Input: directory with models (containing the SBML test suite), first model to be simulated, last model to be simulated, SBMLTestSuiteRunner.Options.all (for testing the models of the test suite with all given integrators) or SBMLTestSuiteRunner.Options.sedml (for testing the models of the test suite using the given SED-ML files) or nothing (for testing the models of the test suite with the RosenbrockSolver solver, should produce only successful tests)

main(String[]) - Static method in class org.simulator.SBMLTestSuiteWrapper

main(String[]) - Static method in class org.simulator.SimulatorTest

Starts a simulation at the command line.

main(String[]) - Static method in class org.simulator.TestBiomodels

* Input: directory with models (containing the biomodels), first model to be simulated, last model to be simulated,

ManhattanDistance - Class in org.simulator.math

Class for computation of the Manhattan distance of two vectors.

ManhattanDistance() - Constructor for class org.simulator.math.ManhattanDistance

Initializes a new distance object

mantissa - Variable in class org.simulator.sbml.astnode.ASTNodeValue

The mantissa of the corresponding ASTNode

math - Variable in class org.simulator.sbml.astnode.FunctionValue

The math of the function definition.

Mathematics - Class in org.simulator.math

This class contains a collection of mathematical functions like the faculty, logarithms and several trigonometric functions.

Mathematics() - Constructor for class org.simulator.math.Mathematics

MatrixOperations - Class in org.simulator.math

Class used to perform matrix operations, focusing on finding vector solutions to the vector equation F(x) = 0.

MatrixOperations() - Constructor for class org.simulator.math.MatrixOperations

MatrixOperations.MatrixException - Exception in org.simulator.math

This exception is thrown when errors in the computation of matrix-related solutions, their eigenvalues or eigenvectors.

MatrixOperations.MatrixException() - Constructor for exception org.simulator.math.MatrixOperations.MatrixException

Constructor for MatrixException

MatrixOperations.MatrixException(String) - Constructor for exception org.simulator.math.MatrixOperations.MatrixException

Constructor for MatrixException with message

MeanFunction - Class in org.simulator.math

In this class functions for the computation of an overall distance based on the distance values determined for each column of a table are defined.

MeanFunction() - Constructor for class org.simulator.math.MeanFunction

meanFunction - Variable in class org.simulator.math.QualityMeasure

metric - Variable in class org.simulator.math.Relative_N_Metric

The metric the relative distance is based on.

min(int, int, int) - Static method in class org.simulator.math.Mathematics

This just computes the minimum of three integer values.

minus(ASTNodeValue[], int, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

MinusValue - Class in org.simulator.sbml.astnode

This class can compute and store the value of a minus node.

MinusValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.MinusValue

model - Variable in class org.simulator.sbml.SBMLinterpreter

The model to be simulated.

MultiTable - Class in org.simulator.math.odes

This data structure contains the an array of sorted time points and a matrix organized in one column per quantity for which data (measurement or simulation) are gathered.

MultiTable() - Constructor for class org.simulator.math.odes.MultiTable

Constructs an empty MultiTable object.

MultiTable(double[], double[][], String[]) - Constructor for class org.simulator.math.odes.MultiTable

Constructs a data object for the given values.

MultiTable(double[], double[][], String[], String[]) - Constructor for class org.simulator.math.odes.MultiTable

MultiTable.Block - Class in org.simulator.math.odes

A MultiTable.Block is a data structure with a two-dimensional double array of actual data together with identifiers for each column.

MultiTable.Block.Column - Class in org.simulator.math.odes

A column of the MultiTable.Block matrix.

MultTableSEDMLWrapper - Class in org.simulator.sedml

This class adapts the native results to an interface that the SED-ML processor can use to post-process results.

MultTableSEDMLWrapper(MultiTable) - Constructor for class org.simulator.sedml.MultTableSEDMLWrapper