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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
 

Generated at April 19 2013
Version 1.3 Revision 424
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