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M

main(String[]) - Static method in class sbrt.ext.mma.algebra.MathematicaSolver
Used for testing purposes.
main(String[]) - Static method in class sbrt.ext.R.stat.RCorrelator
Used for testing purposes.
main(String[]) - Static method in class sbrt.kernel.math.HashLinearComb
Used for testing purposes.
main(String[]) - Static method in class sbrt.kernel.math.stat.comp.KendallTau
Tests the Kendall Tau A and B computers.
main(String[]) - Static method in class sbrt.kernel.math.stat.comp.MannWhitneyU
Used for testing.
main(String[]) - Static method in class sbrt.kernel.utilities.Util
Used for testing purposes.
main(String[]) - Static method in class sbrt.Sbrt
Parses the provided command line arguments and executes the application they specify.
main(String[]) - Static method in class sbrt.shell.proc.fba.MetatoolInputReader
Used for testing purposes.
main(String[]) - Static method in class sbrt.shell.text.fba.BiggBracketParserV1
Used for testing purposes.
MAJOR - Static variable in class sbrt.Sbrt
Indicates the major version number of the Systems Biology Research Tool.
make(Collection<String>, IrrevRxnFluxome) - Static method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns an irreversible reaction fluxome composed of the reactions in the provided fluxome with the names in the provided collection.
make(Collection<String>, MixedFluxome) - Static method in class sbrt.kernel.fba.MixedFluxomeV1
Returns a mixed fluxome composed of the reactions in the provided fluxome with the names in the provided collection.
make(LinearSystemSolution<V>, Map<? extends V, Interval>, double) - Static method in class sbrt.kernel.math.geom.HashConvexPolytope
Constructs a new convex poltyope from the provided linear system solution and variable bounds.
make(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.ProcessManagerFactory
Prints a formatted string representation of the provided input to the provided print writer and returns its corresponding process manager.
make(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.ProgramSolverFactory
Uses the information contained in the provided input to create a new program solver object.
makeFluxome(T) - Method in interface sbrt.kernel.fba.comp.FluxomeReducer
Returns a sub-fluxome of the one provided.
makeFluxome(IrrevRxnFluxome) - Method in class sbrt.kernel.fba.comp.MsFluxomeReducer
Returns the sub-fluxome resulting from network reduction.
makeFluxome(IrrevRxnFluxome) - Method in class sbrt.kernel.fba.comp.WwFluxomeReducer
Returns the sub-fluxome resulting from network reduction.
ManagerInput<K,V> - Interface in sbrt.shell.mng
This interface is used to represent the input to KernelProcessManager objects.
MannWhitneyResults - Class in sbrt.kernel.math.stat.comp
This class is used to store the results of a Mann-Whitney U test.
MannWhitneyResults(double, double, int, int) - Constructor for class sbrt.kernel.math.stat.comp.MannWhitneyResults
Constructs a new set of results for a Mann-Whitney U test.
MannWhitneyResults(double, int, int) - Constructor for class sbrt.kernel.math.stat.comp.MannWhitneyResults
Constructs a new set of results for a Mann-Whitney U test.
MannWhitneyU - Class in sbrt.kernel.math.stat.comp
This class is used to compute Mann-Whitney U statistics.
MannWhitneyU() - Constructor for class sbrt.kernel.math.stat.comp.MannWhitneyU
 
MannWhitneyUManager - Class in sbrt.shell.mng.stat
This class is used to manage Mann-Whitney tests.
MannWhitneyUManager() - Constructor for class sbrt.shell.mng.stat.MannWhitneyUManager
 
MapEntryFormat<K,V> - Interface in sbrt.shell.text
This interface is used to represent formats for map entries.
MapFormat<K,V> - Interface in sbrt.shell.text
This interface is used to represent formats for maps.
MapInputFile<K,V> - Interface in sbrt.shell.io
This interface is used to represent input files that contain maps.
MapManagerInput<K,V> - Class in sbrt.shell.mng
This class is a concrete implemenation of ManagerInput.
MapManagerInput(Map<K, V>, String) - Constructor for class sbrt.shell.mng.MapManagerInput
Constructs a new manager input from the provided map and name.
MapManagerInput(Map<K, V>) - Constructor for class sbrt.shell.mng.MapManagerInput
Constructs a new manager input from the provided map with a null name.
MapOutputFile<K,V> - Interface in sbrt.shell.io
This interface is used to represent output files that maps can be written to.
MapTextFile<K,V> - Interface in sbrt.shell.io
This interface is used to represent text-based files that contain maps.
MapTextInputFile<K,V> - Interface in sbrt.shell.io
This interface is used to represent text-based input files that contain maps.
MapTextOutputFile<K,V> - Interface in sbrt.shell.io
This interface is used to represent output files that maps can be written to as text.
MathematicaException - Exception in sbrt.ext.mma
This class is used to wrap exceptions thrown by Mathematica.
MathematicaException(MathLinkException) - Constructor for exception sbrt.ext.mma.MathematicaException
Constructs an external software exception.
MathematicaException(String, MathLinkException) - Constructor for exception sbrt.ext.mma.MathematicaException
Constructs an external software exception.
MathematicaSolver<V> - Class in sbrt.ext.mma.algebra
This class is used to solve systems of linear equations using Mathematica.
MathematicaSolver(String[]) - Constructor for class sbrt.ext.mma.algebra.MathematicaSolver
Creates a new linear system solver.
MathematicaSolver(String) - Constructor for class sbrt.ext.mma.algebra.MathematicaSolver
Creates a new linear system solver.
MathExpr<V> - Interface in sbrt.kernel.math
This interface is used to represent mathematical expressions.
MathExprFormat<E extends MathExpr<V>,V> - Interface in sbrt.shell.text.math
This interface is used to represent formats for linear combinations.
Matrix<R,C,E> - Interface in sbrt.kernel.math.algebra
This interface is used to represent matrices.
MatrixBuilder<R,C,E> - Interface in sbrt.kernel.math.algebra
This interface is used to represent mutable matrices.
MatrixConverterManager - Class in sbrt.shell.mng.algebra
This class is used to convert matrices to linear combinations.
MatrixConverterManager() - Constructor for class sbrt.shell.mng.algebra.MatrixConverterManager
 
MatrixElement<R,C,E> - Class in sbrt.kernel.math.algebra
This class is used to represent matrix elements.
MatrixElement(S, T, U) - Constructor for class sbrt.kernel.math.algebra.MatrixElement
Constructs a new matrix element.
MatrixElement(IndexPair<R, C>, U) - Constructor for class sbrt.kernel.math.algebra.MatrixElement
Constructs a new matrix element.
MatrixElementFormat<R,C,E> - Interface in sbrt.shell.text.math
This interface is used to represent formats for matrix elements.
MatrixElementFormatV1<R,C> - Class in sbrt.shell.text.math
This class is a concrete implementation of MatrixElementFormat.
MatrixElementFormatV1(SimpleFormat<R>, SimpleFormat<C>) - Constructor for class sbrt.shell.text.math.MatrixElementFormatV1
Constructs a new matrix element format.
MatrixMultiplier - Class in sbrt.kernel.math.algebra
This class is used to multiply matrices.
MatrixMultiplier() - Constructor for class sbrt.kernel.math.algebra.MatrixMultiplier
 
MatrixTransposer - Class in sbrt.kernel.math.algebra
This class is used to transpose matrices.
MatrixTransposer() - Constructor for class sbrt.kernel.math.algebra.MatrixTransposer
 
MatrixWrap<R,C,E> - Class in sbrt.kernel.math.algebra
This class is used to wrap mutable matrices as an immutable matrix.
MatrixWrap(Matrix<R, C, E>) - Constructor for class sbrt.kernel.math.algebra.MatrixWrap
Constructs a new wrapper around the provided matrix.
MAX_OBSTRUCTED_MOVES - Static variable in class sbrt.shell.mng.geom.CdHarManager
The keyword used to denote the maximum number of obstructed moves to allow.
METATOOL_INPUT_FILE - Static variable in class sbrt.shell.mng.fba.MetatoolOutputReaderManager
The keyword used to denote a Metatool input file.
METATOOL_OUTPUT_FILE - Static variable in class sbrt.shell.mng.fba.MetatoolOutputReaderManager
The keyword used to denote a Metatool output file.
MetatoolInputReader - Class in sbrt.shell.proc.fba
This class is used to parse Metatool input files for the purpose of converting them to FBA Reaction Files.
MetatoolInputReader.Results - Class in sbrt.shell.proc.fba
This class is used to store the results of parsing a Metatool input file.
MetatoolInputReaderManager - Class in sbrt.shell.mng.fba
This class is used to manage the conversion of input files for Metatool into SBRT FBA Reaction Files.
MetatoolInputReaderManager() - Constructor for class sbrt.shell.mng.fba.MetatoolInputReaderManager
 
MetatoolInputWriter - Class in sbrt.shell.proc.fba
This class is used to write input files for Metatool.
MetatoolInputWriter() - Constructor for class sbrt.shell.proc.fba.MetatoolInputWriter
Creates a new Metatool input file writer.
MetatoolInputWriterManager - Class in sbrt.shell.mng.fba
This class is used to manage the writing of input files for Metatool.
MetatoolInputWriterManager() - Constructor for class sbrt.shell.mng.fba.MetatoolInputWriterManager
 
MetatoolOutputReader - Class in sbrt.shell.proc.fba
This class is used to parse Metatool output files for the purpose of creating SBRT compliant files.
MetatoolOutputReader() - Constructor for class sbrt.shell.proc.fba.MetatoolOutputReader
Creates a new Metatool output file reader.
MetatoolOutputReaderManager - Class in sbrt.shell.mng.fba
This class is used to manage the writing of input files for Metatool.
MetatoolOutputReaderManager() - Constructor for class sbrt.shell.mng.fba.MetatoolOutputReaderManager
 
METEXT - Static variable in class sbrt.shell.proc.fba.MetatoolInputReader
The Metatool keyword -METEXT.
METINT - Static variable in class sbrt.shell.proc.fba.MetatoolInputReader
The Metatool keyword -METINT.
MIN_CHORD_LENGTH - Static variable in class sbrt.shell.mng.geom.CdHarManager
The keyword used to denote the minimum chord length.
MINOR - Static variable in class sbrt.Sbrt
Indicates the minor version number of the Systems Biology Research Tool.
MissingVariableException - Exception in sbrt.kernel.math
This class is used to indicate that a varible is missing.
MissingVariableException(Object) - Constructor for exception sbrt.kernel.math.MissingVariableException
Constructs an exception to indicate the provided variable is missing.
MixedFluxome - Interface in sbrt.kernel.fba
This interface is used to represent fluxomes that contain multiple types of chemical reactions.
MixedFluxomeFormatV1 - Class in sbrt.shell.text.fba
This class is used to format irreversible reaction fluxome files.
MixedFluxomeFormatV1() - Constructor for class sbrt.shell.text.fba.MixedFluxomeFormatV1
Constructs a new irreversible reaction fluxome format.
MixedFluxomeV1 - Class in sbrt.kernel.fba
This class is a concrete implementation of MixedFluxome.
MixedFluxomeV1(Map<String, ? extends ChemRxn>, Map<String, Or<And<String>>>) - Constructor for class sbrt.kernel.fba.MixedFluxomeV1
Constructs a new mixed fluxome from the provided internal and exchange reactions and catalysts.
MixedFluxomeV1(Map<String, ? extends ChemRxn>) - Constructor for class sbrt.kernel.fba.MixedFluxomeV1
Constructs a new mixed fluxome from the provided internal and exchange reactions.
MMaExprInterpretter - Class in sbrt.ext.mma.algebra
This class is intended for use solely by the class MathematicaSolver.
MonitoredProcess<R> - Interface in sbrt.kernel
This interface is used to represent monitored processes.
MsFluxIntervalComputer<F extends IrrevRxnFluxome> - Class in sbrt.kernel.fba.comp
This class is used to compute Mahadevan-Schilling flux intervals.
MsFluxIntervalComputer(FbaOptimizer<F>, Map<String, Set<LinearComb<String>>>) - Constructor for class sbrt.kernel.fba.comp.MsFluxIntervalComputer
Constructs a new Mahadevan-Schilling flux interval computer.
MsFluxIntervalComputer(FbaOptimizer<F>, Map<String, Set<LinearComb<String>>>, double) - Constructor for class sbrt.kernel.fba.comp.MsFluxIntervalComputer
Constructs a new Mahadevan-Schilling flux interval computer.
MsFluxIntervalManager - Class in sbrt.shell.mng.fba
This class is used to manage Mahadevan-Schilling flux interval processes.
MsFluxIntervalManager() - Constructor for class sbrt.shell.mng.fba.MsFluxIntervalManager
 
MsFluxomeReducer - Class in sbrt.kernel.fba.comp
This class is used to reduce the size of fluxomes for the purpose of identifying the steady state cycles they contain.
MsFluxomeReducer(ProgramSolver<Object, Object>) - Constructor for class sbrt.kernel.fba.comp.MsFluxomeReducer
Constructs a fluxome reducer from the provided linear program solver.
MsFluxomeReducerManager - Class in sbrt.shell.mng.fba
This class is used to manage the MS fluxome reduction algorithm.
MsFluxomeReducerManager() - Constructor for class sbrt.shell.mng.fba.MsFluxomeReducerManager
 
MultiOutputFiles<F extends OutputFile<R>,R> - Class in sbrt.shell.io
This class is used to create multiple output files.
MultiOutputFiles(Iterator<F>) - Constructor for class sbrt.shell.io.MultiOutputFiles
Constructs a new multiple output files results manager.
MultipleCorrelationAnalysis<V,T extends CorrResult> - Class in sbrt.kernel.math.stat.proc
This class is used to perform multiple correlation analyses.
MultipleCorrelationAnalysis(Correlator<V, T>) - Constructor for class sbrt.kernel.math.stat.proc.MultipleCorrelationAnalysis
Constructs a new correlation process.
MultipleVectorsConverterManager - Class in sbrt.shell.mng.algebra
This class is used to convert files containing multiple vectors into a series of files, each containing a single vector.
MultipleVectorsConverterManager() - Constructor for class sbrt.shell.mng.algebra.MultipleVectorsConverterManager
 
multiply(SparseDoubleMatrix<R, C>, SparseDoubleMatrix<C, T>, DoubleMatrixBuilder<R, T>) - Method in class sbrt.kernel.math.algebra.MatrixMultiplier
Fills product with matrixA * matrixB.
multiply(double) - Method in class sbrt.kernel.math.HashLinearComb
Multiplies this linear combination by the provided constant.
multiply(double) - Method in interface sbrt.kernel.math.LinearComb
Multiplies this linear combination by the provided constant.
MutableProgressMonitor - Interface in sbrt.kernel.utilities
This interface is used to represent mutable progress montiors.
MwUAnalysis<V> - Class in sbrt.kernel.math.stat.proc
This class is used to perform Mann-Whitney U tests.
MwUAnalysis() - Constructor for class sbrt.kernel.math.stat.proc.MwUAnalysis
Constructs a new Mann-Whitney U analysis.

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