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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.
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
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C
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