Uses of Interface
sbrt.kernel.math.algebra.SparseDoubleMatrix

Packages that use SparseDoubleMatrix
sbrt.kernel.fba Provides classes and interfaces for creating objects relevant to Flux Balance Analysis. 
sbrt.kernel.fba.comp Provides classes and interfaces for performing Flux Balance Analysis computations. 
sbrt.kernel.fba.proc Provides classes and interfaces for executing Flux Balance Analysis processes. 
sbrt.kernel.math.algebra Provides classes and interfaces for creating objects relevant to algebra. 
sbrt.shell.io Provides classes and interfaces for reading and writing files. 
 

Uses of SparseDoubleMatrix in sbrt.kernel.fba
 

Methods in sbrt.kernel.fba that return SparseDoubleMatrix
 SparseDoubleMatrix<java.lang.String,java.lang.String> MixedFluxomeV1.getStoichMatrix()
          Returns the stoichiometry matrix of this fluxome.
 SparseDoubleMatrix<java.lang.String,java.lang.String> Fluxome.getStoichMatrix()
          Returns the stoichiometry matrix of this fluxome.
 SparseDoubleMatrix<java.lang.String,java.lang.String> IrrevRxnFluxomeV1.getStoichMatrix()
          Returns the stoichiometry matrix of this fluxome.
 

Uses of SparseDoubleMatrix in sbrt.kernel.fba.comp
 

Methods in sbrt.kernel.fba.comp that return SparseDoubleMatrix
 SparseDoubleMatrix<?,java.lang.String> CycleComputer.getCycles(F fluxome)
          Returns the set of all steady state cycles contained in the provided fluxome.
 SparseDoubleMatrix<?,java.lang.String> SlpCycleComputer.getCycles(IrrevRxnFluxome fluxome)
          Returns the set of all steady state cycles contained in the provided fluxome.
 SparseDoubleMatrix<?,java.lang.String> SlpExCurrComputerV2.getMatrix(IrrevRxnFluxome fluxome)
          Returns the extreme current matrix for the provided fluxome.
 SparseDoubleMatrix<?,java.lang.String> ExtremeCurrentComputer.getMatrix(IrrevRxnFluxome fluxome)
          Returns the extreme current matrix for the provided fluxome.
 SparseDoubleMatrix<?,java.lang.String> SlpExCurrComputerV2.getMatrix(IrrevRxnFluxome fluxome, MutableProgressMonitor pm)
          Returns the extreme current matrix for the provided fluxome.
 SparseDoubleMatrix<?,java.lang.String> ExtremeCurrentComputer.getMatrix(IrrevRxnFluxome fluxome, MutableProgressMonitor pm)
          Returns the extreme current matrix for the provided fluxome.
 

Uses of SparseDoubleMatrix in sbrt.kernel.fba.proc
 

Methods in sbrt.kernel.fba.proc that return SparseDoubleMatrix
 SparseDoubleMatrix<java.lang.String,java.lang.String> NetworkInfoProcess.Results.getStoichMatrix()
          Returns the stoichiometry matrix of the fluxome.
 

Uses of SparseDoubleMatrix in sbrt.kernel.math.algebra
 

Subinterfaces of SparseDoubleMatrix in sbrt.kernel.math.algebra
 interface SmdMatrix<R,C>
          This interface is used to represent sparse mutable matrices containing strictly double precision numbers as elements.
 

Classes in sbrt.kernel.math.algebra that implement SparseDoubleMatrix
 class AbstractSmdMatrix<R,C>
          This abstract class is a skeleton implementation of SmdMatrix.
 class HashMatrix<R,C>
          This class is a java.util.LinkedHashMap based implementation of SmdMatrix.
 class RowOrTreeMatrix<R extends Comparable<? super R>,C extends Comparable<? super C>>
          This class is a java.util.TreeMap based implementation of SmdMatrix.
 class SparseDoubleMatrixWrap<R,C>
          This class is used to wrap mutable matrices as an immutable SparseDoubleMatrix.
 class TreeMatrix<R extends Comparable<? super R>,C extends Comparable<? super C>>
          This class is a java.util.TreeMap based implementation of SmdMatrix.
 

Methods in sbrt.kernel.math.algebra that return SparseDoubleMatrix
 SparseDoubleMatrix<R,C> SparseDoubleMatrix.getColumn(java.lang.Object columnIndex)
          Returns the column corresponding to the provided column index.
 SparseDoubleMatrix<R,C> SparseDoubleMatrixWrap.getColumn(java.lang.Object columnIndex)
          Returns the column corresponding to the provided column index.
 SparseDoubleMatrix<R,C> SparseDoubleMatrix.getRow(java.lang.Object rowIndex)
          Returns the row corresponding to the provided row index.
 SparseDoubleMatrix<R,C> SparseDoubleMatrixWrap.getRow(java.lang.Object rowIndex)
          Returns the row corresponding to the provided row index.
 

Methods in sbrt.kernel.math.algebra with parameters of type SparseDoubleMatrix
<R,C,T> void
MatrixMultiplier.multiply(SparseDoubleMatrix<R,C> matrixA, SparseDoubleMatrix<C,T> matrixB, DoubleMatrixBuilder<R,T> product)
          Fills product with matrixA * matrixB.
<R,C,T> void
MatrixMultiplier.multiply(SparseDoubleMatrix<R,C> matrixA, SparseDoubleMatrix<C,T> matrixB, DoubleMatrixBuilder<R,T> product)
          Fills product with matrixA * matrixB.
 void SmdMatrix.setElements(SparseDoubleMatrix<? extends R,? extends C> m)
          Sets the corresponding elements of this matrix to those of the provided matrix.
 void AbstractSmdMatrix.setElements(SparseDoubleMatrix<? extends R,? extends C> m)
          Sets the corresponding elements of this matrix to those of the provided matrix.
 

Constructors in sbrt.kernel.math.algebra with parameters of type SparseDoubleMatrix
SparseDoubleMatrixWrap(SparseDoubleMatrix<R,C> m)
          Constructs a new wrapper around the provided matrix.
 

Uses of SparseDoubleMatrix in sbrt.shell.io
 

Methods in sbrt.shell.io that return SparseDoubleMatrix
static SparseDoubleMatrix<java.lang.Integer,java.lang.String> ComiFile.getMatrix(ComiFile<java.lang.String,java.lang.Double> file)
          Reads the provided column-oriented map input file and returns its contents as a sparse matrix.