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T

TabListFormat<E> - Class in sbrt.shell.text
This class is used to define a format for tab-delimited lists.
TabListFormat(SimpleFormat<E>) - Constructor for class sbrt.shell.text.TabListFormat
Constructs a new tab-delimited list format with the provided element format.
TabListFormat(Formatter<E>, Parser<E>) - Constructor for class sbrt.shell.text.TabListFormat
Constructs a new tab-delimited list format with the provided element format.
TabSetFormat<E> - Class in sbrt.shell.text
This class is used to define a format for tab-delimited sets.
TabSetFormat(SimpleFormat<E>) - Constructor for class sbrt.shell.text.TabSetFormat
Constructs a new tab-delimited set format with the provided element format.
TabSetFormat(Formatter<E>, Parser<E>) - Constructor for class sbrt.shell.text.TabSetFormat
Constructs a new tab-delimited set format with the provided element format.
TAU_A - Static variable in class sbrt.shell.mng.stat.KendallTauManager
The value used to denote a Kendall's TauA correlation coefficient.
TAU_B - Static variable in class sbrt.shell.mng.stat.KendallTauManager
The value used to denote a Kendall's TauB correlation coefficient.
TauResult - Class in sbrt.kernel.math.stat.comp
This class is used to store the results of a correlation computation.
TauResult(double, double, int) - Constructor for class sbrt.kernel.math.stat.comp.TauResult
Constructs a new correlation results.
Taxicab - Class in sbrt.kernel.math.geom.comp
This class is used to compute Taxicab distances.
Taxicab() - Constructor for class sbrt.kernel.math.geom.comp.Taxicab
 
terms() - Method in class sbrt.kernel.math.HashLinearComb
Returns the number of terms contained in this linear combination.
terms() - Method in interface sbrt.kernel.math.Polynomial
Returns the number of terms contained in this polynomial.
TEXT - Static variable in class sbrt.shell.io.FileFormat
Used to denote a plain-text file.
TextAreaOutputStream - Class in sbrt.shell.gui
An output stream that writes its output to a javax.swing.JTextArea control.
TextAreaOutputStream(JTextArea) - Constructor for class sbrt.shell.gui.TextAreaOutputStream
Creates a new instance of TextAreaOutputStream which writes to the specified instance of javax.swing.JTextArea control.
TextFileLineIterator<E> - Class in sbrt.shell.io
This class is used to iterate over the lines of an input file.
TextFileLineIterator(TextInputFile<E>) - Constructor for class sbrt.shell.io.TextFileLineIterator
Constructs a new text file line iterator using the provided text input file.
TextInputFile<E> - Class in sbrt.shell.io
This class is used to read input files containing text.
TextInputFile(String, Parser<E>) - Constructor for class sbrt.shell.io.TextInputFile
Constructs a new text input file using the provided arguments.
TextInputFile(String, FileFormat, Parser<E>) - Constructor for class sbrt.shell.io.TextInputFile
Constructs a new text input file using the provided arguments.
TextInputFile(String, FileFormat, Parser<E>, Collection<Character>) - Constructor for class sbrt.shell.io.TextInputFile
Constructs a new text input file using the provided arguments.
TextOutputFile<T> - Class in sbrt.shell.io
This class is used to represent output files containing plain text.
TextOutputFile(String, Formatter<T>) - Constructor for class sbrt.shell.io.TextOutputFile
Constructs a new text output file using the provided arguments.
TextOutputFile(String, FileFormat, Formatter<T>) - Constructor for class sbrt.shell.io.TextOutputFile
Constructs a new text output file using the provided arguments.
TextPaneGui - Class in sbrt.shell.gui
This class is used to create a GUI for the SBRT.
TextPaneGui() - Constructor for class sbrt.shell.gui.TextPaneGui
Constructs a new text pane GUI for the SBRT.
TextPaneOutputStream - Class in sbrt.shell.gui
An output stream that writes its output to a javax.swing.JTextPane.
TextPaneOutputStream(JTextPane, String) - Constructor for class sbrt.shell.gui.TextPaneOutputStream
Creates a new instance of TextAreaOutputStream which writes to the specified instance of javax.swing.JTextArea control.
TILDE - Static variable in class sbrt.shell.text.SpecialChars
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toArray() - Method in class sbrt.kernel.math.graph_theory.Path
Returns an array representation of this path.
toArray() - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.toArray().
toArray(T[]) - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.toArray(Object[]).
toArray() - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.toArray().
toArray(T[]) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.toArray(Object[]).
toArray() - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.toArray().
toArray(T[]) - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.toArray(Object[]).
toLinearCombs() - Method in class sbrt.kernel.math.algebra.AbstractSmdMatrix
Returns this matrix as a list of linear combinations.
toLinearCombs() - Method in interface sbrt.kernel.math.algebra.DoubleMatrix
Returns this matrix as a list of linear combinations.
toLinearCombs() - Method in class sbrt.kernel.math.algebra.DoubleMatrixWrap
Returns this matrix as a list of linear combinations.
toList() - Method in class sbrt.kernel.math.graph_theory.Path
Returns a list representation of this path.
toMap() - Method in class sbrt.kernel.math.algebra.HashLinearSystemSolution
Returns this solution as a map.
toMap() - Method in interface sbrt.kernel.math.algebra.LinearSystemSolution
Returns this solution as a map.
toMap() - Method in class sbrt.shell.io.ProcessInputFile
Returns the information contained in this file as a map.
toMap() - Method in interface sbrt.shell.mng.ManagerInput
Returns the information contained in this input as a map.
toMap() - Method in class sbrt.shell.mng.MapManagerInput
Returns the information contained in this input as a map.
toString() - Method in class sbrt.ext.cplex.CplexSolver
Returns the name of this program solver.
toString() - Method in class sbrt.ext.R.stat.RCorrelator.Result
Returns a string representation of this result.
toString() - Method in class sbrt.kernel.fba.AbstractRxn
Returns an appropriate string representation of this reaction.
toString() - Method in interface sbrt.kernel.fba.ChemRxn
Returns an appropriate string representation of this chemical reaction.
toString() - Method in class sbrt.kernel.fba.IrrevRxn
Returns an appropriate string representation of this irreversible reaction.
toString() - Method in class sbrt.kernel.fba.proc.FbaProcess
Returns a string representation of this process.
toString() - Method in class sbrt.kernel.fba.RevExchRxn
Returns a string representation of this exchange reaction.
toString() - Method in class sbrt.kernel.fba.RevRxn
Returns an appropriate string representation of this reversible reaction.
toString() - Method in class sbrt.kernel.fba.SinkRxn
Returns a string representation of this sink reaction.
toString() - Method in class sbrt.kernel.fba.SourceRxn
Returns a string representation of this source reaction.
toString() - Method in class sbrt.kernel.math.AbstractLinearComb.Term
Returns an appropriate string representation of this term.
toString() - Method in class sbrt.kernel.math.AbstractPolynomial
Returns a string representation of this polynomial.
toString() - Method in class sbrt.kernel.math.algebra.AbstractMdMatrix
Returns a string representation of this matrix.
toString() - Method in interface sbrt.kernel.math.algebra.Matrix
Returns a string representation of this matrix.
toString() - Method in class sbrt.kernel.math.algebra.MatrixWrap
Returns a string representation of this matrix.
toString() - Method in class sbrt.kernel.math.geom.ParallelHyperplanes
Returns a string representation of this pair of bounding parallel hyperplanes.
toString() - Method in class sbrt.kernel.math.graph_theory.DirectedGraph.Edge
Returns an appropriate string representation of this edge.
toString() - Method in class sbrt.kernel.math.graph_theory.Path
Returns a string representation of this path.
toString() - Method in class sbrt.kernel.math.Interval
Returns a string representation of this interval.
toString() - Method in interface sbrt.kernel.math.LinearComb
Returns an appropriate string representation of this linear combination.
toString() - Method in interface sbrt.kernel.math.MathExpr
Returns an appropriate string representation of this mathematical expression.
toString() - Method in enum sbrt.kernel.math.optimization.OptSense
Returns an appropriate string representation of this optimization sense.
toString() - Method in enum sbrt.kernel.math.optimization.ProgramSolverStatus
Returns an appropriate string representation of this program solver status.
toString() - Method in interface sbrt.kernel.math.Polynomial.Term
Returns an appropriate string representation of this term.
toString() - Method in interface sbrt.kernel.math.Polynomial
Returns an appropriate string representation of this polynomial.
toString() - Method in class sbrt.kernel.math.stat.comp.MannWhitneyResults
Returns a string represenation of these results.
toString() - Method in class sbrt.kernel.math.stat.comp.TauResult
Returns a string represenation of these correlation results.
toString() - Method in class sbrt.kernel.utilities.And
Returns a string representation of this "and" relationship.
toString() - Method in class sbrt.kernel.utilities.Or
Returns a string representation of this "and" relationship.
toString() - Method in class sbrt.kernel.utilities.UnmodifiableCollection
Returns toString() on the underlying collection.
toString() - Method in class sbrt.kernel.utilities.UnmodifiableList
Returns toString() on the underlying list.
toString() - Method in class sbrt.kernel.utilities.UnmodifiableMap
Returns toString() on the underlying map.
toString() - Method in class sbrt.kernel.utilities.UnmodifiableSet
Returns toString() on the underlying set.
toString() - Method in class sbrt.shell.io.FileFormat
Returns a string representation of this file format.
toString() - Method in class sbrt.shell.io.ProcessInputFile
Returns a string representation of the information contained in this file.
total() - Method in class sbrt.kernel.fba.FluxConstraints
Returns the total number of elements contained in this set of constraints.
translate(String, String) - Method in class sbrt.shell.proc.fba.SimpleRxnFileReader
Translates a simple reaction file into an FBA Reaction File.
translate(String, String, PrintWriter) - Method in class sbrt.shell.proc.fba.SimpleRxnFileReader
Translates a simple reaction file into an FBA Reaction File.
transpose(Matrix<R, C, E>, MatrixBuilder<? super C, ? super R, E>) - Method in class sbrt.kernel.math.algebra.MatrixTransposer
Fills emptyMatrix with the transpose of matrix.
TreeMatrix<R extends java.lang.Comparable<? super R>,C extends java.lang.Comparable<? super C>> - Class in sbrt.kernel.math.algebra
This class is a java.util.TreeMap based implementation of SmdMatrix.
TreeMatrix() - Constructor for class sbrt.kernel.math.algebra.TreeMatrix
Constructs an emtpy TreeMatrix.
TrueFalseFormat - Class in sbrt.shell.text
This class is used to define a format for true/false values.
TrueFalseFormat() - Constructor for class sbrt.shell.text.TrueFalseFormat
Constructs a new true/false format object.

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