Constant Field Values


Contents
sbrt.*

sbrt.ProcessRunner
public static final java.lang.String ERROR_LOG "sbrt_error_log.txt"

sbrt.Sbrt
public static final java.lang.String GUI_ARG "-g"
public static final int MAJOR 2
public static final int MINOR 0
public static final int REVISION 0
public static final java.lang.String USAGE "usage: sbrt process_file.txt"
public static final java.lang.String VERSION_ARG "-v"

sbrt.kernel.*

sbrt.kernel.fba.comp.AbstractFluxIntervalComputer<F extends Fluxome>
public static final double ZERO_CUTOFF 1.0E-9

sbrt.kernel.fba.comp.CdHarFluxComp<F extends Fluxome>
public static final double DEFAULT_COEFF_CUTOFF 1.0E-9
public static final double DEFAULT_MIN_CHORD 5.0E-9
public static final double DEFAULT_TOLERANCE 1.0E-9

sbrt.kernel.fba.comp.FbaOptimizer<F extends Fluxome>
public static final double DEFAULT_CONST_TOL 0.0
public static final int DEFAULT_SAFETY_LEVEL 1

sbrt.kernel.fba.comp.InitialPointComputer<F extends Fluxome>
public final double DEFAULT_ZERO_CUTOFF 1.0E-9

sbrt.kernel.fba.proc.RevRxnBreakerProcess
public static final java.lang.String FORWARD_SUFFIX "_Forward"
public static final java.lang.String REVERSE_SUFFIX "_Reverse"
public static final java.lang.String SINK_SUFFIX "_Sink"
public static final java.lang.String SOURCE_SUFFIX "_Source"

sbrt.shell.*

sbrt.shell.ProcessManagerFactory
public static final java.lang.String PROCESS "Process"
public static final java.lang.String PROCESS_NAME_FILE "Process Name File"

sbrt.shell.ProgramSolverFactory
public static final java.lang.String CPLEX "CPLEX"
public static final java.lang.String GLPK "GLPK"
public static final java.lang.String PARAM_FILE "Program Solver Parameter File"
public static final java.lang.String SOLVER "Program Solver"

sbrt.shell.mng.AbstractProcessManager
public static final java.lang.String ALGORITHM "Algorithm"
public static final java.lang.String COMPLETED "Completed: "
public static final java.lang.String DATA_HEADERS "Data Headers"
public static final java.lang.String ELAPSED_TIME "Elapsed time: "
public static final java.lang.String FILE_FORMAT "File Format"
public static final java.lang.String INPUT_FILE "Input File"
public static final java.lang.String INPUT_FILE_FORMAT "Input File Format"
public static final java.lang.String INPUT_FILE_NAME_FILE "Input File Name File"
public static final java.lang.String ITERATIONS "Iterations"
public static final java.lang.String OUTPUT_FILE_FORMAT "Output File Format"
public static final java.lang.String OUTPUT_FILE_NAME "Output File Name"
public static final java.lang.String OUTPUT_FILE_NAME_FILE "Output File Name File"
public static final java.lang.String PERCENT_COMPLETED "Percent completed: "
public static final java.lang.String SEED "Seed"
public static final java.lang.String ZERO_CUTOFF "Zero Cutoff"

sbrt.shell.mng.algebra.LinearSolverManager
public static final java.lang.String EQUATIONS_FILE "Equations File"
public static final java.lang.String KERNEL_LINK_CMD "Kernel Link Command"

sbrt.shell.mng.comb.SingleElementUnionManager
public static final java.lang.String SETS_FILE "Sets File"

sbrt.shell.mng.fba.BiggSbmlReaderManager
public static final java.lang.String GENE_FILE_NAME "Gene File Name"
public static final java.lang.String RXN_FILE_NAME "Reaction File Name"
public static final java.lang.String SBML_INPUT_FILE "SBML Input File"

sbrt.shell.mng.fba.CatalystDeletionManager
public static final java.lang.String CATALYST_DELETION_FILE "Catalyst Deletion File"

sbrt.shell.mng.fba.FbaManager
public static final java.lang.String CONSTRAINT_TOLERANCE "Constraint Tolerance"
public static final double DEFAULT_CONSTRAINT_TOLERANCE 1.0E-9
public static final java.lang.String FLUX_VECTOR_FILE "Flux Vector File"
public static final java.lang.String FLUX_VECTOR_FILE_NAME "Flux Vector File Name"
public static final java.lang.String RXN_CATALYST_FILE "Reaction-Catalyst File"
public static final java.lang.String RXN_FILE "Reaction File"
public static final java.lang.String SYSTEM_SOLUTION_FILE "System Solution File"

sbrt.shell.mng.fba.FbaOptManager
public static final java.lang.String CONSTRAINTS_FILE "Constraints File"
public static final int DEFAULT_SAFETY_LEVEL 1
public static final java.lang.String OBJECTIVE_FUNCTION "Objective Function"
public static final java.lang.String OPTIMIZATION_SENSE "Optimization Sense"
public static final java.lang.String SAFETY_LEVEL "Safety Level"

sbrt.shell.mng.fba.FluxActivityManager
public static final java.lang.String ACTIVITY_COUNT_FILE_NAME "Activity Count File Name"
public static final java.lang.String ACTIVITY_VECTOR_FILE_NAME "Activity Vector File Name"
public static final java.lang.String FLUX_VECTOR_FILE_FORMAT "Flux Vector File Format"

sbrt.shell.mng.fba.FluxCapManager
public static final java.lang.String CYCLE_FILE "Cycle File"

sbrt.shell.mng.fba.FluxPlasticityManager
public static final java.lang.String ALWAYS_ACTIVE_FILE_NAME "Always-Active Reaction File Name"
public static final java.lang.String FLUX_INTERVAL_FILE "Flux Interval File"
public static final java.lang.String NEVER_ACTIVE_FILE_NAME "Never-Active Reaction File Name"
public static final java.lang.String POT_ACTIVE_FILE_NAME "Potentially-Active Reaction File Name"

sbrt.shell.mng.fba.InitialPointManager
public static final double DEFAULT_P 1.0E15
public static final java.lang.String FLUX_INTERVAL_FILE "Flux Interval File"
public static final java.lang.String P_MAX "P Max"
public static final java.lang.String P_VECTOR_FILE_NAME "P Vector File Name"

sbrt.shell.mng.fba.IntervalVariationManager
public static final java.lang.String CV_FILE "Constraint Variation File"
public static final java.lang.String FLUX_INTERVAL_FILE "Flux Interval File"

sbrt.shell.mng.fba.MetatoolOutputReaderManager
public static final java.lang.String ELEM_MODE_FILE_NAME "Elementary Mode File Name"
public static final java.lang.String METATOOL_INPUT_FILE "Metatool Input File"
public static final java.lang.String METATOOL_OUTPUT_FILE "Metatool Output File"

sbrt.shell.mng.fba.MsFluxIntervalManager
public static final java.lang.String FLUX_CAP_FILE "Flux Cap File"

sbrt.shell.mng.fba.NetworkInfoManager
public static final java.lang.String CATALYST_FILE_NAME "Catalyst File Name"
public static final java.lang.String CHEM_SPECIES_FILE_NAME "Chemical Species File Name"
public static final java.lang.String EQUATION_FILE_NAME "Equation File Name"
public static final java.lang.String EQUIV_RXN_FILE_NAME "Equivalent Reaction File Name"
public static final java.lang.String RXN_NAME_FILE_NAME "Reaction Name File Name"
public static final java.lang.String RXN_OUTPUT_FILE_NAME "Reaction Output File Name"
public static final java.lang.String S_MATRIX_FILE_NAME "Stoichiometry Matrix File Name"

sbrt.shell.mng.fba.ObjectiveFunctionManager
public static final java.lang.String OBJ_FUNCT_FILE "Objective Function File"
public static final java.lang.String OBJ_FUNCT_FILE_FORMAT "Objective Function File Format"

sbrt.shell.mng.fba.PalssonSbmlReaderManager
public static final java.lang.String FLUX_BOUNDS_FILE_NAME "Flux Bounds File Name"
public static final java.lang.String FLUX_VECTOR_FILE_NAME "Flux Vector File Name"
public static final java.lang.String GENE_FILE_NAME "Gene File Name"
public static final java.lang.String PROTEIN_FILE_NAME "Protein File Name"
public static final java.lang.String RXN_FILE_NAME "Reaction File Name"
public static final java.lang.String SBML_INPUT_FILE "SBML Input File"

sbrt.shell.mng.fba.RandomConstraintsManager
public static final java.lang.String INACTIVE "Inactive Constraint"
public static final java.lang.String IRREV_CONSTRAINT "Irreversible Constraint"
public static final java.lang.String NUM_ACTIVE_FLUXES "Number of Active Fluxes"
public static final java.lang.String REV_CONSTRAINT "Reversible Constraint"

sbrt.shell.mng.fba.RandomFluxVectorManager
public static final java.lang.String ALGORITHM "Random Flux Vector Algorithm"

sbrt.shell.mng.fba.RxnDeletionManager
public static final java.lang.String RXN_DELETION_FILE "Reaction Deletion File"

sbrt.shell.mng.fba.SimpleRxnFileTransManager
public static final java.lang.String INPUT_RXN_FILE "Input Reaction File"

sbrt.shell.mng.geom.CdHarManager
public static final java.lang.String CONSTRAINT_TOLERANCE "Constraint Tolerance"
public static final double DEFAULT_CONSTRAINT_TOLERANCE 1.0E-9
public static final double DEFAULT_MIN_CHORD_LENGTH 1.0E-6
public static final java.lang.String INITIAL_POINT_FILE "Initial Point File"
public static final java.lang.String MAX_OBSTRUCTED_MOVES "Maximum Obstructed Moves"
public static final java.lang.String MIN_CHORD_LENGTH "Minimum Chord Length"
public static final java.lang.String PLANES_FILE "Parallel Hyperplanes File"
public static final java.lang.String POINTS_PER_POINT "Points Per Point"

sbrt.shell.mng.graph_theory.CycleIdManager
public static final java.lang.String EDGE_FILE "Edge File"

sbrt.shell.mng.graph_theory.GraphInfoManager
public static final java.lang.String NODE_FILE_NAME "Node File Name"

sbrt.shell.mng.graph_theory.PathIdManager
public static final java.lang.String EDGE_FILE "Edge File"

sbrt.shell.mng.stat.CorrelationManager
public static final java.lang.String CORR_COEFF "Correlation Coefficient"
public static final java.lang.String KENDALLS_TAU "Kendall\'s tau"
public static final java.lang.String PEARSONS_R "Pearson\'s r"
public static final java.lang.String SPEARMANS_RHO "Spearman\'s rho"
public static final java.lang.String X_FILE_NAME "X Value File Name"
public static final java.lang.String Y_FILE_NAME "Y Value File Name"

sbrt.shell.mng.stat.KendallTauManager
public static final java.lang.String TAU_A "Kendall\'s Tau A"
public static final java.lang.String TAU_B "Kendall\'s Tau B"

sbrt.shell.mng.stat.MannWhitneyUManager
public static final java.lang.String SAMPLE_A_FILE "Sample A File"
public static final java.lang.String SAMPLE_B_FILE "Sample B File"

sbrt.shell.mng.utilities.IntervalComparisonManager
public static final java.lang.String FILE_1 "File 1"
public static final java.lang.String FILE_2 "File 2"

sbrt.shell.mng.utilities.VariableParticipationManager
public static final java.lang.String EXPRESSION_FILE "Expression File"

sbrt.shell.mng.utilities.VectorComparisonManager
public static final java.lang.String FILE "File"

sbrt.shell.proc.fba.MetatoolInputReader
public static final java.lang.String CAT "-CAT"
public static final java.lang.String ENZIRREV "-ENZIRREV"
public static final java.lang.String ENZREV "-ENZREV"
public static final java.lang.String METEXT "-METEXT"
public static final java.lang.String METINT "-METINT"

sbrt.shell.proc.fba.MetatoolInputWriter
public static final java.lang.String SURR "Surroundings"

sbrt.shell.proc.fba.PalssonSbmlReader
public static final java.lang.String NOT_PROVIDED "Not_Provided"

sbrt.shell.text.SpecialChars
public static final char AMPERSAND 38
public static final char ASTERICK 42
public static final char AT 64
public static final char BACK_SLASH 92
public static final char CARET 94
public static final char COLON 58
public static final char COMMA 44
public static final char DASH 45
public static final char DOLLAR 36
public static final char DOT 46
public static final char EQUALS 61
public static final char EXCLAMATION 33
public static final char FORWARD_SLASH 47
public static final char GREATER_THAN 62
public static final char HASH 35
public static final char LEFT_BRACE 123
public static final char LEFT_BRACKET 91
public static final char LEFT_PAREN 40
public static final char LESS_THAN 60
public static final char PERCENT 37
public static final char PIPE 124
public static final char PLUS 43
public static final char QUESTION 63
public static final char RIGHT_BRACE 125
public static final char RIGHT_BRACKET 93
public static final char RIGHT_PAREN 41
public static final char SEMICOLON 59
public static final char TILDE 126

sbrt.shell.text.chem.IrrevRxnFormatV1
public static final java.lang.String ARROW "-->"

sbrt.shell.text.chem.RevRxnFormatV1
public static final java.lang.String ARROW "<==>"

sbrt.shell.text.fba.BiggRxnNodeParser
public static final java.lang.String RXN_NODE_NAME "reaction"

sbrt.shell.text.fba.FbaOptHeaderFormatterV1
public static final java.lang.String OBJ_VALUE "Objective_Value"

sbrt.shell.text.fba.FbaOptHeaderParserV1
public static final java.lang.String OBJ_VALUE "Objective_Value"

sbrt.shell.text.fba.IrrevRxnFormatV1
public static final java.lang.String ARROW "-->"
public static final java.lang.String SURR "Surroundings"

sbrt.shell.text.fba.IrrevRxnFormatV2
public static final java.lang.String ARROW "-->"
public static final java.lang.String SURR "Surroundings"

sbrt.shell.text.fba.PalssonRxnNodeParser
public static final java.lang.String RXN_NODE_NAME "reaction"

sbrt.shell.text.fba.RevRxnFormatV1
public static final java.lang.String ARROW "<==>"
public static final java.lang.String SURR "Surroundings"

sbrt.shell.text.fba.RevRxnFormatV2
public static final java.lang.String ARROW "<==>"
public static final java.lang.String SURR "Surroundings"

sbrt.shell.text.fba.RxnNameSetFormatV1
public static final java.lang.String ALL_RXNS "All_Reactions"