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sbrt.* |
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sbrt.ProcessRunner | ||
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public static final java.lang.String |
ERROR_LOG |
"sbrt_error_log.txt" |
sbrt.Sbrt | ||
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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.* |
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sbrt.kernel.fba.comp.AbstractFluxIntervalComputer<F extends Fluxome> | ||
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public static final double |
ZERO_CUTOFF |
1.0E-9 |
sbrt.kernel.fba.comp.CdHarFluxComp<F extends Fluxome> | ||
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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> | ||
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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> | ||
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public final double |
DEFAULT_ZERO_CUTOFF |
1.0E-9 |
sbrt.kernel.fba.proc.RevRxnBreakerProcess | ||
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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.* |
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sbrt.shell.ProcessManagerFactory | ||
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public static final java.lang.String |
PROCESS |
"Process" |
public static final java.lang.String |
PROCESS_NAME_FILE |
"Process Name File" |
sbrt.shell.ProgramSolverFactory | ||
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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 | ||
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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 | ||
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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 | ||
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public static final java.lang.String |
SETS_FILE |
"Sets File" |
sbrt.shell.mng.fba.BiggSbmlReaderManager | ||
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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 | ||
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public static final java.lang.String |
CATALYST_DELETION_FILE |
"Catalyst Deletion File" |
sbrt.shell.mng.fba.FbaManager | ||
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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 | ||
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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 | ||
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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 | ||
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public static final java.lang.String |
CYCLE_FILE |
"Cycle File" |
sbrt.shell.mng.fba.FluxPlasticityManager | ||
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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 | ||
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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 | ||
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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 | ||
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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 | ||
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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 | ||
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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 | ||
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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 | ||
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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 | ||
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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 | ||
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public static final java.lang.String |
EXPRESSION_FILE |
"Expression File" |
sbrt.shell.mng.utilities.VectorComparisonManager | ||
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public static final java.lang.String |
FILE |
"File" |
sbrt.shell.proc.fba.MetatoolInputReader | ||
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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 | ||
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public static final java.lang.String |
SURR |
"Surroundings" |
sbrt.shell.proc.fba.PalssonSbmlReader | ||
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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 | ||
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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 | ||
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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 | ||
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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" |
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