Constant Field Values

Contents

• org.systemsbiology.*

org.systemsbiology.*

org.systemsbiology.chem.Compartment

public static final double

DEFAULT_VOLUME

1.0d

org.systemsbiology.chem.Constants

public static final double

AVOGADRO_CONSTANT

6.02214199E23d

org.systemsbiology.chem.DelayedReactionSolver

public static final int	DEFAULT_NUM_HISTORY_BINS	400
public static final int	MIN_NUM_HISTORY_BINS	10

org.systemsbiology.chem.ISimulator

public static final int

MIN_NUM_RESULTS_TIME_POINTS

2

org.systemsbiology.chem.Model

public static final String	INTERNAL_SYMBOL_PREFIX	"___"
public static final String	NAMESPACE_IDENTIFIER	"::"

org.systemsbiology.chem.ModelBuilderCommandLanguage

public static final String

CLASS_ALIAS

"command-language"

org.systemsbiology.chem.ModelExporterCommandLanguage

public static final String

CLASS_ALIAS

"command-language"

org.systemsbiology.chem.ModelExporterHumanReadable

public static final String

CLASS_ALIAS

"human-readable"

org.systemsbiology.chem.ModelExporterOrrellColumnFormat

public static final String

CLASS_ALIAS

"orrell-column-format"

org.systemsbiology.chem.ReservedSymbolMapperChemCommandLanguage

public static final String	SYMBOL_AVOGADRO	"Navo"
public static final String	SYMBOL_TIME	"time"

org.systemsbiology.chem.Simulator

protected static final long	DEFAULT_MIN_NUM_MILLISECONDS_FOR_UPDATE	1000l
protected static final int	NULL_REACTION	-1

org.systemsbiology.chem.SimulatorDeterministicBase

public static final boolean	DEFAULT_FLAG_GET_FINAL_SYMBOL_FLUCTUATIONS	false
public static final double	DEFAULT_MAX_ALLOWED_ABSOLUTE_ERROR	0.01d
public static final double	DEFAULT_MAX_ALLOWED_RELATIVE_ERROR	1.0E-4d
protected static final int	DEFAULT_NUM_HISTORY_BINS	400

org.systemsbiology.chem.SimulatorDeterministicRungeKuttaAdaptive

public static final String

CLASS_ALIAS

"ODE-RK5-adaptive"

org.systemsbiology.chem.SimulatorDeterministicRungeKuttaFixed

public static final String

CLASS_ALIAS

"ODE-RK5-fixed"

org.systemsbiology.chem.SimulatorStochasticBase

public static final int	DEFAULT_ENSEMBLE_SIZE	1
public static final boolean	DEFAULT_FLAG_GET_FINAL_SYMBOL_FLUCTUATIONS	false
public static final int	DEFAULT_NUM_HISTORY_BINS	400

org.systemsbiology.chem.SimulatorStochasticGibsonBruck

public static final String

CLASS_ALIAS

"gibson-bruck"

org.systemsbiology.chem.SimulatorStochasticGillespie

public static final String

CLASS_ALIAS

"gillespie-direct"

org.systemsbiology.chem.SimulatorStochasticTauLeapBase

public static final String

CLASS_ALIAS

"gillespie-tauleap"

org.systemsbiology.chem.SimulatorStochasticTauLeapComplex

public static final String

CLASS_ALIAS

"tauleap-complex"

org.systemsbiology.chem.SimulatorStochasticTauLeapSimple

public static final String

CLASS_ALIAS

"tauleap-simple"

org.systemsbiology.chem.app.ModelViewerCytoscape

public static final String

CLASS_ALIAS

"cytoscape"

org.systemsbiology.chem.app.ModelViewerHumanReadable

public static final String	CLASS_ALIAS	"human-readable"
public static final int	HEIGHT	600
public static final int	WIDTH	500

org.systemsbiology.chem.app.SimulationResultsPlot

public static final int

MAX_NUM_SYMBOLS_TO_PLOT

20

org.systemsbiology.chem.odetojava.SimulatorOdeToJavaBase

public static final boolean	DEFAULT_FLAG_GET_FINAL_SYMBOL_FLUCTUATIONS	false
public static final double	DEFAULT_MAX_ALLOWED_ABSOLUTE_ERROR	1.0E-4d
public static final double	DEFAULT_MAX_ALLOWED_RELATIVE_ERROR	1.0E-4d
protected static final int	DEFAULT_NUM_HISTORY_BINS	400

org.systemsbiology.chem.odetojava.SimulatorOdeToJavaRungeKuttaAdaptive

public static final String

CLASS_ALIAS

"ODEtoJava-dopr54-adaptive"

org.systemsbiology.chem.odetojava.SimulatorOdeToJavaRungeKuttaImplicit

public static final String

CLASS_ALIAS

"ODEtoJava-imex443-stiff"

org.systemsbiology.chem.sbml.ModelBuilderMarkupLanguage

public static final String

CLASS_ALIAS

"markup-language"

org.systemsbiology.chem.sbml.ModelExporterMarkupLanguage

public static final String	CLASS_ALIAS	"markup-language"
public static final String	DEFAULT_REACTION_PARAMETER_SYMBOL_NAME	"__RATE__"

org.systemsbiology.chem.sbw.SimulationDriverModule

public static final String	CATEGORY_NAME	"Analysis"
public static final String	MODULE_DISPLAY_NAME	"Simulation Driver"
public static final String	MODULE_UNIQUE_NAME	"org.systemsbiology.chem.sbw.gui"

org.systemsbiology.chem.sbw.SimulationDriverService

public static final String	SERVICE_DESCRIPTION	"Simulation Service"
public static final String	SERVICE_NAME	"asim"

org.systemsbiology.gui.SortStatus

public static final int	CODE_ASCENDING	1
public static final int	CODE_DESCENDING	-1
public static final int	CODE_NONE	0

org.systemsbiology.inference.EvidenceWeightedInferer

public static final int

MIN_NUM_BINS

2

org.systemsbiology.inference.EvidenceWeightedInfererDriver

public static final double	ALPHA_VALUE_DEVIATION_WARNING_THRESHOLD	0.5d
public static final double	DEFAULT_INITIAL_SIGNIFICANCE_CUTOFF	0.05d
public static final int	DEFAULT_NUM_BINS	100
public static final double	DEFAULT_QUANTILE_THRESHOLD	0.05d
public static final double	DEFAULT_SEPARATION_THRESHOLD	1.0E-7d

org.systemsbiology.inference.EvidenceWeightType

public static final int	CODE_LINEAR	0
public static final int	CODE_POWER	1
public static final int	CODE_UNIFORM	2

org.systemsbiology.inference.ObservationsData

public static final String

NULL_OBSERVATION_STRING

"null"

org.systemsbiology.inference.ObservationsTableModel

public static final String

COLUMN_NAME_ELEMENT

"element"

org.systemsbiology.inference.PreferencesHandler

public static final String

KEY_DELIMITER

"delimiter"

org.systemsbiology.inference.SignificanceCalculationMethod

public static final int	CODE_CDF_NONPARAMETRIC	0
public static final int	CODE_CDF_PARAMETRIC	2
public static final int	CODE_PDF_NONPARAMETRIC	1
public static final int	CODE_PDF_PARAMETRIC	3

org.systemsbiology.inference.SignificanceCalculator

public static final double

DEFAULT_MISSING_DATA_SIGNIFICANCE

-1.0d

org.systemsbiology.inference.SignificancesData

public static final double	DEFAULT_SIGNIFICANCE_MISSING_DATA	-1.0d
public static final String	NULL_SIGNIFICANCE_STRING	"null"

org.systemsbiology.math.SignificantDigitsCalculator

public static final int

SIGNIFICANT_DIGITS_UNKNOWN

-1

org.systemsbiology.math.Symbol

public static final int

NULL_ARRAY_INDEX

-1

org.systemsbiology.math.SymbolEvaluator

protected static final int

NULL_ARRAY_INDEX

-1

org.systemsbiology.math.probability.Lorentz

public static final double

RATIO_WIDTH_TO_STDEV

0.5d

org.systemsbiology.util.AppConfig

public static final String

CONFIG_FILE_NAME

"AppConfig.xml"

org.systemsbiology.util.CommandLineApp

protected static final String	HELP_ARG	"-help"
public static final String	NULL_MODIFIER	"null"

org.systemsbiology.util.IAliasableClass

public static final String

CLASS_ALIAS

"classalias"