- general - package general
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- getAddedInteractions() - Method in class interaction.InteractionNetwork
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- getArgument() - Method in class gui.ArgumentComponent
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- getBinaryEntities() - Method in class interaction.InteractionNetwork
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- getBioNetwork() - Method in class general.Bind
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- getClasses(String) - Static method in class applications.gui.GraphicalFlexflux
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Scans all classes accessible from the context class loader which belong
to the given package.
- getCoeffs() - Method in class general.Objective
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- getColumnClass(int) - Method in class analyses.result.MyTableModel
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- getCondition() - Method in class interaction.Interaction
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- getConsequence() - Method in class interaction.Interaction
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- getConstraints() - Method in class general.Bind
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- getDeadReactions() - Method in class analyses.result.DRResult
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- getDeadReactions() - Method in class general.Bind
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- getEntities() - Method in class general.Constraint
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- getEntities() - Method in class general.Objective
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- getEntities() - Method in class interaction.InteractionNetwork
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- getEntity(String) - Method in class interaction.InteractionNetwork
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- getEntity() - Method in class interaction.Unique
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- getEntityNames() - Method in class general.Constraint
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- getEssentialReactions() - Method in class analyses.result.FVAResult
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- getExchangeInteractions() - Method in class general.Bind
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- getGPRInteractions() - Method in class interaction.InteractionNetwork
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- getGroupIndex() - Method in class analyses.result.ReacAnalysisResult
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- getGroupIndex() - Method in class analyses.result.TwoReacsAnalysisResult
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- getIntEntities() - Method in class interaction.InteractionNetwork
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- getInteractionNetwork() - Method in class general.Bind
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- getInteractionsEntities() - Method in class general.Bind
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- getInteractionsEntitiesCause() - Method in class general.Bind
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- getInteractionToCheck() - Method in class interaction.InteractionNetwork
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- getIntToConstraint() - Method in class general.Bind
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- getInvolvedEntities() - Method in class interaction.InversedRelation
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- getInvolvedEntities() - Method in class interaction.Relation
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- getInvolvedEntities() - Method in class interaction.RelationWithList
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- getInvolvedEntities() - Method in class interaction.Unique
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- getItemPaint(int, int) - Method in class analyses.result.ReacAnalysisResult.MyRenderer
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- getLb() - Method in class general.Constraint
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- getList() - Method in class interaction.RelationWithList
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- getMap() - Method in class analyses.result.FVAResult
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- getMaximize() - Method in class general.Objective
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- getName() - Method in class general.Objective
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- getNewColor(PlotCanvas) - Method in class analyses.result.TwoReacsAnalysisResult
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- getNewEssentialEntities() - Method in class analyses.PhenotypicPhaseComparator
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- getNewEssentialEntitiesPanel() - Method in class analyses.PhenotypicPhaseComparator
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- getNoLongerEssentialEntities() - Method in class analyses.PhenotypicPhaseComparator
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- getNoLongerEssentialEntitiesPanel() - Method in class analyses.PhenotypicPhaseComparator
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- getNot() - Method in class general.Constraint
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- getNotTransformedUniques() - Method in class interaction.InteractionNetwork
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- getNumEntities() - Method in class interaction.InteractionNetwork
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- getObjective() - Method in class general.Bind
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- getObjValue() - Method in class analyses.result.FBAResult
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- getObjValue() - Method in class analyses.result.FVAResult
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- getOverWritesBounds() - Method in class general.Constraint
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- getReactionsPanel(List<BioEntity>) - Method in class analyses.result.FVAResult
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Creates a JPanel for reactions.
- getRightComponent(String, String) - Method in class gui.MainFrame
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- getScore() - Method in class analyses.result.ReacAnalysisResult
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- getScore() - Method in class analyses.result.TwoReacsAnalysisResult
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Adds up all the distance of the experimental values to the calculated
line.
- getShadowPriceGroups() - Method in class analyses.result.ReacAnalysisResult
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- getShadowPriceGroups() - Method in class analyses.result.TwoReacsAnalysisResult
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- getSimpleConstraints() - Method in class general.Bind
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- getSolvedValue(BioEntity) - Method in class general.Bind
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Return the value of the last solve for a given entity.
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class analyses.result.CompFVAResult.MyTableCellRenderer
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- getThreadFactory() - Method in class general.Bind
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- getTransformation() - Method in class interaction.UniqueProbability
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- getUb() - Method in class general.Constraint
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- getValue() - Method in class gui.ArgumentComponent
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- getValue() - Method in class gui.BooleanComponent
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- getValue() - Method in class gui.ChoiceComponent
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- getValue() - Method in class gui.FileComponent
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- getValue() - Method in class gui.StringComponent
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- getValueForEntity(BioEntity) - Method in class analyses.result.KOResult
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- getValuesForEntity(BioEntity) - Method in class analyses.result.FVAResult
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Get the values for an entity
- getValuesforTime(double) - Method in class analyses.result.RFBAResult
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- GLPKBind - Class in general
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GLPK version of Bind.
- GLPKBind(boolean) - Constructor for class general.GLPKBind
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- GLPKBind(List<Constraint>, Map<BioEntity, Constraint>, InteractionNetwork, BioNetwork, boolean) - Constructor for class general.GLPKBind
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- go(boolean) - Method in class general.Bind
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Make the solver perform the solves.
- go(boolean) - Method in class general.CplexBind
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- go(boolean) - Method in class general.GLPKBind
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- goWithConstraints(List<Constraint>, boolean) - Method in class general.Bind
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Performs the solver solve with constraints.
- gprInteractions(boolean) - Method in class general.Bind
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Adds GPR interactions to the problem.
- GPRInteractions - Variable in class interaction.InteractionNetwork
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List of GPR interactions.
- GraphicalFlexflux - Class in applications.gui
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Main class for FlexFlux GUI
- GraphicalFlexflux() - Constructor for class applications.gui.GraphicalFlexflux
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- groupIndex - Variable in class analyses.result.ReacAnalysisResult
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Map to get the group index of a shadow-price value.
- groupIndex - Variable in class analyses.result.TwoReacsAnalysisResult
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Map to get the group index of a shadow-price value.
- gui - package gui
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- GuiRunAnalysis - Class in gui
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- GuiRunAnalysis(String[]) - Constructor for class gui.GuiRunAnalysis
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