Index

A

addAdvice() (synbioweaver.core.Aspect method) addCircuit() (synbioweaver.core.Aspect method) (synbioweaver.core.Circuit method) (synbioweaver.core.Weaver method) addElemTypeAdvice() (synbioweaver.core.Weaver method) addPart() (synbioweaver.core.Aspect method) (synbioweaver.core.Circuit method) (synbioweaver.core.Weaver method) addReaction() (synbioweaver.core.Weaver method) addTypeAdvice() (synbioweaver.core.Aspect method) addWeaverOutput() (synbioweaver.core.Aspect method) Advice (class in synbioweaver.core) AFTER (synbioweaver.core.PointCut attribute) ANY (synbioweaver.core.MoleculeSignatureElement attribute) (synbioweaver.core.PartSignatureElement attribute)

args (synbioweaver.core.AspectValueError attribute) (synbioweaver.core.CircuitValueError attribute) (synbioweaver.core.InvalidAdviceMethodError attribute) (synbioweaver.core.InvalidPointCutError attribute) (synbioweaver.core.InvalidPointCutExpressionError attribute) (synbioweaver.core.InvalidPointCutOperatorError attribute) (synbioweaver.core.InvalidSignatureError attribute) (synbioweaver.core.InvalidSymbolNameError attribute) (synbioweaver.core.InvalidWeaverOutputMethodError attribute) (synbioweaver.core.MoleculeValueError attribute) (synbioweaver.core.PartInitializationError attribute) (synbioweaver.core.PartValueError attribute) (synbioweaver.core.PrecedenceOutOfRangeError attribute) (synbioweaver.core.SymbolExistsWarning attribute) Aspect (class in synbioweaver.core) AspectValueError

B

BEFORE (synbioweaver.core.PointCut attribute)

C

checkAndSetMolecule() (in module synbioweaver.core) checkAndSetOperator() (synbioweaver.core.PointCut method) checkBaseClassesMatch() (in module synbioweaver.core) checkIfTypeReturnInstance() (in module synbioweaver.core) Circuit (class in synbioweaver.core) CircuitValueError CLASSONLY (synbioweaver.core.MoleculeSignatureElement attribute) (synbioweaver.core.PartSignatureElement attribute)

CodingRegion (class in synbioweaver.core) ConstitutivePromoter (class in synbioweaver.core) constructMoleculeListAndAddTypeAdvice() (synbioweaver.core.Weaver method) createMolecule() (synbioweaver.core.Aspect method) (synbioweaver.core.Circuit method) (synbioweaver.core.Weaver method)

D

declareNewMolecule() (in module synbioweaver.core)

declareNewPart() (in module synbioweaver.core)

E

ExecutionNode (class in synbioweaver.core) exportMolecule() (synbioweaver.core.Aspect method) (synbioweaver.core.Circuit method) (synbioweaver.core.Weaver method)

expressionUses() (synbioweaver.core.PointCutExpressionAnd method) (synbioweaver.core.PointCutExpressionConcatenate method) (synbioweaver.core.PointCutExpressionNot method) (synbioweaver.core.PointCutExpressionOperator method) (synbioweaver.core.PointCutExpressionOr method)

G

getAdviceList() (synbioweaver.core.Aspect method) getAfterNodes() (synbioweaver.core.Circuit method) (synbioweaver.core.CodingRegion method) (synbioweaver.core.ConstitutivePromoter method) (synbioweaver.core.ExecutionNode method) (synbioweaver.core.HybridPromoter method) (synbioweaver.core.Molecule method) (synbioweaver.core.NegativePromoter method) (synbioweaver.core.Part method) (synbioweaver.core.PositivePromoter method) (synbioweaver.core.Promoter method) (synbioweaver.core.Protein method) (synbioweaver.core.RBS method) (synbioweaver.core.RNACodingRegion method) (synbioweaver.core.Terminator method) getAfterPart() (synbioweaver.core.Circuit method) (synbioweaver.core.CodingRegion method) (synbioweaver.core.ConstitutivePromoter method) (synbioweaver.core.HybridPromoter method) (synbioweaver.core.NegativePromoter method) (synbioweaver.core.Part method) (synbioweaver.core.PositivePromoter method) (synbioweaver.core.Promoter method) (synbioweaver.core.RBS method) (synbioweaver.core.RNACodingRegion method) (synbioweaver.core.Terminator method) getBeforeNodes() (synbioweaver.core.Circuit method) (synbioweaver.core.CodingRegion method) (synbioweaver.core.ConstitutivePromoter method) (synbioweaver.core.ExecutionNode method) (synbioweaver.core.HybridPromoter method) (synbioweaver.core.Molecule method) (synbioweaver.core.NegativePromoter method) (synbioweaver.core.Part method) (synbioweaver.core.PositivePromoter method) (synbioweaver.core.Promoter method) (synbioweaver.core.Protein method) (synbioweaver.core.RBS method) (synbioweaver.core.RNACodingRegion method) (synbioweaver.core.Terminator method)

getBeforePart() (synbioweaver.core.Circuit method) (synbioweaver.core.CodingRegion method) (synbioweaver.core.ConstitutivePromoter method) (synbioweaver.core.HybridPromoter method) (synbioweaver.core.NegativePromoter method) (synbioweaver.core.Part method) (synbioweaver.core.PositivePromoter method) (synbioweaver.core.Promoter method) (synbioweaver.core.RBS method) (synbioweaver.core.RNACodingRegion method) (synbioweaver.core.Terminator method) getCodingFor() (synbioweaver.core.CodingRegion method) (synbioweaver.core.RNACodingRegion method) getInducers() (synbioweaver.core.HybridPromoter method) getMoleculeObject() (synbioweaver.core.Weaver method) getRegulatedBy() (synbioweaver.core.HybridPromoter method) (synbioweaver.core.NegativePromoter method) (synbioweaver.core.PositivePromoter method) getRepressors() (synbioweaver.core.HybridPromoter method) getTypeAdviceList() (synbioweaver.core.Aspect method) getWeaverOutputList() (synbioweaver.core.Aspect method)

H

HybridPromoter (class in synbioweaver.core)

I

importMolecule() (synbioweaver.core.Aspect method) (synbioweaver.core.Circuit method) (synbioweaver.core.Weaver method) InvalidAdviceMethodError InvalidPointCutError InvalidPointCutExpressionError InvalidPointCutOperatorError

InvalidSignatureError InvalidSymbolNameError InvalidWeaverOutputMethodError isInducer() (synbioweaver.core.HybridPromoter method) isMoleculeAdvice() (synbioweaver.core.TypeAdvice method) isPartAdvice() (synbioweaver.core.TypeAdvice method) isRepressor() (synbioweaver.core.HybridPromoter method) isWithin() (synbioweaver.core.PointCutContext method)

L

left (synbioweaver.core.PointCutExpressionAnd attribute) (synbioweaver.core.PointCutExpressionConcatenate attribute) (synbioweaver.core.PointCutExpressionNot attribute) (synbioweaver.core.PointCutExpressionOperator attribute) (synbioweaver.core.PointCutExpressionOr attribute)

M

mainAspect() (synbioweaver.core.Aspect method) mainCircuit() (synbioweaver.core.Circuit method) match() (synbioweaver.core.MoleculeSignature method) (synbioweaver.core.MoleculeSignatureElement method) (synbioweaver.core.NotOnStack method) (synbioweaver.core.OnStack method) (synbioweaver.core.PartSignature method) (synbioweaver.core.PartSignatureElement method) (synbioweaver.core.PointCut method) (synbioweaver.core.PointCutExpressionAnd method) (synbioweaver.core.PointCutExpressionConcatenate method) (synbioweaver.core.PointCutExpressionNode method) (synbioweaver.core.PointCutExpressionNot method) (synbioweaver.core.PointCutExpressionOperator method) (synbioweaver.core.PointCutExpressionOr method) matchNamespaces() (synbioweaver.core.MoleculeSignature method) (synbioweaver.core.PartSignature method) MAXPRECEDENCE (synbioweaver.core.Advice attribute) message (synbioweaver.core.AspectValueError attribute) (synbioweaver.core.CircuitValueError attribute) (synbioweaver.core.InvalidAdviceMethodError attribute) (synbioweaver.core.InvalidPointCutError attribute) (synbioweaver.core.InvalidPointCutExpressionError attribute) (synbioweaver.core.InvalidPointCutOperatorError attribute) (synbioweaver.core.InvalidSignatureError attribute) (synbioweaver.core.InvalidSymbolNameError attribute) (synbioweaver.core.InvalidWeaverOutputMethodError attribute) (synbioweaver.core.MoleculeValueError attribute) (synbioweaver.core.PartInitializationError attribute) (synbioweaver.core.PartValueError attribute) (synbioweaver.core.PrecedenceOutOfRangeError attribute) (synbioweaver.core.SymbolExistsWarning attribute)

MINPRECEDENCE (synbioweaver.core.Advice attribute) Molecule (class in synbioweaver.core) moleculeGraph() (synbioweaver.core.Weaver.WeaverOutput method) molecules() (synbioweaver.core.Weaver.WeaverOutput method) MoleculeSignature (class in synbioweaver.core) MoleculeSignatureElement (class in synbioweaver.core) MoleculeValueError

N

NegativePromoter (class in synbioweaver.core) NotOnStack (class in synbioweaver.core) numberOfMatchingParts() (synbioweaver.core.NotOnStack method) (synbioweaver.core.OnStack method) (synbioweaver.core.PartSignature method) (synbioweaver.core.PointCutExpressionAnd method) (synbioweaver.core.PointCutExpressionConcatenate method) (synbioweaver.core.PointCutExpressionNode method) (synbioweaver.core.PointCutExpressionNot method) (synbioweaver.core.PointCutExpressionOperator method) (synbioweaver.core.PointCutExpressionOr method)

O

OnStack (class in synbioweaver.core)

output() (synbioweaver.core.Weaver method)

P

Part (class in synbioweaver.core) PartInitializationError PartSignature (class in synbioweaver.core) PartSignatureElement (class in synbioweaver.core) PartValueError PointCut (class in synbioweaver.core) PointCutContext (class in synbioweaver.core) PointCutExpressionAnd (class in synbioweaver.core)

PointCutExpressionConcatenate (class in synbioweaver.core) PointCutExpressionNode (class in synbioweaver.core) PointCutExpressionNot (class in synbioweaver.core) PointCutExpressionOperator (class in synbioweaver.core) PointCutExpressionOr (class in synbioweaver.core) PositivePromoter (class in synbioweaver.core) PrecedenceOutOfRangeError Promoter (class in synbioweaver.core) Protein (class in synbioweaver.core)

R

RBS (class in synbioweaver.core) reactionFrom() (synbioweaver.core.Aspect method) (synbioweaver.core.Circuit method) (synbioweaver.core.Weaver method) reactionTo() (synbioweaver.core.Aspect method) (synbioweaver.core.Circuit method) (synbioweaver.core.Weaver method) readAspectsConstructAdviceLists() (synbioweaver.core.Weaver method)

REPLACE (synbioweaver.core.PointCut attribute) right (synbioweaver.core.PointCutExpressionAnd attribute) (synbioweaver.core.PointCutExpressionConcatenate attribute) (synbioweaver.core.PointCutExpressionNot attribute) (synbioweaver.core.PointCutExpressionOperator attribute) (synbioweaver.core.PointCutExpressionOr attribute) RNACodingRegion (class in synbioweaver.core) runAfterAdvice() (synbioweaver.core.Weaver method) runBeforeAndReplaceAdvice() (synbioweaver.core.Weaver method)

S

setAfterPart() (synbioweaver.core.Circuit method) (synbioweaver.core.CodingRegion method) (synbioweaver.core.ConstitutivePromoter method) (synbioweaver.core.HybridPromoter method) (synbioweaver.core.NegativePromoter method) (synbioweaver.core.Part method) (synbioweaver.core.PositivePromoter method) (synbioweaver.core.Promoter method) (synbioweaver.core.RBS method) (synbioweaver.core.RNACodingRegion method) (synbioweaver.core.Terminator method) setBeforePart() (synbioweaver.core.Circuit method) (synbioweaver.core.CodingRegion method) (synbioweaver.core.ConstitutivePromoter method) (synbioweaver.core.HybridPromoter method) (synbioweaver.core.NegativePromoter method) (synbioweaver.core.Part method) (synbioweaver.core.PositivePromoter method) (synbioweaver.core.Promoter method) (synbioweaver.core.RBS method) (synbioweaver.core.RNACodingRegion method) (synbioweaver.core.Terminator method)

setWeaver() (synbioweaver.core.Aspect method) (synbioweaver.core.Circuit method) sortAdviceList() (synbioweaver.core.Weaver method) SUBCLASS (synbioweaver.core.MoleculeSignatureElement attribute) (synbioweaver.core.PartSignatureElement attribute) SymbolExistsWarning synbioweaver.core (module)

T

Terminator (class in synbioweaver.core)

TypeAdvice (class in synbioweaver.core)

W

weave() (synbioweaver.core.Circuit method) (synbioweaver.core.CodingRegion method) (synbioweaver.core.ConstitutivePromoter method) (synbioweaver.core.HybridPromoter method) (synbioweaver.core.NegativePromoter method) (synbioweaver.core.Part method) (synbioweaver.core.PositivePromoter method) (synbioweaver.core.Promoter method) (synbioweaver.core.RBS method) (synbioweaver.core.RNACodingRegion method) (synbioweaver.core.Terminator method)

Weaver (class in synbioweaver.core) Weaver.MoleculeReactionFrom (class in synbioweaver.core) Weaver.MoleculeReactionTo (class in synbioweaver.core) Weaver.WeaverOutput (class in synbioweaver.core)