A B C D E F G H I K M N O P R S T U V

A

addHeader(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Adds the header.

addOntologyLink(String, String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase

Adds an link into an ontology.

ALGEBRAIC_RULE - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule

The flag ALGEBRAIC_RULE.

annotateDeletion(TreeNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

annotateInsertion(TreeNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

annotateMove(TreeNode, TreeNode, Element, ChangeFactory, boolean) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

annotatePatch(String, ChangeFactory) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

annotateUpdateAttribute(TreeNode, TreeNode, String, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

annotateUpdateText(TextNode, TextNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

annotationPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a machine readable annotation.

ASSIGNMENT_RULE - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule

The flag ASSIGNMENT_RULE.

B

BASE_UNITS - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLUnit

those are BASE_UNITS.

BivesSBMLParseException - Exception in de.unirostock.sems.bives.sbml.exception

The Class BivesSBMLParseException.

BivesSBMLParseException(String) - Constructor for exception de.unirostock.sems.bives.sbml.exception.BivesSBMLParseException

Instantiates a new BiVeS exception signalling an error while parsing an SBML document.

C

canBeReactantOrProduct() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies

Can this species take part in a reaction as a reactant or product?

canHaveAssignmentRule() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies

Is this species allowed to have an assignment rule.

connect() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector

connect() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor

contributorPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a machine readable annotation.

creationDatePath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a machine readable annotation.

creatorPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a machine readable annotation.

D

de.unirostock.sems.bives.sbml.algorithm - package de.unirostock.sems.bives.sbml.algorithm

de.unirostock.sems.bives.sbml.api - package de.unirostock.sems.bives.sbml.api

de.unirostock.sems.bives.sbml.exception - package de.unirostock.sems.bives.sbml.exception

de.unirostock.sems.bives.sbml.parser - package de.unirostock.sems.bives.sbml.parser

descriptionPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a human readable annotation.

doc - Variable in class de.unirostock.sems.bives.sbml.api.SBMLSingle

The doc.

doc1 - Variable in class de.unirostock.sems.bives.sbml.api.SBMLDiff

The original document.

doc2 - Variable in class de.unirostock.sems.bives.sbml.api.SBMLDiff

The modified document.

documentNode - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

The document node.

E

eventPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to an event definition.

extractOntologyLinks(DocumentNode, SBMLModel) - Static method in class de.unirostock.sems.bives.sbml.parser.SBMLMeta

Extract ontology links from an annotation element.

F

flagMetaModifcations(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase

Flags occuring modifcations of the meta information (notes, annotations) to the given MarkupElement.

flatten() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle

flatten() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDocument

functionPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a function definition.

G

generateHTMLReport() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Generate html report.

getAnnotation() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase

Gets the annotation.

getCompartment() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

Gets the compartment.

getCompartment() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies

Gets the compartment that hosts this species.

getCompartment(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the compartment.

getCompartments() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the compartments.

getCompartmentType(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the compartment type.

getCompartmentTypes() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the compartment types.

getConstraints() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the constraints.

getDocument() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLValidator

getDocument() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the SBML document.

getDocumentNode() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

Gets the document node.

getEvents() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the events.

getFromMetaId(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets an entity given its meta id.

getFromNode(TreeNode) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets an entity given its tree node.

getFunctionDefinitions() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the function definitions.

getHierarchyDotGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getHierarchyDotGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle

getHierarchyGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getHierarchyGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle

getHierarchyGraphML() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getHierarchyGraphML() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle

getHierarchyJsonGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getHierarchyJsonGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle

getHTMLReport() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getID() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject

Gets the id.

getID() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the id of the model.

getInitialAmount() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies

Returns the initial amount of this species or null if not defined.

getInitialAssignments() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the initial assignments.

getInitialConcentration() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies

Returns the initial concentration of this species or null if not defined.

getKineticLaw() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

Gets the kinetic law.

getLevel() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDocument

Gets the level.

getListOfModifiersNode() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

Gets the list of modifiers node.

getListOfProductsNode() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

Gets the list of products node.

getListOfReactantsNode() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

Gets the list of reactants node.

getMarkDownReport() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint

Gets the math.

getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment

Gets the math.

getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay

Gets the math.

getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority

Gets the math.

getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger

Gets the math.

getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition

Gets the math.

getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment

Gets the math.

getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw

Gets the math.

getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRule

Gets the math.

getMessage() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint

Gets the message.

getMetaId() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase

Gets the meta id.

getModel() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDocument

Gets the model.

getModel() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

Gets the model.

getModifiers() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

Gets the modifiers.

getName() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject

Gets the name.

getName() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the name of the model.

getNameAndId() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject

Gets the name (if defined) and the id as: NAME (ID).

getNameOrId() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject

Gets the name (if defined) or the id (if name undefined).

getNotes() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase

Gets the notes.

getOntologyLinks() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase

Gets the links that point to an ontology.

getOntologyMappings() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the ontology mappings which group entities by there pointers into ontologies.

getParameter(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets a specific parameter.

getParameters() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the parameters.

getProducts() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

Gets the products.

getReactants() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

Gets the reactants.

getReaction(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets a specific reaction.

getReactions() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the reactions.

getReactionsDotGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getReactionsDotGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle

getReactionsGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getReactionsGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle

getReactionsGraphML() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getReactionsGraphML() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle

getReactionsJsonGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getReactionsJsonGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle

getReactionsSbgnJsonGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getReport() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffInterpreter

Gets the produced report.

getReport(Typesetting) - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getReStructuredTextReport() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

getRules() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the rules.

getRuleType() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRule

Gets the rule type.

getSBOTerm() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase

Gets the SBO term.

getSidName(SBMLSBase) - Static method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the SId.

getSpecies() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the species.

getSpecies() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference

Gets the corresponding species.

getSpecies(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the species.

getSpeciesReference(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the species reference.

getSpeciesType(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the species type.

getSpeciesTypes() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the species types.

getSymbol() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment

Gets the symbol.

getUnitDefinition(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the unit definition.

getUnitDefinitions() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Gets the unit definitions.

getValue() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter

Gets the value.

getVariable() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule

Gets the corresponding variable.

getVariable() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment

Gets the variable of interest.

getVariable() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRateRule

Gets the variable of interest.

getVersion() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDocument

Gets the version.

graphProducer - Variable in class de.unirostock.sems.bives.sbml.api.SBMLDiff

The graph producer.

graphProducer - Variable in class de.unirostock.sems.bives.sbml.api.SBMLSingle

The graph producer.

H

hasBoundaryCondition() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies

Checks for a boundary condition.

hasOnlySubstanceUnits() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies

Checks if this species has only substance units.

I

id - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject

The id.

id - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference

The id of this species reference.

init() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector

init() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor

interprete() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffInterpreter

interpreter - Variable in class de.unirostock.sems.bives.sbml.api.SBMLDiff

The interpreter.

isBaseUnit() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition

Checks if this is a base unit.

isConstant() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter

Checks if the parameter is constant.

isConstant() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies

Checks if this species is constant.

isFast() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

Checks if this reaction is fast.

isReversible() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

Checks if this reaction is reversible.

K

kineticsPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a kinetic law.

M

mapNode(DocumentNode, SBMLSBase) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Map node model node to its entity.

mapTrees(boolean, boolean, boolean) - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff

markup() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter

markup() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnit

markup() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition

math - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule

The math.

modificationDatePath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a machine readable annotation.

modifyCompartments(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Modify compartments.

modifyCompartmentTypes(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Modify compartment types.

modifyContraints(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Modify contraints.

modifyEvents(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Modify events.

modifyFunctions(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Modify functions.

modifyInitialAssignments(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Modify initial assignments.

modifyParameter(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Modify parameter.

modifyReaction(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Modify reaction.

modifyRules(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Modify rules.

modifySpecies(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Modify species.

modifySpeciesTypes(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Modify species types.

modifyUnits(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Modify units.

N

name - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject

The name.

name - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference

The name.

O

ontologyLink - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

P

parameterPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a parameter.

PREDEFINED_UNITS - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLUnit

those are predefined units.

processRnA() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer

Process Reaction Network of the original document.

processRnB() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer

Process Reaction Network of the modified document.

produceHierarchyGraph() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer

produceReactionNetwork() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer

R

RATE_RULE - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule

The flag RATE_RULE.

reactionsModifierSpeciesReference - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

reactionsPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a reaction.

reactionsSpeciesReference - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

registerSpeciesReference(String, SBMLSimpleSpeciesReference) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Registers a species reference.

report() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference

Typeset this reference.

report() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference

report(MarkupElement, boolean) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

Typeset this reaction.

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAlgebraicRule

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartment

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartmentType

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEvent

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRateRule

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference

Report a delete.

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesType

reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition

reportDelete(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment

Report delete.

reportDelete(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay

Report delete.

reportDelete(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority

Report delete.

reportDelete(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger

Report delete.

reportDelete(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw

Report delete.

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAlgebraicRule

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartment

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartmentType

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEvent

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRateRule

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference

Report an insert.

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesType

reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition

reportInsert(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment

Report insert.

reportInsert(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay

Report insert.

reportInsert(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority

Report insert.

reportInsert(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger

Report insert.

reportInsert(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw

Report insert.

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAlgebraicRule

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartment

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartmentType

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEvent

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRateRule

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesType

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition

reportModification(SimpleConnectionManager, SBMLEventAssignment, SBMLEventAssignment, MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment

Report modification on this entity.

reportModification(SimpleConnectionManager, SBMLEventDelay, SBMLEventDelay, MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay

Report modifications on the entity.

reportModification(SimpleConnectionManager, SBMLEventPriority, SBMLEventPriority, MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority

Report modifications on the entity.

reportModification(SimpleConnectionManager, SBMLEventTrigger, SBMLEventTrigger, MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger

Report modifications.

reportModification(SimpleConnectionManager, SBMLKineticLaw, SBMLKineticLaw, MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw

Report modification of the entities.

reportModification(SimpleConnectionManager, SBMLSimpleSpeciesReference, SBMLSimpleSpeciesReference) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference

Report modification between two versions of this species reference.

reportModification(SimpleConnectionManager, SBMLSpeciesReference, SBMLSpeciesReference) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference

Report the modifications of this species reference.

resolveSymbol(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Resolve certain symbol.

resolveSymbole(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel

Deprecated.

as of version 1.3.6, replaced by SBMLModel.resolveSymbol(String)

resolveVariable(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment

Resolve variable.

resolveVariable(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRule

Resolves a variable.

rulePath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a rule.

S

SBMLAlgebraicRule - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLAlgebraicRule used to express equations that are neither assignments of model variables nor rates of change.

SBMLAlgebraicRule(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLAlgebraicRule

Instantiates a new SBML algebraic rule.

SBMLAnotation - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLAnotation ,a container for optional software-generated content not meant to be shown to humans.

SBMLAnotation(DocumentNode) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLAnotation

Instantiates a new SBML anotation.

SBMLAssignmentRule - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLAssignmentRule used to express equations that set the values of variables.

SBMLAssignmentRule(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule

Instantiates a new SBML assignment rule.

SBMLCompartment - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLCompartment, a bounded space in which species are located.

SBMLCompartment(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLCompartment

Instantiates a new SBML compartment.

SBMLCompartmentType - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLCompartmentType, a grouping construct used to establish a relationship between multiple SBMLCompartments.

SBMLCompartmentType(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLCompartmentType

Instantiates a new SBML compartment type.

SBMLConnector - Class in de.unirostock.sems.bives.sbml.algorithm

The Class SBMLConnector to connect SBML documents.

SBMLConnector(Connector) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector

Instantiates a new SBML connector.

SBMLConnector(Connector, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector

Instantiates a new SBML connector.

SBMLConnector(SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector

Instantiates a new SBML connector.

SBMLConnector(SBMLDocument, SBMLDocument, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector

Instantiates a new SBML connector.

SBMLConnectorPreprocessor - Class in de.unirostock.sems.bives.sbml.algorithm

The Class SBMLConnectorPreprocessor to pre-compute a mapping.

SBMLConnectorPreprocessor(Connector) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor

Instantiates a new sBML connector preprocessor.

SBMLConnectorPreprocessor(Connector, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor

Instantiates a new sBML connector preprocessor.

SBMLConnectorPreprocessor(SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor

Instantiates a new sBML connector preprocessor.

SBMLConnectorPreprocessor(SBMLDocument, SBMLDocument, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor

Instantiates a new sBML connector preprocessor.

SBMLConstraint - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLConstraint, a mechanism for stating the assumptions under which a model is designed to operate.

SBMLConstraint(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLConstraint

Instantiates a new SBML constraint.

SBMLDiff - Class in de.unirostock.sems.bives.sbml.api

The Class SBMLDiff to compare two SBML models.

SBMLDiff(SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff

Instantiates a new SBML differ.

SBMLDiff(SBMLDocument, SBMLDocument, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff

Instantiates a new SBML differ.

SBMLDiff(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff

Instantiates a new SBML differ.

SBMLDiff(TreeDocument, TreeDocument, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff

Instantiates a new SBML differ.

SBMLDiff(File, File) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff

Instantiates a new SBML differ.

SBMLDiff(File, File, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff

Instantiates a new SBML differ.

SBMLDiff(String, String) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff

Instantiates a new SBML differ.

SBMLDiff(String, String, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff

Instantiates a new SBML differ.

SBMLDiffAnnotator - Class in de.unirostock.sems.bives.sbml.algorithm

SBMLDiffAnnotator() - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

SBMLDiffInterpreter - Class in de.unirostock.sems.bives.sbml.algorithm

The Class SBMLDiffInterpreter to interpret a mapping of SBML models.

SBMLDiffInterpreter(SimpleConnectionManager, SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffInterpreter

Instantiates a new SBML diff interpreter.

SBMLDiffReport - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLDiffReport creates a report about the differences between two versions of an SBML document.

SBMLDiffReport() - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport

Instantiates a new sBML diff report.

SBMLDocument - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLDocument representing a document holding an SBMLModel.

SBMLDocument(TreeDocument) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLDocument

Instantiates a new SBML document.

SBMLEvent - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLEvent describes the time and form of instantaneous, discontinuous state changes in the model.

SBMLEvent(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEvent

Instantiates a new sBML event.

SBMLEventAssignment - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLEventAssignment.

SBMLEventAssignment(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment

Instantiates a new SBML event assignment.

SBMLEventDelay - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLEventDelay.

SBMLEventDelay(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay

Instantiates a new SBML event delay.

SBMLEventPriority - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLEventPriority.

SBMLEventPriority(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority

Instantiates a new SBML event priority.

SBMLEventTrigger - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLEventTrigger.

SBMLEventTrigger(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger

Instantiates a new SBML event trigger.

SBMLFunctionDefinition - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLFunctionDefinition associates an identifier with a function definition.

SBMLFunctionDefinition(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition

Instantiates a new SBML function definition.

SBMLGenericIdNameObject - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLGenericIdNameObject representing a generic object that has an id and a name.

SBMLGenericIdNameObject(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject

Instantiates a new SBML generic id-name-object.

SBMLGenericObject - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLGenericObject representing a generic SBML object.

SBMLGenericObject(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

Instantiates a new generic SBML object.

SBMLGraphProducer - Class in de.unirostock.sems.bives.sbml.algorithm

The Class SBMLGraphProducer to create the graphs.

SBMLGraphProducer(SimpleConnectionManager, SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer

Instantiates a new SBML graph producer for difference graphs.

SBMLGraphProducer(SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer

Instantiates a new SBML graph producer for single document graphs.

SBMLInitialAssignment - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLInitialAssignment assigning initial values to entities in a model.

SBMLInitialAssignment(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment

Instantiates a new SBML initial assignment.

SBMLKineticLaw - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLKineticLaw defines the speed at which the process defined by the reaction takes place.

SBMLKineticLaw(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw

Instantiates a new SBML kinetic law.

SBMLListOf - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLListOf represents a list of something in SBML.

SBMLListOf(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLListOf

Instantiates a new SBML list of ...

SBMLMeta - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLMeta to handle annotations and stuff.

SBMLMeta() - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLMeta

sbmlModel - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

The sbml model.

SBMLModel - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLModel representing a model encoded in SBML.

SBMLModel(DocumentNode, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLModel

Instantiates a new SBML model.

SBMLParameter - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLParameter is used to define a symbol associated with a value; this symbol can then be used in mathematical formulas in a model.

SBMLParameter(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLParameter

Instantiates a new SBML parameter.

SBMLRateRule - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLRateRule used to express equations that determine the rates of change of variables.

SBMLRateRule(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLRateRule

Instantiates a new SBML rate rule.

SBMLReaction - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLReaction represents any kind of process that can change the quantity of one or more species in a model.

SBMLReaction(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLReaction

Instantiates a new SBML reaction.

SBMLRule - Class in de.unirostock.sems.bives.sbml.parser

The abstract Class SBMLRule.

SBMLRule(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLRule

Instantiates a new SBML rule.

SBMLSBase - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLSBase.

SBMLSBase(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSBase

Instantiates a new SBMLS base.

SBMLSimpleSpeciesReference - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLSimpleSpeciesReference representing a link to a species (mainly for modifiers, parent class for substrates and products).

SBMLSimpleSpeciesReference(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference

Instantiates a new SBML simple species reference.

SBMLSingle - Class in de.unirostock.sems.bives.sbml.api

The Class SBMLSingle to study single SBML documents.

SBMLSingle(SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLSingle

Instantiates a new object to study single SBML documents.

SBMLSingle(TreeDocument) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLSingle

Instantiates a new object.

SBMLSingle(File) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLSingle

Instantiates a new object to study single SBML documents.

SBMLSingle(String) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLSingle

Instantiates a new object to study single SBML documents.

SBMLSpecies - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLSpecies representing a species in an SBML document.

SBMLSpecies(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSpecies

Instantiates a new SBML species.

SBMLSpeciesReference - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLSpeciesReference representing a link to a species.

SBMLSpeciesReference(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference

Instantiates a new SBML species reference.

SBMLSpeciesType - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLSpeciesType representing type of species (level < 3).

SBMLSpeciesType(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesType

Instantiates a new SBML species type.

SBMLUnit - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLUnit representing a factor based on a unit:

SBMLUnit(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLUnit

Instantiates a new SBML unit derived from a base unit.

SBMLUnitDefinition - Class in de.unirostock.sems.bives.sbml.parser

The Class SBMLUnitDefinition.

SBMLUnitDefinition(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition

Instantiates a new SBML unit definition.

SBMLUnitDefinition(String, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition

Instantiates a new SBML base unit.

SBMLValidator - Class in de.unirostock.sems.bives.sbml.algorithm

The Class SBMLValidator validates SBML code.

SBMLValidator() - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLValidator

species - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference

The species it is linking to.

speciesPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a species.

T

type - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule

The type flag encoding the type of rule.

U

unitsPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

The XPATH to a reaction.

V

validate(TreeDocument) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLValidator

validate(File) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLValidator

validate(String) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLValidator

A B C D E F G H I K M N O P R S T U V