All Differences

Removals

Additions

Changes

Bold is New, strike is deleted

A  B C D E F G I L M N O P Q R S T U V X Y Z TOP
accept
  type  (SBase) in org.sbml.jsbml.KineticLaw
  type  (SBase) in org.sbml.jsbml.Model
  type  (SBase) in org.sbml.jsbml.ext.comp.CompModelPlugin
  type  (SBase) in org.sbml.jsbml.ext.spatial.SpatialModelPlugin
addAdditionalGraphicalObject (GraphicalObject)
addAllChangeListeners
  type  (Collection<TreeNodeChangeListener>, boolean) in org.sbml.jsbml.AbstractTreeNode
  type  (Collection<TreeNodeChangeListener>, boolean) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
addPlugin
  type  (String, SBasePlugin) in org.sbml.jsbml.AbstractSBase
  type  (String, SBasePlugin) in org.sbml.jsbml.SBase
addReferenceGlyph (ReferenceGlyph)
addSampledField (SampledField)
AdvectionCoefficient
  AdvectionCoefficient (int, int) constructor
  AdvectionCoefficient (String, int, int) constructor
all_L3_namespaces
AnalyticVolume.FunctionKind
ArraysParser

B  A C D E F G I L M N O P Q R S T U V X Y Z TOP
base
BASE_UNIT_SUFFIX
BoundaryCondition.BoundaryKind

C  A B D E F G I L M N O P Q R S T U V X Y Z TOP
checkBrackets (ASTNode)
checkDenominatorBrackets (ASTNode)
clone
  type  () in org.sbml.jsbml.ext.fbc.ListOfObjectives
  type  () in org.sbml.jsbml.ext.groups.ListOfMemberConstraint
  type  () in org.sbml.jsbml.util.ListOfWithName
complementA
complementB
compression
coordinate
CoordinateKind
CoordinateReference
coordinateReference1
coordinateReference2
createGeneralGlyph
  type  () in org.sbml.jsbml.ext.layout.GeneralGlyph
  type  (String) in org.sbml.jsbml.ext.layout.GeneralGlyph
createGroup
  type  (String) in org.sbml.jsbml.ext.groups.GroupsModelPlugin
  type  (String, String[]) in org.sbml.jsbml.ext.groups.GroupsModelPlugin
createMemberWithIdRef
  type  (String) in org.sbml.jsbml.ext.groups.Group
  type  (String, String) in org.sbml.jsbml.ext.groups.Group
createMemberWithMetaIdRef
  type  (String) in org.sbml.jsbml.ext.groups.Group
  type  (String, String) in org.sbml.jsbml.ext.groups.Group
createMixedGeometry
  type  () in org.sbml.jsbml.ext.spatial.Geometry
  type  (String) in org.sbml.jsbml.ext.spatial.Geometry
createPluginFor (SBase)
createReferenceGlyph ()
createReferenceGlyphForList
  type  () in org.sbml.jsbml.ext.layout.GeneralGlyph
  type  (String) in org.sbml.jsbml.ext.layout.GeneralGlyph
createSampledField
  type  () in org.sbml.jsbml.ext.spatial.Geometry
  type  (String) in org.sbml.jsbml.ext.spatial.Geometry
CSGPrimitive.PrimitiveKind
CSGSetOperator.SetOperation
CVTermTests

D  A B C E F G I L M N O P Q R S T U V X Y Z TOP
data
DiffusionCoefficient
  DiffusionCoefficient (int, int) constructor
  DiffusionCoefficient (String, int, int) constructor
DiffusionCoefficient.DiffusionKind
diffusionKind

E  A B C D F G I L M N O P Q R S T U V X Y Z TOP
equals (Object)

F  A B C D E G I L M N O P Q R S T U V X Y Z TOP
filterCVTerms
  type  (Qualifier, boolean, String[]) in org.sbml.jsbml.AbstractSBase
  type  (Qualifier, boolean, String[]) in org.sbml.jsbml.SBase
filterResources
  type  (String[]) in org.sbml.jsbml.CVTerm
  type  (Pattern[]) in org.sbml.jsbml.CVTerm
FormulaCompilerLibSBML
formulaToString (ASTNode, FormulaCompiler)

G  A B C D E F I L M N O P Q R S T U V X Y Z TOP
Geometry (String, int, int) constructor
Geometry.GeometryKind
getActivator ()
getBoundaryMaximum ()
getBoundaryMinimum ()
getChild (int)
getChildElement (String, String)
getChildElements (String, String)
getComplementA ()
getComplementB ()
getCompression ()
getCoordinate ()
getCoordinateReference1 ()
getCoordinateReference2 ()
getData ()
getDataString ()
getDiffusionKind ()
getDomainType ()
getEventAssignment (String)
getExtensionCount
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.SBase
getExternalModelDefinition
  type  (int) in org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
  type  (String) in org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
getFluxBoundCount ()
getIdManager (SBase)
getInterpolation ()
getIsActive ()
getListOfSampledFields ()
getMemberConstraintCount ()
getModelDefinition
  type  (int) in org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
  type  (String) in org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
getNamespaceFor (int, int, int)
getNumCompartmentGlyphs ()
getNumExternalModelDefinitions ()
getNumFluxBound ()
getNumGroups ()
getNumLayouts ()
getNumMemberConstraints ()
getNumMembers ()
getNumModelDefinitions ()
getNumObjective ()
getNumPorts ()
getNumReactionGlyphs ()
getNumReplacedElements ()
getNumSpeciesGlyphs ()
getNumSubmodels ()
getNumTextGlyphs ()
getObjectiveCount ()
getPackageName ()
getPackageNamespaces ()
getPort
  type  (int) in org.sbml.jsbml.ext.comp.CompModelPlugin
  type  (String) in org.sbml.jsbml.ext.comp.CompModelPlugin
getProcess ()
getReplacedElement
  type  (int) in org.sbml.jsbml.ext.comp.CompSBasePlugin
  type  (String) in org.sbml.jsbml.ext.comp.CompSBasePlugin
getSideProduct ()
getSideSubstrate ()
getSpatialDimensions ()
getSpeciesReferenceGlyph (String)
getSubmodel
  type  (int) in org.sbml.jsbml.ext.comp.CompModelPlugin
  type  (String) in org.sbml.jsbml.ext.comp.CompModelPlugin
getType ()
getVariable ()
getVariableInstance ()
GraphicalPrimitive1D (int, int) constructor
GraphicalPrimitive2D (int, int) constructor

I  A B C D E F G L M N O P Q R S T U V X Y Z TOP
IdManager
initDefaults (int, int, boolean)
interpolation
isActive
  type  () in org.sbml.jsbml.ext.spatial.GeometryDefinition
 in  org.sbml.jsbml.ext.spatial.SpatialConstants
isAssociation (int)
isDissociation (int)
isPackageEnabledOrDisabled (String)
isProcess (int)
isRequired ()
isSetBoundaryMaximum ()
isSetBoundaryMinimum ()
isSetComplementA ()
isSetComplementB ()
isSetCompression ()
isSetCoordinate ()
isSetCoordinateReference1 ()
isSetCoordinateReference2 ()
isSetData ()
isSetDiffusionKind ()
isSetDomainType ()
isSetInterpolation ()
isSetIsActive ()
isSetListOfSampledFields ()
isSetSpatialDimensions ()
isSetSpatialRef ()
isSetType ()
isSetVariable ()
isVector ()

L  A B C D E F G I M N O P Q R S T U V X Y Z TOP
lambdaBody (List<ASTNode>)
LEFT_BRACES
 in  org.sbml.jsbml.text.parser.FormulaParserConstants
 in  org.sbml.jsbml.text.parser.FormulaParserLL3Constants
LEFT_BRACKET
 in  org.sbml.jsbml.text.parser.FormulaParserConstants
 in  org.sbml.jsbml.text.parser.FormulaParserLL3Constants
ListOfWithName (ListOfWithName<SBase>) constructor
LocalStyle
  LocalStyle (int, int, RenderGroup) constructor
  LocalStyle (String, int, int, RenderGroup) constructor
  LocalStyle (RenderGroup) constructor
logicalOperation (String, List<ASTNode>)

M  A B C D E F G I L N O P Q R S T U V X Y Z TOP
main (String[])
metaIds ()
MixedGeometry
ModelBuilder

N  A B C D E F G I L M O P Q R S T U V X Y Z TOP
numBvars
numPiece

O  A B C D E F G I L M N P Q R S T U V X Y Z TOP
of (Comparable<? super L>, Comparable<? super V>)
OrdinalMapping
org.sbml.jsbml.ext.arrays
org.sbml.jsbml.ext.arrays.compiler
org.sbml.jsbml.ext.arrays.flattening
org.sbml.jsbml.ext.arrays.test
org.sbml.jsbml.ext.arrays.util
org.sbml.jsbml.ext.arrays.validator
org.sbml.jsbml.ext.arrays.validator.constraints
org.sbml.jsbml.ext.fbc.test
org.sbml.jsbml.ext.groups.test
org.sbml.jsbml.ext.layout.test
org.sbml.jsbml.ext.qual.test
org.sbml.jsbml.ext.render.test
org.sbml.jsbml.math.test

P  A B C D E F G I L M N O Q R S T U V X Y Z TOP
Pair
ParametricObject.PolygonKind
ParseException (Throwable) constructor
PROPERTY_UNDEFINED_EXCEPTION_MSG_SBASE
PROPERTY_UNDEFINED_EXCEPTION_MSG_TREE_NODE
PropertyUndefinedError (String, TreeNode) constructor

Q  A B C D E F G I L M N O P R S T U V X Y Z TOP
QualitativeModel (QualModelPlugin) constructor
QualModelPlugin

R  A B C D E F G I L M N O P Q S T U V X Y Z TOP
register
  type  (SBase) in org.sbml.jsbml.KineticLaw
  type  (SBase) in org.sbml.jsbml.Model
  type  (SBase) in org.sbml.jsbml.ext.comp.CompModelPlugin
  type  (SBase) in org.sbml.jsbml.ext.spatial.SpatialModelPlugin
relation (ASTNode, String, ASTNode)
removeAdjacentDomain (String)
removeAllTreeNodeChangeListeners
  type  (boolean) in org.sbml.jsbml.AbstractTreeNode
  type  (boolean) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
removeAnalyticVolume (String)
removeBasePoint1 ()
removeBasePoint2 ()
removeCompartmentGlyph
  type  (CompartmentGlyph) in org.sbml.jsbml.ext.layout.Layout
  type  (int) in org.sbml.jsbml.ext.layout.Layout
  type  (String) in org.sbml.jsbml.ext.layout.Layout
removeCoordinateComponent (String)
removeCSGNode (String)
removeCVTerm
  type  (CVTerm) in org.sbml.jsbml.AbstractSBase
  type  (int) in org.sbml.jsbml.AbstractSBase
  type  (CVTerm) in org.sbml.jsbml.Annotation
  type  (int) in org.sbml.jsbml.Annotation
  type  (CVTerm) in org.sbml.jsbml.SBase
  type  (int) in org.sbml.jsbml.SBase
 in  org.sbml.jsbml.util.TreeNodeChangeEvent
removeDomain (String)
removeDomainType (String)
removeEnd ()
removeEventAssignment (EventAssignment)
removeGeneralGlyph
  type  (int) in org.sbml.jsbml.ext.layout.GeneralGlyph
  type  (GraphicalObject) in org.sbml.jsbml.ext.layout.GeneralGlyph
  type  (int) in org.sbml.jsbml.ext.layout.Layout
  type  (String) in org.sbml.jsbml.ext.layout.Layout
  type  (GeneralGlyph) in org.sbml.jsbml.ext.layout.Layout
removeGeometryDefinition (String)
removeReactionGlyph
  type  (ReactionGlyph) in org.sbml.jsbml.ext.layout.Layout
  type  (int) in org.sbml.jsbml.ext.layout.Layout
  type  (String) in org.sbml.jsbml.ext.layout.Layout
removeSampledField
  type  (SampledField) in org.sbml.jsbml.ext.spatial.Geometry
  type  (int) in org.sbml.jsbml.ext.spatial.Geometry
  type  (String) in org.sbml.jsbml.ext.spatial.Geometry
removeSampledVolume (String)
removeSingletons ()
removeSpeciesGlyph
  type  (SpeciesGlyph) in org.sbml.jsbml.ext.layout.Layout
  type  (int) in org.sbml.jsbml.ext.layout.Layout
  type  (String) in org.sbml.jsbml.ext.layout.Layout
removeStart ()
removeTextGlyph
  type  (TextGlyph) in org.sbml.jsbml.ext.layout.Layout
  type  (int) in org.sbml.jsbml.ext.layout.Layout
  type  (String) in org.sbml.jsbml.ext.layout.Layout
RenderCurve
RenderGroup
RIGHT_BRACES
 in  org.sbml.jsbml.text.parser.FormulaParserConstants
 in  org.sbml.jsbml.text.parser.FormulaParserLL3Constants
RIGHT_BRACKET
 in  org.sbml.jsbml.text.parser.FormulaParserConstants
 in  org.sbml.jsbml.text.parser.FormulaParserLL3Constants

S  A B C D E F G I L M N O P Q R T U V X Y Z TOP
SampledField
  SampledField (int, int) constructor
  SampledField (String, int, int) constructor
SampledField.CompressionKind
SampledField.DataKind
SampledField.InterpolationKind
selector (Object[])
setAreaUnits (Kind)
setBoundaryMaximum (Boundary)
setBoundaryMinimum (Boundary)
setCaseSensitive (boolean)
setComplementA (String)
setComplementB (String)
setCompression (CompressionKind)
setCoordinate (CoordinateKind)
setCoordinateReference1 (CoordinateKind)
setCoordinateReference2 (CoordinateKind)
setData
  type  (String) in org.sbml.jsbml.ext.spatial.SampledField
  type  (XMLNode) in org.sbml.jsbml.ext.spatial.SampledField
setDiffusionKind (DiffusionKind)
setDomainType (String)
setExtendedSBase (SBase)
setExtentUnits (Kind)
setInterpolation (InterpolationKind)
setIsActive (boolean)
setLengthUnits (Kind)
setListOfReferenceGlyph (ListOf<ReferenceGlyph>)
setListOfSampledFields (ListOf<SampledField>)
setNotesKeyToUserObject (String)
setPolygonType (PolygonKind)
setPrimitiveType (PrimitiveKind)
setSpatialDimensions (int)
setSubstanceUnits (Kind)
setTimeUnits (Kind)
setType (CoordinateKind)
setUp ()
setVariable (String)
setVolumeUnits (Kind)
spatialDimensions
SpatialTest
SPLITTER
stringToType
Style
  Style (int, int, RenderGroup) constructor
  Style (String, int, int, RenderGroup) constructor
  Style (RenderGroup) constructor

T  A B C D E F G I L M N O P Q R S U V X Y Z TOP
test_CVTerm_removeResources ()
TestSBase
toFormula (FormulaCompiler)
Transformation (int, int) constructor
Transformation2D (int, int) constructor

U  A B C D E F G I L M N O P Q R S T V X Y Z TOP
unregister
  type  (SBase) in org.sbml.jsbml.ext.comp.CompModelPlugin
  type  (SBase) in org.sbml.jsbml.ext.spatial.SpatialModelPlugin
unregisterChild
  type  (SBase) in org.sbml.jsbml.AbstractSBase
  type  (SBase) in org.sbml.jsbml.SBase
unsetBoundaryMaximum ()
unsetBoundaryMinimum ()
unsetComplementA ()
unsetComplementB ()
unsetCompression ()
unsetCoordinate ()
unsetCoordinateReference1 ()
unsetCoordinateReference2 ()
unsetData ()
unsetDiffusionKind ()
unsetGraphicalObject ()
unsetInterpolation ()
unsetIsActive ()
unsetListOfSampledFields ()
unsetListOfSpeciesReferencesGlyph ()
unsetType ()

V  A B C D E F G I L M N O P Q R S T U X Y Z TOP
valuePairOf (Comparable<? super L>, Comparable<? super V>)
vector
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.ASTNodeCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FindUnitsCompiler
  type  (Object[]) in org.sbml.jsbml.util.compilers.FormulaCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FormulaCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.LaTeXCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.MathMLCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.UnitsCompiler

X  A B C D E F G I L M N O P Q R S T U V Y Z TOP
x ()

Y  A B C D E F G I L M N O P Q R S T U V X Z TOP
y ()

Z  A B C D E F G I L M N O P Q R S T U V X Y TOP
z ()