A-Index (Omix API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes|All Packages

A

abs() - Method in class omix.util.math.BigFraction
abs(Number) - Static method in class omix.mathxp.util.MathUtilities
Abstract - Annotation Type in omix.lang.reflect.annotation
AbstractAccessManager - Interface in omix.plugin: This interface allows to access features of the Omix Plugin Interface as super type of ApplicationAccessManager and DocumentAccessManager.
AbstractApplicationExtension - Class in omix.util.ext: This class implements the ApplicationExtensionInterface with empty methods.
AbstractApplicationExtension(ApplicationAccessManager) - Constructor for class omix.util.ext.AbstractApplicationExtension: The constructor of the application extension must be called inside a custom implementation of the method ApplicationExtensionFactory.newApplicationExtension(ApplicationAccessManager).
AbstractBioNode - Interface in omix.plugin.model
AbstractBioNode - Interface in omix.plugin.model.writable
AbstractBioNode - Interface in omix.plugin.motifstamp
AbstractBioNode - Interface in omix.plugin.motifstamp.writable
AbstractBioNodeItem - Interface in omix.plugin.diagram
AbstractBioNodeItem - Interface in omix.plugin.diagram.writable
AbstractCategoryChart - Class in omix.lang.chart: This class is superclass of all category charts.
AbstractComposedXYDataset<C extends AbstractComposedXYDataset.Coordinate> - Class in omix.lang.chart.data: This class represents a X,Y coordinate dataset that has been composed by the user.
AbstractComposedXYDataset.Coordinate - Class in omix.lang.chart.data
AbstractConfigWidget - Class in omix.util.ui: This abstract class can be derived to realize a member widget of the configuration dialog window.
AbstractConfigWidget() - Constructor for class omix.util.ui.AbstractConfigWidget: Same as AbstractConfigWidget(null, null)
AbstractConfigWidget(QWidget) - Constructor for class omix.util.ui.AbstractConfigWidget: Same as AbstractConfigWidget(parent, null)
AbstractConfigWidget(QWidget, Settings) - Constructor for class omix.util.ui.AbstractConfigWidget: Sets the parent widget and the settings variable of the config widget.
AbstractConfigWidget(Settings) - Constructor for class omix.util.ui.AbstractConfigWidget: Same as AbstractConfigWidget(null, settings)
AbstractControlPoint - Interface in omix.plugin.model.points: Generalizes all possible control points of a curve.
AbstractControlPoint - Interface in omix.plugin.model.writable.points
AbstractCSVTable<T> - Class in omix.lang.io: This class is superclass for all data type bound CVS table classes.
AbstractCSVTable(File, String, String, String, String, boolean, int, Charset) - Constructor for class omix.lang.io.AbstractCSVTable: Creates a new table that reads the given file from a start line.
AbstractCurvePoint - Interface in omix.plugin.model.points: Generalizes all curve describing points.
AbstractCurvePoint - Interface in omix.plugin.model.writable.points
AbstractDataMatrix - Class in omix.util.data: This class implements listener management of a data matrix and serves as abstract adapter class for DataMatrixInterface.
AbstractDataMatrix() - Constructor for class omix.util.data.AbstractDataMatrix
AbstractDiagramComponent - Interface in omix.plugin.diagram: This interface generalizes AbstractItem and Group as allowed members of a network diagram and additionally of a group.
AbstractDocumentExtension - Class in omix.util.ext: This class implements the DocumentExtensionInterface with empty methods.
AbstractDocumentExtension(DocumentAccessManager) - Constructor for class omix.util.ext.AbstractDocumentExtension: The constructor of the application extension must be called inside a custom implementation of the method DocumentExtensionFactory.newDocumentExtension(DocumentAccessManager).
AbstractDomReader - Class in omix.util.io: This class is an abstract definition of a reader using DOM (Package org.w3c.dom).
AbstractDomReader(URLConnection, InputUtilities) - Constructor for class omix.util.io.AbstractDomReader
AbstractDomWriter - Class in omix.util.io: This class is an abstract definition of a writer using DOM (Package org.w3c.dom).
AbstractDomWriter(URLConnection, OutputUtilities) - Constructor for class omix.util.io.AbstractDomWriter
AbstractDoubleVec<T extends AbstractDoubleVec<T>> - Class in omix.util.math.vector: Describes a vector in N dimensional space with double precision.
AbstractDoubleVec() - Constructor for class omix.util.math.vector.AbstractDoubleVec: Default constructor
AbstractEdge - Interface in omix.plugin.model
AbstractEdge - Interface in omix.plugin.model.writable
AbstractEdge - Interface in omix.plugin.motifstamp
AbstractEdge - Interface in omix.plugin.motifstamp.writable
AbstractEdgeItem - Interface in omix.plugin.diagram
AbstractEdgeItem - Interface in omix.plugin.diagram.writable
AbstractErrorIndicator - Class in omix.lang.chart.util: This class is superclass for all error indicators.
AbstractErrorIndicator() - Constructor for class omix.lang.chart.util.AbstractErrorIndicator
AbstractFloatVec<T extends AbstractFloatVec<T>> - Class in omix.util.math.vector: Describes a vector in N dimensional space with float precision.
AbstractFloatVec() - Constructor for class omix.util.math.vector.AbstractFloatVec: Default constructor
AbstractItem - Interface in omix.plugin.diagram: This class generalizes all types of visible network components as well as the network and the model.
AbstractItem - Interface in omix.plugin.diagram.writable
AbstractItem - Interface in omix.plugin.motifstamp
AbstractItem - Interface in omix.plugin.motifstamp.writable
AbstractLineChartProperties - Class in omix.lang.chart.util
AbstractLineChartProperties() - Constructor for class omix.lang.chart.util.AbstractLineChartProperties
AbstractMathConstant - Class in omix.mathxp
AbstractMathConstant() - Constructor for class omix.mathxp.AbstractMathConstant
AbstractMathConstant(int, int) - Constructor for class omix.mathxp.AbstractMathConstant
AbstractMathReference - Class in omix.mathxp
AbstractMathReference() - Constructor for class omix.mathxp.AbstractMathReference
AbstractMathReference(int, int) - Constructor for class omix.mathxp.AbstractMathReference
AbstractMathReference(AbstractMathReference) - Constructor for class omix.mathxp.AbstractMathReference
AbstractMathReference(UnitInterface) - Constructor for class omix.mathxp.AbstractMathReference
AbstractMathReference(UnitInterface, int, int) - Constructor for class omix.mathxp.AbstractMathReference
AbstractModelComponent - Interface in omix.plugin.model
AbstractModelComponent - Interface in omix.plugin.model.writable
AbstractModelIODomHandler - Class in omix.util.io: This class can be used to realize a ModelIOHandlerInterface for Omix with DOM (Package org.w3c.dom).
AbstractModelIODomHandler() - Constructor for class omix.util.io.AbstractModelIODomHandler: Empty constructor
AbstractModelIOHandler - Class in omix.util.io: This class can be used to realize a ModelIOHandlerInterface for Omix.
AbstractModelIOHandler() - Constructor for class omix.util.io.AbstractModelIOHandler: Empty constructor
AbstractModelItem - Interface in omix.plugin.diagram
AbstractModelItem - Interface in omix.plugin.diagram.writable
AbstractMultiplePieChart - Class in omix.lang.chart
AbstractMultiplePieChart() - Constructor for class omix.lang.chart.AbstractMultiplePieChart
AbstractMultiplePieChart(CategoryDataset) - Constructor for class omix.lang.chart.AbstractMultiplePieChart
AbstractNode - Interface in omix.plugin.model
AbstractNode - Interface in omix.plugin.model.writable
AbstractNode - Interface in omix.plugin.motifstamp
AbstractNode - Interface in omix.plugin.motifstamp.writable
AbstractNodeItem - Interface in omix.plugin.diagram
AbstractNodeItem - Interface in omix.plugin.diagram.writable
AbstractOVLType - Interface in omix.plugin.ovl: Generalizes OVLItemExtension and OVLClass.
AbstractPieChart - Class in omix.lang.chart: This class is superclass of all pie charts.
AbstractPieChart.DataExtractOrder - Enum in omix.lang.chart
AbstractReader - Class in omix.util.io: This class can be subclassed in order to realize a file reader.
AbstractReader(URLConnection, InputUtilities) - Constructor for class omix.util.io.AbstractReader: Called with the parameters of ModelIOHandlerInterfaceV2#read(String, URLConnection, omix.plugin.io.WritableModel, InputUtilities)
AbstractSideBox - Interface in omix.lang.model.accessory.annotation: This accessory represents charts as side items in the network diagram.
AbstractSideBox - Interface in omix.plugin.model.accessory.annotation
AbstractSideBox - Interface in omix.plugin.model.writable.accessory.annotation
AbstractSideBoxItem - Interface in omix.plugin.diagram.accessory.annotation
AbstractSideBoxItem - Interface in omix.plugin.diagram.writable.accessory.annotation
AbstractStackableChart - Class in omix.lang.chart: This class is superclass of all category charts that can be stacked.
AbstractStackableChart() - Constructor for class omix.lang.chart.AbstractStackableChart
AbstractStackableChart(CategoryDataset) - Constructor for class omix.lang.chart.AbstractStackableChart
AbstractStackableChart(CategoryDataset, StackMode) - Constructor for class omix.lang.chart.AbstractStackableChart
AbstractStackableChart(StackMode) - Constructor for class omix.lang.chart.AbstractStackableChart
AbstractTable<T> - Class in omix.lang.io: This class represents a general table format with cells which are accessible by the horizontal header text and an index.
AbstractTable(File) - Constructor for class omix.lang.io.AbstractTable: Constructs a table object from the given file.
AbstractTable(InputStream) - Constructor for class omix.lang.io.AbstractTable: Constructs a table object from the given input stream.
AbstractTableXYDataset<T extends XYTableDataReference> - Class in omix.lang.chart.data: This class represents a X,Y coordinate dataset that bases on a table from the DataManager.
AbstractTitle - Class in omix.lang.chart.util: This class is superclass for title and legend.
AbstractTitle.Position - Enum in omix.lang.chart.util
AbstractVec<T extends AbstractVec<T>> - Class in omix.util.math.vector: Describes a vector in N dimensional space.
AbstractVec() - Constructor for class omix.util.math.vector.AbstractVec: Default constructor
AbstractVisibleComponent - Interface in omix.plugin.model
AbstractVisibleComponent - Interface in omix.plugin.model.writable
AbstractWriter - Class in omix.util.io: This class can be subclassed in order to realize a file writer.
AbstractWriter(URLConnection, OutputUtilities) - Constructor for class omix.util.io.AbstractWriter: Called with the parameters of ModelIOHandlerInterface.write(String, URLConnection, omix.plugin.network.Model, OutputUtilities)
AbstractXYChart<T extends XYDataset> - Class in omix.lang.chart: This class us superclass of all X,Y coordinate charts in Omix.
AbstractXYZChart<T extends XYZDataset> - Class in omix.lang.chart: This class is superclass of all X,Y,Z coordinate charts.
Academic - omix.util.licensing.LicenseType
accelerationAt(double) - Method in class omix.util.math.curves.ArcSectionComputer2D: returns the acceleration (second derivative) of the curve at the parameter t
accelerationAt(double) - Method in class omix.util.math.curves.BezierSectionComputer: returns the acceleration (second derivative) of the curve at the parameter t
accelerationAt(double) - Method in class omix.util.math.curves.CurveSectionComputer: returns the acceleration (second derivative) of the curve at the parameter t.
accessManager() - Method in class omix.util.ext.AbstractApplicationExtension: The access manager permits access to various features of the Omix Plugin Interface.
accessManager() - Method in class omix.util.ext.AbstractDocumentExtension: The access manager permits access to various features of the Omix Plugin Interface.
Accessory - Interface in omix.lang.model.accessory: This type represents all accessories available in OVL.
Accessory - Interface in omix.plugin.model.accessory
Accessory - Interface in omix.plugin.model.writable.accessory
ACCESSORY - omix.plugin.ovl.annotation.OVLTarget.OVLElementType
accessoryAnchorFloating() - Method in interface omix.plugin.diagram.AbstractEdgeItem
accessoryAnchorFloating() - Method in interface omix.plugin.diagram.AbstractNodeItem
accessoryAnchorFloating() - Method in interface omix.plugin.diagram.CompartmentItem
accessoryAnchorFloating() - Method in interface omix.plugin.diagram.PathwayItem
accessoryAnchorPlacement() - Method in interface omix.plugin.diagram.AbstractEdgeItem
accessoryAnchorPlacement() - Method in interface omix.plugin.diagram.AbstractNodeItem
accessoryAnchorPlacement() - Method in interface omix.plugin.diagram.CompartmentItem
accessoryAnchorPlacement() - Method in interface omix.plugin.diagram.PathwayItem
AccessoryAnchorPlacement - Enum in omix.util
accessoryAnchorX() - Method in interface omix.plugin.diagram.AbstractEdgeItem
accessoryAnchorX() - Method in interface omix.plugin.diagram.AbstractNodeItem
accessoryAnchorX() - Method in interface omix.plugin.diagram.CompartmentItem
accessoryAnchorX() - Method in interface omix.plugin.diagram.PathwayItem
accessoryAnchorY() - Method in interface omix.plugin.diagram.AbstractEdgeItem
accessoryAnchorY() - Method in interface omix.plugin.diagram.AbstractNodeItem
accessoryAnchorY() - Method in interface omix.plugin.diagram.CompartmentItem
accessoryAnchorY() - Method in interface omix.plugin.diagram.PathwayItem
accessoryExists(String) - Method in interface omix.plugin.ovl.OVLItemExtension: Determines if accessory exists in type definition or supertypes.
accessoryExists(String, String) - Method in interface omix.plugin.model.AbstractVisibleComponent
accessoryExists(String, String) - Method in interface omix.plugin.model.Model
accessoryFloating() - Method in interface omix.plugin.diagram.AbstractEdgeItem
accessoryFloating() - Method in interface omix.plugin.diagram.AbstractNodeItem
accessoryFloating() - Method in interface omix.plugin.diagram.CompartmentItem
accessoryFloating() - Method in interface omix.plugin.diagram.PathwayItem
AccessoryItem - Interface in omix.plugin.diagram.accessory
AccessoryItem - Interface in omix.plugin.diagram.writable.accessory
AccessoryItemOwner - Interface in omix.plugin.diagram.accessory
AccessoryItemOwner - Interface in omix.plugin.diagram.writable.accessory
accessoryOrientation() - Method in interface omix.plugin.diagram.AbstractEdgeItem
accessoryOrientation() - Method in interface omix.plugin.diagram.AbstractNodeItem
accessoryOrientation() - Method in interface omix.plugin.diagram.CompartmentItem
accessoryOrientation() - Method in interface omix.plugin.diagram.PathwayItem
AccessoryOwner - Interface in omix.plugin.model.accessory
AccessoryOwner - Interface in omix.plugin.model.writable.accessory
accessorySpacing() - Method in interface omix.plugin.diagram.AbstractEdgeItem
accessorySpacing() - Method in interface omix.plugin.diagram.AbstractNodeItem
accessorySpacing() - Method in interface omix.plugin.diagram.CompartmentItem
accessorySpacing() - Method in interface omix.plugin.diagram.PathwayItem
acosh(double) - Static method in class omix.mathxp.util.MathUtilities
acsch(double) - Static method in class omix.mathxp.util.MathUtilities
actions() - Method in interface omix.plugin.data.DataMatrixInterface
actions() - Method in class omix.plugin.ui.PopupMenuAction
actions() - Method in class omix.util.data.AbstractDataMatrix
activate() - Method in interface omix.plugin.DocumentExtensionInterface: This method is invoked when the document is activated in the multi document area.
activatePlugin(String) - Method in interface omix.plugin.model.writable.Model: Activates the given plugin on the network model document.
activatePlugin(String) - Method in interface omix.plugin.ovl.OVLFieldConverterUtilities: Activates a certain plugin on the network model document.
activationArrowShape() - Method in interface omix.lang.model.EffectorEdge: The shape of the edge's arrow when it shows activation.
activationArrowShape() - Method in interface omix.plugin.model.EffectorEdge: The shape of the edge's arrow when it shows activation.
activationArrowShape() - Method in interface omix.plugin.model.LinkEdge.EffectorEdgeAppearance: The shape of the edge's arrow when it shows activation.
activationArrowShape() - Method in interface omix.plugin.motifstamp.writable.EffectorEdge: The shape of the edge's arrow when it shows activation.
activationBrush() - Method in interface omix.lang.model.EffectorEdge: The paint brush of the edge's arrow when it shows activation.
activationBrush() - Method in interface omix.plugin.model.EffectorEdge: The paint brush of the edge's arrow when it shows activation.
activationBrush() - Method in interface omix.plugin.model.LinkEdge.EffectorEdgeAppearance: The paint brush of the edge's arrow when it shows activation.
activationBrush() - Method in interface omix.plugin.motifstamp.writable.EffectorEdge: The paint brush of the edge's arrow when it shows activation.
add(int, E) - Method in class omix.util.collections.WeakList
add(int, T) - Method in class omix.util.collections.HashList
add(E) - Method in class omix.util.collections.WeakList
add(E) - Method in class omix.util.collections.WeakSet
add(Number) - Method in class omix.util.math.BigFraction
add(Number, Number) - Static method in class omix.mathxp.util.MathUtilities
add(Number, MathContext) - Method in class omix.util.math.BigFraction
add(String, Object) - Method in class omix.plugin.type.TypeSerializationHandlerInterface.ComponentMapSerialization
add(MathExpression, MathExpression, List<Error>) - Method in class omix.mathxp.util.ExpressionUtilities.SummandList
add(ExpressionUtilities.SummandList, List<Error>) - Method in class omix.mathxp.util.ExpressionUtilities.SummandList
add(T) - Method in class omix.util.collections.HashList
Add - omix.plugin.model.util.ChangeEvent.EventType
ADD - omix.mathxp.MathOperation.Operator
addAction(QAction) - Method in class omix.plugin.ui.PopupMenuAction
addAll(int, Collection<? extends E>) - Method in class omix.util.collections.WeakList
addAll(int, Collection<? extends T>) - Method in class omix.util.collections.HashList
addAll(Collection<? extends E>) - Method in class omix.util.collections.WeakCollection
addAll(Collection<? extends T>) - Method in class omix.util.collections.HashList
addAll(Collection<? super T>, T...) - Static method in class omix.util.collections.Collections
addCategory(int, String) - Method in class omix.lang.chart.data.ComposedCategoryDataset
addCategory(int, String) - Method in class omix.lang.chart.util.ErrorComposedDataset
addCategory(String) - Method in class omix.lang.chart.data.ComposedCategoryDataset
addCategory(String) - Method in class omix.lang.chart.util.ErrorComposedDataset
addChangeListener(ChangeListener) - Method in interface omix.plugin.diagram.AbstractItem
addChangeListener(ChangeListener) - Method in interface omix.plugin.diagram.Diagram
addChangeListener(ChangeListener) - Method in interface omix.plugin.model.AbstractModelComponent
addChangeListener(ChangeListener) - Method in interface omix.plugin.model.Model: Adds a ChangeListener which is triggered when the composition of the network changes.
addChangeListener(ModelChangeListener) - Method in interface omix.plugin.model.Model: Adds a ModelChangeListener which is triggered when the composition of the network changes.
addChangeListener(ModelChangeListener) - Method in interface omix.plugin.model.writable.Model: Adds a NetworkChangeListener which is triggered when the composition of the network changes.
addChartChangeListener(ChartChangeListener) - Method in class omix.lang.chart.Chart
addChartChangeListener(ChartChangeListener) - Method in class omix.lang.chart.data.TableDataReference
addClosingWidgetListener(ClosingWidgetInterface.ClosingWidgetListener) - Method in interface omix.plugin.type.util.ClosingWidgetInterface: Registers a listener
addComponent(AbstractModelComponent) - Method in interface omix.plugin.model.writable.Model: Created diagram items have to be inserted into the metabolic network before taking any effect.
OVL definitions do not become part of a diagram component until the item is added to the diagram.
After adding a Metabolite or Metabolite to the diagram, a ModelMetaboliteType is simultaneously added to the Model.
addContextMenuEntryProvider(ContextMenuEntryProvider) - Method in interface omix.plugin.model.Model
addCustomShape(String, List<? extends AbstractCurvePoint>) - Method in interface omix.plugin.model.writable.Model: Creates a new custom shape available for nodes or edge markers.
AddCustomShapes - omix.plugin.model.util.ModelCapability
addDataManagerChangeListener(DataManager.DataManagerChangeListener) - Method in interface omix.plugin.data.DataManager
addDataMatrixChangeListener(DataMatrixChangeListener) - Method in interface omix.plugin.data.DataMatrixInterface: Adds a change listener to the data matrix.
addDataMatrixChangeListener(DataMatrixChangeListener) - Method in interface omix.plugin.data.Table
addDataMatrixChangeListener(DataMatrixChangeListener) - Method in class omix.util.data.AbstractDataMatrix: Adds a change listener to the data matrix.
addDataReference(T) - Method in class omix.lang.chart.data.TableDataset: Adds an additional table data reference to the dataset.
addDatasetChangeListener(DatasetChangeListener) - Method in class omix.lang.chart.data.ComposedDataset: Add a dataset change listener.
addDatasetChangeListener(DatasetChangeListener) - Method in interface omix.lang.chart.data.Dataset: Add a dataset change listener.
addDatasetChangeListener(DatasetChangeListener) - Method in class omix.lang.chart.data.TableDataset: Add a dataset change listener.
addDataSourceChangeListener(DataSourceChangeListener) - Method in interface omix.plugin.data.DataSourceInterface
addDateSource(String, DataSourceInterface) - Method in interface omix.plugin.data.writable.DataSourceManager
addDiagram(Diagram) - Method in interface omix.plugin.model.writable.Model
AddDiagrams - omix.plugin.model.util.ModelCapability
addDockWidget(QDockWidget) - Method in interface omix.plugin.AbstractAccessManager: Adds a dock widget to the Omix mainwindow.
addDockWidget(QDockWidget, Qt.DockWidgetArea) - Method in interface omix.plugin.AbstractAccessManager: Adds a dock widget to the Omix mainwindow.
Added - omix.util.ui.AnnotationChangeEvent.ChangeType
addEdge(E, N, N) - Method in class omix.util.math.graph.Graph: Edges can be added by specifying a reference to any kind of external edge connecting two nodes.
addError(String) - Method in class omix.plugin.io.util.MessageCollector: Adds an error message.
addError(UnitCheckMessageCollectorInterface.UnitCheckMessage) - Method in interface omix.mathxp.util.UnitCheckMessageCollectorInterface
addErrorTableReference(ErrorTableDataset.ErrorTableReference) - Method in class omix.lang.chart.util.ErrorTableDataset
addExponent(MathExpression, List<Error>) - Method in class omix.mathxp.util.ExpressionUtilities.Multiplier
addIndex(String, Integer) - Method in class omix.lang.io.AbstractTable: inserts a column identifier in association with the column index.
addItem(Component) - Method in interface omix.lang.model.accessory.annotation.ItemGroup: Add item to the item list.
addItem(AbstractItem) - Method in interface omix.plugin.diagram.writable.Diagram: Created diagram items have to be inserted into the metabolic network before taking any effect.
OVL definitions do not become part of a diagram component until the item is added to the diagram.
After adding a MetaboliteItem or Metabolite to the diagram, a MetaboliteType is simultaneously added to the Model.
addItem(Guideline) - Method in interface omix.plugin.diagram.writable.Diagram
addItem(PatternItem) - Method in interface omix.plugin.diagram.writable.Diagram
addItem(AbstractItem) - Method in interface omix.plugin.motifstamp.writable.MotifStamp
addItemContextMenuEntries(Object, Field, QMenu) - Method in interface omix.plugin.model.util.ContextMenuEntryProvider: This method is called whenever the user causes a context menu to be shown on a VoD branch.
addItemContextMenuEntries(DataAnnotation, QMenu) - Method in interface omix.plugin.model.util.ContextMenuEntryProvider: This method is called whenever the user causes a context menu to be shown on an accessory.
addItemContextMenuEntries(AbstractItem, QMenu) - Method in interface omix.plugin.model.util.ContextMenuEntryProvider: This method is called whenever the user causes a context menu to be shown.
addItemContextMenuEntries(DataAnnotationItem, QMenu) - Method in interface omix.plugin.model.util.ContextMenuEntryProvider
addItemContextMenuEntries(AbstractModelComponent, QMenu) - Method in interface omix.plugin.model.util.ContextMenuEntryProvider
AddItems - omix.plugin.model.util.ModelCapability
additiveExpression() - Method in class omix.mathxp.parser.MathExpressionsParser
addMenu(QMenu) - Method in interface omix.plugin.AbstractAccessManager: Adds a menu to the menubar of Omix.
addMenuItem(QAction) - Method in interface omix.plugin.AbstractAccessManager: Adds an action to the extras menu of Omix.
addMenuItem(QAction, PluginMenuItemType) - Method in interface omix.plugin.AbstractAccessManager: Adds an action to the menubar of Omix according to the PluginMenuItemType parameter.
addModelComponent(AbstractModelComponent) - Method in interface omix.plugin.model.accessory.annotation.ItemGroup: Add item to the item list.
addMotifStamp(MotifStamp) - Method in interface omix.plugin.model.writable.Model
AddMotifStamps - omix.plugin.model.util.ModelCapability
addMultiplicator(MathExpression, List<Error>) - Method in class omix.mathxp.util.ExpressionUtilities.Summand
addNode(N) - Method in class omix.util.math.graph.Graph: Nodes can be added by specifying a reference to any kind of external graph component.
addProperty(String, String, Class<?>) - Method in interface omix.plugin.vod.VoDObject
addPropertyChangeListener(PropertyChangeListener) - Method in class omix.lang.chart.util.ChartStyleElement
addPropertyChangeListener(PropertyChangeListener) - Method in interface omix.plugin.diagram.AbstractItem
addPropertyChangeListener(PropertyChangeListener) - Method in interface omix.plugin.diagram.Guideline
addPropertyChangeListener(PropertyChangeListener) - Method in interface omix.plugin.model.AbstractModelComponent
addPropertyChangeListener(PropertyChangeListener) - Method in interface omix.plugin.model.Model
addPropertyChangeListener(PropertyChangeListener) - Method in interface omix.plugin.model.points.AbstractCurvePoint
addPublicIdentifier(PublicIdentifier) - Method in interface omix.plugin.model.writable.Compartment: Adds a public identifier to the item.
addPublicIdentifier(PublicIdentifier) - Method in interface omix.plugin.model.writable.MetaboliteType: Adds a public identifier to the item.
addPublicIdentifier(PublicIdentifier) - Method in interface omix.plugin.model.writable.Model: Adds a public identifier to the model.
addPublicIdentifier(PublicIdentifier) - Method in interface omix.plugin.model.writable.Pathway: Adds a public identifier to the item.
addPublicIdentifier(PublicIdentifier) - Method in interface omix.plugin.model.writable.Reaction: Adds a public identifier to the item.
addRenderingHints(Map<?, ?>) - Method in class omix.util.ui.QPaintGraphics2D
addResizeListener(TypeGraphicsHandlerInterface.ValuePainterInterface.ResizeListenerInterface) - Method in interface omix.plugin.type.TypeGraphicsHandlerInterface.ValuePainterInterface
addSender(ValueChangeSender) - Method in interface omix.lang.reflect.ValueChangeListener: This method is called from inside ValueChangeSender.connect(ValueChangeListener...) in order to install a bidirectional connection.
addSender(ValueChangeSender) - Method in class omix.util.ui.EventBasedItemPropertyChangeListener: This method is called from inside ValueChangeSender.connect(ValueChangeListener...) in order to install a bidirectional connection.
addSender(ValueChangeSender) - Method in class omix.util.ui.EventBasedValueChangeListener: This method is called from inside ValueChangeSender.connect(ValueChangeListener...) in order to install a bidirectional connection.
addSender(ValueChangeSender) - Method in class omix.util.ValueChangeAdapter: This method is called from inside ValueChangeSender.connect(ValueChangeListener...) in order to install a bidirectional connection.
addSeries(int, String) - Method in class omix.lang.chart.data.ComposedCategoryDataset
addSeries(int, String) - Method in class omix.lang.chart.util.ErrorComposedDataset
addSeries(String) - Method in class omix.lang.chart.data.ComposedCategoryDataset
addSeries(String) - Method in class omix.lang.chart.util.ErrorComposedDataset
addShutdownHook(Runnable) - Static method in class omix.util.ui.ThreadAffineUtility
addSynonym(String) - Method in interface omix.plugin.model.writable.Compartment: Adds a synonym to the item.
addSynonym(String) - Method in interface omix.plugin.model.writable.MetaboliteType: Adds a synonym to the item.
addSynonym(String) - Method in interface omix.plugin.model.writable.Pathway: Adds a synonym to the item.
addSynonym(String) - Method in interface omix.plugin.model.writable.Reaction: Adds a synonym to the item.
addSynonym(String, String) - Method in interface omix.plugin.model.writable.Compartment: Adds a synonym to the item.
addSynonym(String, String) - Method in interface omix.plugin.model.writable.MetaboliteType: Adds a synonym to the item.
addSynonym(String, String) - Method in interface omix.plugin.model.writable.Pathway: Adds a synonym to the item.
addSynonym(String, String) - Method in interface omix.plugin.model.writable.Reaction: Adds a synonym to the item.
addTableRepresentation(String, String, DataMatrixInterface.Representations) - Method in interface omix.plugin.data.writable.DataSourceManager
addTask(AutoCloseable) - Method in class omix.util.FinallyTasks
addToolBar(QToolBar) - Method in interface omix.plugin.AbstractAccessManager: Adds a toolbar to the mainwindow.
addToolBar(QToolBar, Qt.ToolBarArea) - Method in interface omix.plugin.AbstractAccessManager: Adds a toolbar to the mainwindow.
addToolBarAction(QAction) - Method in interface omix.plugin.AbstractAccessManager: Adds an action to the plugin toolbar of Omix.
addToolBarAction(QAction, PluginToolbarItemType) - Method in interface omix.plugin.AbstractAccessManager: Adds an action to the plugin toolbar of Omix according to the PluginToolbarItemType parameter.
addUpdateListener(TypeGraphicsHandlerInterface.ValuePainterInterface.UpdateListenerInterface) - Method in interface omix.plugin.type.TypeGraphicsHandlerInterface.ValuePainterInterface
addValue(Object) - Method in class omix.lang.JsonArray
addValue(String, double, double) - Method in class omix.lang.chart.data.ComposedXYDataset
addValue(String, double, double, double) - Method in class omix.lang.chart.data.ComposedXYZDataset
addValue(String, int, double, double) - Method in class omix.lang.chart.data.ComposedXYDataset
addValue(String, int, double, double, double) - Method in class omix.lang.chart.data.ComposedXYZDataset
addWarning(String) - Method in class omix.plugin.io.util.MessageCollector: Adds a warning.
addWarning(UnitCheckMessageCollectorInterface.UnitCheckMessage) - Method in interface omix.mathxp.util.UnitCheckMessageCollectorInterface
All - omix.lang.chart.data.Qualifier
All - omix.plugin.model.util.ModelCapability
allCompartments() - Method in interface omix.lang.model.Model: Returns an unchangeable List of all compartment items.
allCompartments() - Method in interface omix.plugin.model.Model: Returns an unchangeable List of all compartment items.
allCompartments() - Method in interface omix.plugin.model.writable.Model: Returns an unchangeable List of all compartment items.
allowsThreadedPixmaps() - Static method in class omix.util.PixmapManager
amd64 - omix.util.SystemInfo.Architecture
AMP - Static variable in class omix.mathxp.parser.MathExpressionsLexer
AMP - Static variable in class omix.mathxp.parser.MathExpressionsParser
ampere - omix.mathxp.units.SIUnit
Analysis - omix.plugin.util.PluginMenuItemType: The "Analysis" menu.
analyze() - Method in class omix.util.math.graph.Graph: Computation of all CCs and SCCs in the graph.
and(Validator) - Method in interface omix.lang.annotation.util.Validator
AND - omix.mathxp.MathOperation.Operator
andExpression() - Method in class omix.mathxp.parser.MathExpressionsParser
angle() - Method in interface omix.plugin.diagram.Guideline
AngledRectangle - omix.lang.StandardShapes: AngledRectangle.
AngledRectangle - Static variable in interface omix.lang.Shape: AngledRectangle.
ANGULAR - omix.plugin.model.points.Smoothness: Arbitrary non-smooth alignment.
annotation - Variable in class omix.util.ui.AnnotationChangeEvent
annotationAdded(Annotation) - Method in interface omix.plugin.ovl.reflect.AnnotationChangeListener
annotationAdded(Annotation) - Method in class omix.util.ItemPropertyChangeListener
annotationAdded(Annotation) - Method in class omix.util.SynchronousItemPropertyChangeListener
annotationAdded(Annotation) - Method in class omix.util.ui.EventBasedItemPropertyChangeListener
annotationAdded(Annotation) - Method in class omix.util.ui.EventBasedValueChangeListener
annotationAdded(Object, String, Annotation) - Method in interface omix.plugin.ovl.reflect.AnnotationChangeListener
annotationAdded(Object, String, Annotation) - Method in class omix.util.ItemPropertyChangeListener
annotationAdded(Object, String, Annotation) - Method in class omix.util.SynchronousItemPropertyChangeListener
annotationAdded(Object, String, Annotation) - Method in class omix.util.ui.EventBasedItemPropertyChangeListener
AnnotationArray<T extends DataAnnotation> - Interface in omix.plugin.model.accessory.annotation
AnnotationArray<T extends DataAnnotation> - Interface in omix.plugin.model.writable.accessory.annotation
AnnotationArrayItem<T extends DataAnnotationItem> - Interface in omix.plugin.diagram.accessory.annotation
AnnotationArrayItem<T extends DataAnnotationItem> - Interface in omix.plugin.diagram.writable.accessory.annotation
AnnotationChangeEvent - Class in omix.util.ui
AnnotationChangeEvent(Object, String, AnnotationChangeEvent.ChangeType, Annotation) - Constructor for class omix.util.ui.AnnotationChangeEvent
AnnotationChangeEvent.ChangeType - Enum in omix.util.ui
AnnotationChangeListener - Interface in omix.plugin.ovl.reflect
annotationRemoved(Annotation) - Method in interface omix.plugin.ovl.reflect.AnnotationChangeListener
annotationRemoved(Annotation) - Method in class omix.util.ItemPropertyChangeListener
annotationRemoved(Annotation) - Method in class omix.util.SynchronousItemPropertyChangeListener
annotationRemoved(Annotation) - Method in class omix.util.ui.EventBasedItemPropertyChangeListener
annotationRemoved(Annotation) - Method in class omix.util.ui.EventBasedValueChangeListener
annotationRemoved(Object, String, Annotation) - Method in interface omix.plugin.ovl.reflect.AnnotationChangeListener
annotationRemoved(Object, String, Annotation) - Method in class omix.util.ItemPropertyChangeListener
annotationRemoved(Object, String, Annotation) - Method in class omix.util.SynchronousItemPropertyChangeListener
annotationRemoved(Object, String, Annotation) - Method in class omix.util.ui.EventBasedItemPropertyChangeListener
AntiAliasing - omix.plugin.paint.PaintHandlerInterface.PaintOption: Anti-aliasing
anyOtherNonsence() - Method in class omix.mathxp.parser.MathExpressionsParser
APIVersion - Class in omix.util: This class represents the minimum Omix API version a plug-in must base on in order to be compatible.
appearance() - Method in interface omix.plugin.model.Link
appearance() - Method in interface omix.plugin.model.LinkEdge
appearance() - Method in interface omix.plugin.model.writable.Link
appearance() - Method in interface omix.plugin.model.writable.LinkEdge
application() - Static method in class omix.util.SystemInfo: This method returns the actual application.
ApplicationAccessManager - Interface in omix.plugin: This interface allows to access features of the Omix Plugin Interface.
ApplicationExtensionFactory - Interface in omix.plugin: This interface must be derived by a custom plugin class in order to implement an application extension.
A custom class implementing ApplicationExtensionFactory can be registered at the Omix Plugin Manager:
ApplicationExtensionInterface - Interface in omix.plugin: This interface can be implemented in order to realize a global extension for Omix.
Applications - Enum in omix.util: This enum represents the Application Product
applicationVersion() - Static method in class omix.util.SystemInfo: This method returns the application version.
apply(Object, JsonArray) - Method in interface omix.lang.FunctionPointer
apply(A) - Method in interface omix.util.ui.ThrowingFunction: This method is called inside of EventLoopParallelAction or ThreadAffineUtility.
apply(A, B) - Method in interface omix.util.ui.ThrowingFunction2: This method is called inside of EventLoopParallelAction or ThreadAffineUtility.
apply(A, B, C) - Method in interface omix.util.ui.ThrowingFunction3: This method is called inside of EventLoopParallelAction or ThreadAffineUtility.
apply(A, B, C, D) - Method in interface omix.util.ui.ThrowingFunction4: This method is called inside of EventLoopParallelAction or ThreadAffineUtility.
apply(A, B, C, D, E) - Method in interface omix.util.ui.ThrowingFunction5: This method is called inside of EventLoopParallelAction or ThreadAffineUtility.
Arc - Interface in omix.plugin.model.points: Represents an arc as curve describing component of an edge.
An arc consists of a center point, radius in X and Y direction, a start angle and a length in degrees.
Arc - Interface in omix.plugin.model.writable.points
arch() - Static method in class omix.util.SystemInfo: This method returns the processor architecture of the current platform.
ArcSectionComputer2D - Class in omix.util.math.curves: This class represents an arc curve section.
ArcSectionComputer2D(Vec2d, double, double, double, double) - Constructor for class omix.util.math.curves.ArcSectionComputer2D: creates a new arc section computation unit.
AreaChart - Class in omix.lang.chart
AreaChart() - Constructor for class omix.lang.chart.AreaChart
AreaChart(CategoryDataset) - Constructor for class omix.lang.chart.AreaChart
AreaChart(CategoryDataset, StackMode) - Constructor for class omix.lang.chart.AreaChart
AreaChart(StackMode) - Constructor for class omix.lang.chart.AreaChart
AreaChartProperties - Class in omix.lang.chart.util
AreaChartProperties() - Constructor for class omix.lang.chart.util.AreaChartProperties
arm - omix.util.SystemInfo.Architecture
Array<T extends Accessory> - Interface in omix.lang.model.accessory: This type represents accessory arrays.
Array<T extends Accessory> - Interface in omix.plugin.model.accessory
Array<T extends Accessory> - Interface in omix.plugin.model.writable.accessory
ArrayItem<T extends AccessoryItem> - Interface in omix.plugin.diagram.accessory
ArrayItem<T extends AccessoryItem> - Interface in omix.plugin.diagram.writable.accessory
ArrayWrapper<T> - Class in omix.util.wrap
arrowShape() - Method in interface omix.lang.model.FluxEdge: The shape of the edge's arrow.
arrowShape() - Method in interface omix.plugin.model.FluxEdge: The shape of the edge's arrow.
arrowShape() - Method in interface omix.plugin.model.LinkEdge.FluxEdgeAppearance: The shape of the edge's arrow.
arrowShape() - Method in interface omix.plugin.motifstamp.writable.FluxEdge: The shape of the edge's arrow.
arrowSize() - Method in interface omix.lang.model.EffectorEdge: The size of the edge's arrow given as multiple of the edge width.
arrowSize() - Method in interface omix.lang.model.FluxEdge: The size of the edge's arrow given as multiple of the edge width.
arrowSize() - Method in interface omix.plugin.model.EffectorEdge: The size of the edge's arrow given as multiple of the edge width.
arrowSize() - Method in interface omix.plugin.model.FluxEdge: The size of the edge's arrow given as multiple of the edge width.
arrowSize() - Method in interface omix.plugin.model.LinkEdge.EffectorEdgeAppearance: The size of the edge's arrow given as multiple of the edge width.
arrowSize() - Method in interface omix.plugin.model.LinkEdge.FluxEdgeAppearance: The size of the edge's arrow given as multiple of the edge width.
arrowSize() - Method in interface omix.plugin.motifstamp.writable.EffectorEdge: The size of the edge's arrow given as multiple of the edge width.
arrowSize() - Method in interface omix.plugin.motifstamp.writable.FluxEdge: The size of the edge's arrow given as multiple of the edge width.
asech(double) - Static method in class omix.mathxp.util.MathUtilities
asFlags() - Method in enum omix.plugin.data.DataMatrixInterface.DeletableFlag
asFlags() - Method in enum omix.plugin.data.DataMatrixInterface.Representation
asFlags() - Method in enum omix.plugin.model.util.ModelCapability
asinh(double) - Static method in class omix.mathxp.util.MathUtilities
asLifoQueue(Deque<T>) - Static method in class omix.util.collections.Collections
asList(Collection<E>) - Static method in class omix.util.collections.Collections
assignValue(Object, Object, OVLFieldConverterUtilities) - Method in interface omix.plugin.ovl.OVLCompatibilityHandlerInterface.OVLFieldConverterInterface
attach(OVLEnvironment) - Method in interface omix.plugin.model.writable.Model: Attaches this writable model to the OVL environment.
atto - omix.mathxp.units.SIPrefix
authenticator() - Method in interface omix.plugin.AbstractAccessManager: An authenticator asking the user for passwords.
authenticator() - Method in interface omix.plugin.data.DataInputUtilities: Returns the authenticator of Omix allowing to prompts the user to enter a login.
authenticator() - Method in interface omix.plugin.data.DataOutputUtilities: Returns the authenticator of Omix allowing to prompts the user to enter a login.
authenticator() - Method in interface omix.plugin.io.util.InputUtilities: Returns the authenticator of Omix allowing to prompts the user to enter a login.
authenticator() - Method in interface omix.plugin.io.util.OutputUtilities: Returns the authenticator of Omix allowing to prompts the user to enter a login.
Authenticator - Interface in omix.plugin.util: This interface allows plugins to ask the user for login information.
Authenticator.DomainUsernamePassword - Class in omix.plugin.util: Represents a domain+username/password answer.
Authenticator.Password - Class in omix.plugin.util: Represents a password answer.
Authenticator.UsernamePassword - Class in omix.plugin.util: Represents a username/password answer.
available(String) - Method in class omix.lang.io.AbstractTable: checks the availability of a column
availableSizes() - Method in interface omix.plugin.model.util.Thumbnails: Returns all available sizes of the thumbnail list.
avg(int) - Method in class omix.lang.io.CSVDoubleTable: returns the average value of a row (index).
avg(int) - Method in class omix.lang.io.CSVIntegerTable: returns the average value of a row (index).
avg(String) - Method in class omix.lang.io.CSVDoubleTable: returns the average value of a column (identifier).
avg(String) - Method in class omix.lang.io.CSVIntegerTable: returns the average value of a column (identifier).
Axis - Class in omix.lang.chart.util: This class represents an axis in charts.
Axis() - Constructor for class omix.lang.chart.util.Axis
AXIS_PARALLEL - omix.plugin.model.points.Smoothness: Alignment parallel to the axes.
Axis.LabelLocation - Enum in omix.lang.chart.util: Used to indicate the location of an axis label.
Axis.Position - Enum in omix.lang.chart.util

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes|All Packages