P-Index (Omix API)

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P

PadSpread - omix.lang.Gradient.Spread: The gradient spreads with the last/first color.
Page - omix.plugin.paint.PaintHandlerInterface.PaintOption: If an image format is a page oriented file format like PDF.
paint() - Method in interface omix.lang.model.accessory.annotation.SideBox: The fill appearance of the item's shape.
paint() - Method in interface omix.lang.model.accessory.annotation.SubNode: Deprecated.

The fill appearance of the item's shape.
paint() - Method in interface omix.lang.model.BioNode: The fill appearance of the item's shape.
paint() - Method in interface omix.lang.model.Compartment: The fill brush of the item's shape.
paint() - Method in interface omix.lang.model.GraphicsBox: The fill appearance of the item's shape.
paint() - Method in interface omix.lang.model.GraphicsItem: Deprecated.

The fill appearance of the item's shape.
paint() - Method in interface omix.lang.model.GraphicsNode: The fill appearance of the item's shape.
paint() - Method in interface omix.lang.model.Link: The fill appearance of the item's shape.
paint() - Method in interface omix.lang.model.MetNode: Deprecated.

The fill appearance of the item's shape.
paint() - Method in interface omix.lang.model.Node: The fill appearance of the item's shape.
paint() - Method in interface omix.plugin.diagram.MetaboliteItem
paint() - Method in interface omix.plugin.model.AbstractNode: The fill appearance of the item's shape.
paint() - Method in interface omix.plugin.model.Compartment: The fill brush of the item's shape.
paint() - Method in interface omix.plugin.model.GraphicsBox: The fill appearance of the item's shape.
paint() - Method in interface omix.plugin.model.GraphicsNode: The fill appearance of the item's shape.
paint() - Method in interface omix.plugin.model.Link: The fill appearance of the item's shape.
paint() - Method in interface omix.plugin.motifstamp.GraphicsNode: The fill appearance of the item's shape.
paint() - Method in interface omix.plugin.motifstamp.Metabolite: The fill appearance of the item's shape.
paint(QPainter, QRect) - Method in interface omix.plugin.type.TypeEditHandlerInterface.CellPainterInterface
paint(QPainter, QRectF) - Method in interface omix.plugin.type.TypeGraphicsHandlerInterface.ValuePainterInterface: Called when an object of specific type shall be painted in accessory ObjectField or in Visualization on Demand (VoD).
paint(QPainter, QStyleOptionGraphicsItem, QWidget) - Method in class omix.mathxp.ui.scene.MathConstant2D
paint(QPainter, QStyleOptionGraphicsItem, QWidget) - Method in class omix.mathxp.ui.scene.MathFunction2D
paint(QPainter, QStyleOptionGraphicsItem, QWidget) - Method in class omix.mathxp.ui.scene.MathOperation2D
paint(QPainter, QStyleOptionGraphicsItem, QWidget) - Method in class omix.mathxp.ui.scene.MathReference2D
paint(QPainter, QStyleOptionGraphicsItem, QWidget) - Method in class omix.mathxp.ui.scene.MathRoot2D
paint(QPainter, QStyleOptionGraphicsItem, QWidget) - Method in class omix.mathxp.ui.scene.MathUnit2D
Paint - Interface in omix.lang: This interface represents the paint of diagram component which can be: Brush Color Gradient Fillpattern Texture Image PaintedProperty
PaintableObject - Interface in omix.lang: A PaintableObject is a type that is carried by a PaintProxy painted in a TypeGraphicsHandlerInterface.
paintCell(FieldInfo, PaintValueUtilities) - Method in interface omix.plugin.type.TypeEditHandlerInterface: Paint an object of specific type inside the table cell.
If the class type is not supported, the method must return null.
Omix iterates the list of installed TypeEditHandlers ordered by time of installation.
PaintDeviceInterface - Interface in omix.plugin.paint: This interface must be implemented in order to realize an image export feature for Omix.
PaintedProperty - Class in omix.lang: This class represents a painted property in Omix diagrams.
PaintedProperty(String) - Constructor for class omix.lang.PaintedProperty
PaintedProperty(String, String) - Constructor for class omix.lang.PaintedProperty
PaintedProperty(String, String, Brush) - Constructor for class omix.lang.PaintedProperty
painter() - Method in class omix.util.ui.QPainterUtil.RestoreMacro
PaintException - Exception in omix.plugin.paint: A PaintException can occur during a paint procedure of a plugin PaintHandler.
PaintException() - Constructor for exception omix.plugin.paint.PaintException: Constructs a new exception with null as its detail message.
PaintException(String) - Constructor for exception omix.plugin.paint.PaintException: Constructs a new exception with the specified detail message.
PaintException(String, Throwable) - Constructor for exception omix.plugin.paint.PaintException: Constructs a new exception with the specified detail message and cause.
PaintException(Throwable) - Constructor for exception omix.plugin.paint.PaintException: Constructs a new exception with the specified cause.
PaintHandlerFactory - Interface in omix.plugin.paint: This interface must be derived by a custom plugin class in order to implement export of network diagrams into images and movies of various types.
A custom class implementing PaintHandlerFactory can be registered at the Omix Plugin Manager:
PaintHandlerInterface - Interface in omix.plugin.paint: This interface can be derived in order to implement exporting the network diagram into images and movies.
PaintHandlerInterface.PaintOption - Enum in omix.plugin.paint: Options of a PaintDevice
PaintProxy<T extends PaintableObject> - Class in omix.lang: A PaintProxy contains a paintable object in Omix diagrams.
PaintProxy(Class<T>, T) - Constructor for class omix.lang.PaintProxy
PaintProxy(Class<T>, T, Brush) - Constructor for class omix.lang.PaintProxy
PaintResponse() - Constructor for class omix.plugin.type.TypeEditHandlerInterface.PaintResponse
PaintValueUtilities - Interface in omix.plugin.type.util: This utility allows access to the OVLReadAccess interface and the Settings interface during the method call TypeEditHandlerInterface.paintCell(FieldInfo, PaintValueUtilities)
palette() - Method in interface omix.plugin.type.util.PaintValueUtilities: Access to the color palette of the painted area
parallelStream() - Method in class omix.util.collections.WeakCollection
Parameter(String) - Constructor for class omix.mathxp.MathLambdaExpression.Parameter
Parameter(String, UnitInterface) - Constructor for class omix.mathxp.MathLambdaExpression.Parameter
PARAMETER - omix.plugin.ovl.annotation.OVLTarget.OVLElementType
ParameterConverter - Interface in omix.util.wrap
parent - Variable in class omix.util.math.graph.SCC
parent() - Method in interface omix.plugin.type.util.CreateGraphicsItemUtilities
parentWidget() - Method in interface omix.plugin.AbstractAccessManager: A parent widget important to create modal dialog windows.
For instance:
QDialog dialog = new QDialog(parentWidget()); dialog.show();
parentWidget() - Method in interface omix.plugin.data.DataInputUtilities: Returns a parent widget allowing to implement modal QDialog windows during the I/O operation.
parentWidget() - Method in interface omix.plugin.data.DataOutputUtilities: Returns a parent widget allowing to implement modal QDialog windows during the I/O operation.
parentWidget() - Method in interface omix.plugin.io.util.InputUtilities: Returns a parent widget allowing to implement modal QDialog windows during the I/O operation.
parentWidget() - Method in interface omix.plugin.io.util.OutputUtilities: Returns a parent widget allowing to implement modal QDialog windows during the I/O operation.
parExpression() - Method in class omix.mathxp.parser.MathExpressionsParser
parse(String) - Method in class omix.util.text.DecimalFormat
Parser - omix.plugin.ovl.OVLCompilerMessage.Type
pascal - omix.mathxp.units.DerivedUnit
password - Variable in class omix.plugin.util.Authenticator.Password
Password(String) - Constructor for class omix.plugin.util.Authenticator.Password
PATCH_VERSION - Static variable in class omix.util.APIVersion
patchVersion - Variable in class omix.util.VersionNumber: PATCH version number
pathway() - Method in interface omix.lang.model.Reaction: Returns the pathway the reaction belongs to.
pathway() - Method in interface omix.plugin.diagram.ReactionItem
pathway() - Method in interface omix.plugin.diagram.writable.ReactionItem
pathway() - Method in interface omix.plugin.model.Link.PathwayLinkAppearance
pathway() - Method in interface omix.plugin.model.Reaction: Returns the pathway the reaction belongs to.
pathway() - Method in interface omix.plugin.model.writable.Link.PathwayLinkAppearance
pathway() - Method in interface omix.plugin.model.writable.Reaction: Returns the pathway the reaction belongs to.
Pathway - omix.plugin.io.ModelComponentProviderInterface.ItemType
Pathway - Interface in omix.lang.model: Represents a pathway in the metabolic network diagram.
Pathway - Interface in omix.plugin.model
Pathway - Interface in omix.plugin.model.writable
pathwayAccessoryAnchorFloating() - Method in interface omix.plugin.model.StyleSheet
pathwayAccessoryAnchorPlacement() - Method in interface omix.plugin.model.StyleSheet
pathwayAccessoryFloating() - Method in interface omix.plugin.model.StyleSheet
pathwayAccessoryOrientation() - Method in interface omix.plugin.model.StyleSheet
pathwayAccessorySpacing() - Method in interface omix.plugin.model.StyleSheet
pathwayBlur() - Method in interface omix.plugin.model.StyleSheet: The item's blur.
pathwayBrush() - Method in interface omix.plugin.model.StyleSheet: The fill brush of the item's shape.
pathwayExists(String) - Method in interface omix.plugin.model.Model: Determines if pathway of certain name exists.
pathwayExists(String) - Method in interface omix.plugin.model.writable.Model: Determines if pathway of certain name exists.
pathwayFont() - Method in interface omix.plugin.model.StyleSheet: The item's text label font.
PathwayItem - Interface in omix.plugin.diagram
PathwayItem - Interface in omix.plugin.diagram.writable
pathwayLabelConfiguration() - Method in interface omix.plugin.model.StyleSheet
pathwayLabelHidden() - Method in interface omix.plugin.model.StyleSheet
pathways() - Method in interface omix.lang.model.MetabolicNetwork: Deprecated.

Returns an unchangeable List of all pathway items.
pathways() - Method in interface omix.lang.model.Model: Returns an unchangeable List of all pathway items.
pathways() - Method in interface omix.plugin.diagram.Diagram: Returns an unchangeable List of all pathway items.
pathways() - Method in interface omix.plugin.diagram.writable.Diagram: Returns an unchangeable List of all pathway items.
pathways() - Method in interface omix.plugin.model.Model: Returns an unchangeable List of all pathway items.
pathways() - Method in interface omix.plugin.model.writable.Model: Returns an unchangeable List of all pathway items.
Pathways - omix.plugin.identity.IdentifierCollection.TargetType
pathwaysHidden() - Method in interface omix.plugin.model.StyleSheet
pathwayStrength() - Method in interface omix.plugin.model.StyleSheet: This field specifies the strength of the contour the pathway paints around its reactions and edges.
pathwayStrokeColor() - Method in interface omix.plugin.model.StyleSheet: The color for the stroke of the item's shape.
pathwayStrokeStyle() - Method in interface omix.plugin.model.StyleSheet: The paint style for the stroke of the item's shape.
pathwayStrokeWidth() - Method in interface omix.plugin.model.StyleSheet: The stroke width of the item's shape.
pathwayTextBlur() - Method in interface omix.plugin.model.StyleSheet: The blur of the item's text.
pathwayTextBrush() - Method in interface omix.plugin.model.StyleSheet: The fill brush of the item's text label.
pathwayTextShadow() - Method in interface omix.plugin.model.StyleSheet: The shadow of the item's text.
pathwayTextStrokeColor() - Method in interface omix.plugin.model.StyleSheet: The color for the stroke of the item's text label.
pathwayTextStrokeWidth() - Method in interface omix.plugin.model.StyleSheet: The stroke width of the item's text label.
pathwayTextTransparency() - Method in interface omix.plugin.model.StyleSheet: The transparency of the item's text.
pathwayTransparency() - Method in interface omix.plugin.model.StyleSheet: The item's transparency.
PatternBranch - Interface in omix.plugin.diagram.pattern
PatternBranch - Interface in omix.plugin.diagram.writable.pattern
patternBranches() - Method in interface omix.plugin.diagram.Diagram
patternBranches() - Method in interface omix.plugin.diagram.writable.Diagram
PatternItem - Interface in omix.plugin.diagram.pattern
PatternItem - Interface in omix.plugin.diagram.writable.pattern
patternObject() - Method in interface omix.plugin.diagram.AbstractEdgeItem
patternObject() - Method in interface omix.plugin.diagram.AbstractNodeItem
patternObject() - Method in interface omix.plugin.diagram.writable.AbstractEdgeItem
patternObject() - Method in interface omix.plugin.diagram.writable.AbstractNodeItem
PatternPath - Interface in omix.plugin.diagram.pattern
PatternPath - Interface in omix.plugin.diagram.writable.pattern
patternPaths() - Method in interface omix.plugin.diagram.Diagram
patternPaths() - Method in interface omix.plugin.diagram.writable.Diagram
Pentagon - omix.lang.StandardMarkerShapes
Pentagon - omix.lang.StandardShapes: Pentagon.
Pentagon - Static variable in interface omix.lang.MarkerShape: Pentagon.
Pentagon - Static variable in interface omix.lang.Shape: Pentagon.
Pentagon2 - omix.lang.StandardShapes: Pentagon2.
Pentagon2 - Static variable in interface omix.lang.Shape: Pentagon2.
PercentageError - Class in omix.lang.chart.util
PercentageError() - Constructor for class omix.lang.chart.util.PercentageError
PercentageError(double) - Constructor for class omix.lang.chart.util.PercentageError
PercentageStacked - omix.lang.chart.StackMode
performAction(UndoableAction) - Method in interface omix.plugin.model.writable.Model
Peta - omix.mathxp.units.SIPrefix
pico - omix.mathxp.units.SIPrefix
PieChart - Class in omix.lang.chart
PieChart() - Constructor for class omix.lang.chart.PieChart
PieChart(CategoryDataset) - Constructor for class omix.lang.chart.PieChart
PieChart3D - Class in omix.lang.chart
PieChart3D() - Constructor for class omix.lang.chart.PieChart3D
PieChart3D(CategoryDataset) - Constructor for class omix.lang.chart.PieChart3D
PieChartProperties - Class in omix.lang.chart.util
PieChartProperties() - Constructor for class omix.lang.chart.util.PieChartProperties
PieChartStyle - Class in omix.lang.chart.util
PieChartStyle() - Constructor for class omix.lang.chart.util.PieChartStyle
PieChartStyle.LinkStyle - Enum in omix.lang.chart.util
PITCH - omix.util.math.vector.Matrix4d.RotationType: Rotation about Y axis.
PITCH - omix.util.math.vector.Matrix4f.RotationType: Rotation about Y axis.
pixmap(QBrush, int) - Static method in class omix.util.PixmapManager
pixmap(String) - Method in class omix.util.PixmapManager
PixmapManager - Class in omix.util
PixmapManager(String) - Constructor for class omix.util.PixmapManager
PixmapManager(String, QStyle) - Constructor for class omix.util.PixmapManager
PlatformFontConverter - Class in omix.util.ui
Player - Interface in omix.lang.model.accessory.trigger: A Player has the same functionality as the Slider and, additionally, buttons to increase or decrease the current value with a defined step size and an automatic play routine.
Player - Interface in omix.plugin.model.accessory.trigger
Player - Interface in omix.plugin.model.writable.accessory.trigger
PlayerItem - Interface in omix.plugin.diagram.accessory.trigger
PlayerItem - Interface in omix.plugin.diagram.writable.accessory.trigger
PluginCompatibilityHandlerFactory - Interface in omix.plugin: This interface must be derived by a custom plug-in class in order to implement compatibility when a plug-in identifier changed.
PluginCompatibilityHandlerInterface - Interface in omix.plugin: This interface allows to implement compatibility features of a plug-in in case of changing plug-in identifier.
PluginMenuItemType - Enum in omix.plugin.util: Menus in the menubar.
PluginToolbarItemType - Enum in omix.plugin.util: Actions on the toolbars.
plus(Matrix2d) - Method in class omix.util.math.vector.Matrix2d: Addition
plus(Matrix2f) - Method in class omix.util.math.vector.Matrix2f: Addition
plus(Matrix4d) - Method in class omix.util.math.vector.Matrix4d: Addition
plus(Matrix4f) - Method in class omix.util.math.vector.Matrix4f: Addition
plus(Vec2d) - Method in class omix.util.math.vector.Vec2d
plus(Vec2f) - Method in class omix.util.math.vector.Vec2f
plus(Vec4d) - Method in class omix.util.math.vector.Vec4d
plus(Vec4f) - Method in class omix.util.math.vector.Vec4f
plus(T) - Method in class omix.util.math.vector.AbstractVec: Addition
PLUS - Static variable in class omix.mathxp.parser.MathExpressionsLexer
PLUS - Static variable in class omix.mathxp.parser.MathExpressionsParser
pointAt(double) - Method in class omix.util.math.curves.ArcSectionComputer2D: returns the point of the curve at the parameter t
pointAt(double) - Method in class omix.util.math.curves.BezierSectionComputer: returns the point of the curve at the parameter t
pointAt(double) - Method in class omix.util.math.curves.CurveSectionComputer: returns the point of the curve at the parameter t.
points() - Method in interface omix.plugin.diagram.AbstractEdgeItem
points() - Method in interface omix.plugin.diagram.GraphicsPathItem
points() - Method in interface omix.plugin.diagram.writable.AbstractEdgeItem
points() - Method in interface omix.plugin.diagram.writable.GraphicsPathItem
points() - Method in interface omix.plugin.model.util.CustomShape: all points defining the shape
PopupMenuAction - Class in omix.plugin.ui: Realizes an action that contains a popup action.
PopupMenuAction() - Constructor for class omix.plugin.ui.PopupMenuAction
PopupMenuAction(QObject) - Constructor for class omix.plugin.ui.PopupMenuAction
popupMode() - Method in class omix.plugin.ui.PopupMenuAction
pow(int) - Method in class omix.util.math.BigFraction
pow(Number, Number) - Static method in class omix.mathxp.util.MathUtilities
POW - omix.mathxp.MathOperation.Operator
power(UnitInterface, int) - Static method in class omix.mathxp.units.UnitUtilities
powerExpression() - Method in class omix.mathxp.parser.MathExpressionsParser
powerN(UnitInterface, Number) - Static method in class omix.mathxp.units.UnitUtilities
preferredEnumerator() - Method in interface omix.plugin.data.DataSourceInterface
prefix - Variable in class omix.mathxp.units.UnitFactor
Private - Annotation Type in omix.lang.reflect.annotation
product - Variable in class omix.util.licensing.LicenseKey
program() - Method in interface omix.plugin.ovl.AbstractOVLType: Returns the OVL Program, this type was defined in.
progressListener() - Method in interface omix.plugin.data.DataInputUtilities: Utility that allows to change the progress displayed in a progress bar during a file I/O operation.
progressListener() - Method in interface omix.plugin.data.DataOutputUtilities: Utility that allows to change the progress displayed in a progress bar during a file I/O operation.
progressListener() - Method in interface omix.plugin.io.util.InputUtilities: Utility that allows to change the progress displayed in a progress bar during a file I/O operation.
progressListener() - Method in interface omix.plugin.io.util.OutputUtilities: Utility that allows to change the progress displayed in a progress bar during a file I/O operation.
ProgressListener - Interface in omix.plugin.io.util: Utility that allows to change the progress displayed in a progress bar during a file I/O operation.
properties() - Method in class omix.lang.chart.AreaChart
properties() - Method in class omix.lang.chart.BarChart
properties() - Method in class omix.lang.chart.BarChart3D
properties() - Method in class omix.lang.chart.BubbleChart
properties() - Method in class omix.lang.chart.Chart
properties() - Method in class omix.lang.chart.ColumnChart
properties() - Method in class omix.lang.chart.ColumnChart3D
properties() - Method in class omix.lang.chart.LineChart
properties() - Method in class omix.lang.chart.LineChart3D
properties() - Method in class omix.lang.chart.MultiplePieChart
properties() - Method in class omix.lang.chart.MultiplePieChart3D
properties() - Method in class omix.lang.chart.MultipleRingChart
properties() - Method in class omix.lang.chart.PieChart
properties() - Method in class omix.lang.chart.PieChart3D
properties() - Method in class omix.lang.chart.RingChart
properties() - Method in class omix.lang.chart.ScatterPlot
properties() - Method in class omix.lang.chart.XYAreaChart
properties() - Method in class omix.lang.chart.XYCurveChart
properties() - Method in class omix.lang.chart.XYLineChart
property() - Method in annotation type omix.lang.annotation.Capabilities.PropertyCapabilities
propertyCapabilities() - Method in annotation type omix.lang.annotation.Capabilities
propertyChange(PropertyChangeEvent) - Method in class omix.lang.chart.Chart
propertyChange(PropertyChangeEvent) - Method in class omix.lang.chart.util.ChartStyleElement
propertyChange(PropertyChangeEvent) - Method in class omix.lang.chart.util.ErrorComposedDataset
propertyChange(PropertyChangeEvent) - Method in class omix.lang.chart.util.ErrorTableDataset
propertyChange(PropertyChangeEvent) - Method in interface omix.util.chart.ChartChangeListener: This method is called whenever a property of the chart or chart style, legend, title or background changes.
propertyNames() - Method in interface omix.plugin.vod.VoDObject
Protected - Annotation Type in omix.lang.reflect.annotation
provideCompartment(Diagram, InputUtilities) - Method in interface omix.plugin.io.ModelComponentProviderInterface
provideMetabolite(Diagram, InputUtilities) - Method in interface omix.plugin.io.ModelComponentProviderInterface
providePathway(Diagram, InputUtilities) - Method in interface omix.plugin.io.ModelComponentProviderInterface
providePublicIdentifiers(Compartment, PublicIdentifierManager) - Method in interface omix.plugin.identity.PublicIdentifierProviderInterface
providePublicIdentifiers(Metabolite, PublicIdentifierManager) - Method in interface omix.plugin.identity.PublicIdentifierProviderInterface
providePublicIdentifiers(MetaboliteType, PublicIdentifierManager) - Method in interface omix.plugin.identity.PublicIdentifierProviderInterface
providePublicIdentifiers(Model, PublicIdentifierManager) - Method in interface omix.plugin.identity.PublicIdentifierProviderInterface
providePublicIdentifiers(Pathway, PublicIdentifierManager) - Method in interface omix.plugin.identity.PublicIdentifierProviderInterface
providePublicIdentifiers(Reaction, PublicIdentifierManager) - Method in interface omix.plugin.identity.PublicIdentifierProviderInterface
provideReaction(Diagram, InputUtilities) - Method in interface omix.plugin.io.ModelComponentProviderInterface
Public - Annotation Type in omix.lang.reflect.annotation
PublicIdentifier - Interface in omix.lang.identity: This type represents a public identifier.
PublicIdentifier - Interface in omix.plugin.identity
publicIdentifierManager() - Method in interface omix.plugin.io.util.InputUtilities: Returns the manager for public model identifiers.
publicIdentifierManager() - Method in interface omix.plugin.ovl.OVLFieldConverterUtilities: Returns the manager for public model identifiers.
PublicIdentifierManager - Interface in omix.plugin.identity
PublicIdentifierProviderFactory - Interface in omix.plugin.identity
PublicIdentifierProviderInterface - Interface in omix.plugin.identity
PushButton - Interface in omix.lang.model.accessory.trigger: A PushButton calls a parameterless method or any parameterized method at user action.
PushButton - Interface in omix.plugin.model.accessory.trigger
PushButton - Interface in omix.plugin.model.writable.accessory.trigger
PushButtonItem - Interface in omix.plugin.diagram.accessory.trigger
PushButtonItem - Interface in omix.plugin.diagram.writable.accessory.trigger
put(int, int, T) - Method in class omix.util.collections.DoubleIndexedMap: put an object in association with two indexes i and j.
put(String, int, double) - Method in class omix.util.math.ScalingDataMap: Put a value into the map identified by a textual key and an index.
put(K, V) - Method in class omix.util.collections.WeakMap
put(K, V) - Method in class omix.util.collections.WeakWeakMap
put(DataMatrixInterface.MetaDataType, Object) - Method in class omix.plugin.data.DataMatrixInterface.MetaData
putAll(Map<? extends K, ? extends V>) - Method in class omix.util.collections.WeakMap
putAll(Map<? extends K, ? extends V>) - Method in class omix.util.collections.WeakWeakMap
pwd() - Method in interface omix.plugin.net.URLConnectionInterface: Returns the current working directory or the connection.

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