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

A

AbstractionRule - Class in pedviz.view.rules: With this Rule it's possible to draw nodes in an abstract way dependent on a given trait.
AbstractionRule(int, Object, Object) - Constructor for class pedviz.view.rules.AbstractionRule: Creates a new AbstractionRule.
AbstractionRule(int) - Constructor for class pedviz.view.rules.AbstractionRule
AbstractionRule() - Constructor for class pedviz.view.rules.AbstractionRule
AbstractionRule3d - Class in pedviz.view.rules: With this Rule it's possible to draw nodes in an abstract way dependent on a given trait.
AbstractionRule3d() - Constructor for class pedviz.view.rules.AbstractionRule3d
actionPerformed(ActionEvent) - Method in class pedviz.rpedviz.RPedviz
addChangeListener(ChangeListener) - Method in interface pedviz.algorithms.Algorithm: Registers a ChangeListener.
addChangeListener(ChangeListener) - Method in class pedviz.algorithms.ErrorChecking
addChangeListener(ChangeListener) - Method in class pedviz.algorithms.FamilySplitter
addChangeListener(ChangeListener) - Method in class pedviz.algorithms.RubberBands
addChangeListener(ChangeListener) - Method in class pedviz.algorithms.SameParents
addChangeListener(ChangeListener) - Method in class pedviz.algorithms.Sugiyama
addChangeListener(ChangeListener) - Method in class pedviz.algorithms.sugiyama.SugiyamaLayout
addChangeListener(ChangeListener) - Method in class pedviz.graph.Layout
addColorRule(String, String, int, int, int) - Method in class pedviz.rpedviz.RPedviz: Adds a ColorRule.
addColorRule(String[], String[], int[], int[], int[]) - Method in class pedviz.rpedviz.RPedviz: Adds a multiple ColorRule.
addColorRule(String[], String[]) - Method in class pedviz.rpedviz.RPedviz: Adds a multiple ColorRule.
addCondition(Condition) - Method in class pedviz.algorithms.filter.Filter: Adds a new condition to the collection.
addEdge(Edge) - Method in class pedviz.graph.Graph: Adds a relation between two nodes.
addEdge(Edge, boolean) - Method in class pedviz.graph.Graph: Adds a relation between two nodes.
addHintAttribute(String) - Method in class pedviz.view.DefaultNodeView: Adds a trait that will be displayed in the hint.
addNode(Node) - Method in class pedviz.graph.Cluster: Adds the given node.
addNode(Node) - Method in class pedviz.graph.Graph: Adds a node to the graph.
addNode(Node, Node) - Method in class pedviz.graph.Graph: Adds a sub node to the given node.
addNode(int, Node) - Method in class pedviz.graph.Hierarchy: Adds the given node at the given level to the hierarchy.
addNodeListener(NodeListener) - Method in class pedviz.view.GraphView: Registers the NodeListener object.
addNodeViewListener(NodeViewListener) - Method in class pedviz.view.NodeView
addQualitativeTrait(String, double, double, double, double) - Method in class pedviz.rpedviz.RPedviz2D: Adds a qualitative trait.
addQualitativeTrait(String, double, double, double, double) - Method in class pedviz.rpedviz.RPedviz3D: Adds a qualitative trait.
addRule(Rule) - Method in class pedviz.rpedviz.RPedviz: Adds a rule.
addRule(Rule) - Method in class pedviz.view.GraphView: Adds a new Rule.
addRule(String, Object, Color) - Method in class pedviz.view.rules.ColorRule: Adds a new trait to this rule.
addSymbol(Symbol) - Method in class pedviz.view.DefaultNodeView: Adds a symbol to the collection of symbols.
addSymbolRule(String, String, String) - Method in class pedviz.rpedviz.RPedviz2D: Adds a SymbolRule
addSymbolRule(String, String, String) - Method in class pedviz.rpedviz.RPedviz3D: Adds a SymbolRule
afterSplit(Graph) - Method in class pedviz.algorithms.sugiyama.RandomSplitter
afterSplit(Graph) - Method in class pedviz.algorithms.sugiyama.SicknessSplitter
afterSplit(Graph) - Method in interface pedviz.algorithms.sugiyama.Splitter: This method will be run after the graph was split.
Algorithm - Interface in pedviz.algorithms: Implementations of this interface represent a graph algorithm.
ALL_DESELECTED - Static variable in class pedviz.view.NodeEvent: All nodes were deselected.
ANCESTORS - Static variable in class pedviz.algorithms.Highlighter: All ancestors of a person.
ANCESTORS - Static variable in class pedviz.view.LODHighlighter: All ancestors of a person.
AND - Static variable in class pedviz.algorithms.filter.Filter: and operator.
Animation - Class in pedviz.view.animations: This abstract class is a superclass for animations on a GraphView.
Animation(GraphView) - Constructor for class pedviz.view.animations.Animation: Creates a new animation for the given GraphView object.
applyRule(NodeView) - Method in class pedviz.view.rules.AbstractionRule
applyRule(NodeView) - Method in class pedviz.view.rules.AbstractionRule3d
applyRule(NodeView) - Method in class pedviz.view.rules.ColorRule
applyRule(NodeView) - Method in class pedviz.view.rules.GradientRule
applyRule(NodeView) - Method in class pedviz.view.rules.HighlightedColorRule
applyRule(NodeView) - Method in class pedviz.view.rules.HintRule
applyRule(NodeView) - Method in class pedviz.view.rules.PositionZRule
applyRule(NodeView) - Method in class pedviz.view.rules.Rule: Override this method, with it you get the NodeView and can adapt it.
applyRule(NodeView) - Method in class pedviz.view.rules.SelectedColorRule
applyRule(NodeView) - Method in class pedviz.view.rules.ShapeRule
ArrayGraphLoader - Class in pedviz.loader: This Loader class allow you to load a graph from a string array.
ArrayGraphLoader(String, String, String[]) - Constructor for class pedviz.loader.ArrayGraphLoader: Constructs a CsvGraphLoader

B

beforeSplit(Graph) - Method in class pedviz.algorithms.sugiyama.RandomSplitter
beforeSplit(Graph) - Method in class pedviz.algorithms.sugiyama.SicknessSplitter
beforeSplit(Graph) - Method in interface pedviz.algorithms.sugiyama.Splitter: This method will be run before the graph will be split.
BETWEEN - Static variable in interface pedviz.algorithms.filter.Condition: Check on interval.
BlinkAnimation - Class in pedviz.view.animations: This animation lets a collection of nodes blink.
BlinkAnimation(GraphView, Set<Node>, Color, Color) - Constructor for class pedviz.view.animations.BlinkAnimation: Creates a new BlinkAnimation object for the given GraphView object.
BlinkAnimation(GraphView, Set<Node>) - Constructor for class pedviz.view.animations.BlinkAnimation: Creates a new BlinkAnimation object for the given GraphView object.
BOTH - Static variable in class pedviz.view.rules.Rule: can be used in GraphView2D and GraphView3D.
buildHierarchie(HierarchieBuilder) - Method in class pedviz.graph.Graph: Builds a hierarchy based on the given HierarchieBuilder object.
buildHirarchie(Graph) - Method in interface pedviz.algorithms.HierarchieBuilder: Starts the algorithm and assigns every node from the Graph object a layer.
buildHirarchie(Graph) - Method in class pedviz.algorithms.HierarchieUpDown

C

calcWidth(int, int) - Method in class pedviz.view.NodeView: Calcs the node's width.
centerGraph() - Method in class pedviz.view.GraphView: Centers the graph and fits the size on.
centerGraph() - Method in class pedviz.view.GraphView2D
centerGraph() - Method in class pedviz.view.GraphView3D
check(Node) - Method in interface pedviz.algorithms.filter.Condition: Checks if the condition for the given node is valid.
check(Node) - Method in class pedviz.algorithms.filter.NumberCondition
check(Node) - Method in class pedviz.algorithms.filter.TextCondition
clear() - Method in class pedviz.graph.Graph: Removes all nodes, edges and sub nodes.
clone() - Method in class pedviz.graph.Node: Clones the Node object.
clone() - Method in class pedviz.view.NodeView: Clones the NodeView.
close() - Method in interface pedviz.loader.Database: Closes the db connection.
close() - Method in class pedviz.loader.HSQLDatabase
close() - Method in class pedviz.loader.MultiDatabase
close() - Method in class pedviz.loader.MySQLDatabase
close() - Method in class pedviz.loader.PostgreSQLDatabase
Cluster - Class in pedviz.graph: This class can contain any nodes you like.
Cluster() - Constructor for class pedviz.graph.Cluster: Creates a new and empty Cluster.
Cluster(Vector<Node>) - Constructor for class pedviz.graph.Cluster: Creates a new and empty Cluster.
Cluster(Set<Node>) - Constructor for class pedviz.graph.Cluster: Creates a new and empty Cluster.
ColorRule - Class in pedviz.view.rules: With this Rule you can define the color for a node, dependent on a given trait.
ColorRule(String, Object, Color) - Constructor for class pedviz.view.rules.ColorRule: Constructs a new ColorRule with the given trait id, trait value and the given color.
compareTo(Object) - Method in class pedviz.algorithms.GraphError
compareTo(Object) - Method in class pedviz.algorithms.sugiyama.SugiyamaNodeView
compareTo(Object) - Method in class pedviz.view.NodeView: Compares two nodeviews.
compareTo(Object) - Method in class pedviz.view.Symbol: Compares two symbols.
Condition - Interface in pedviz.algorithms.filter: Implementations of this interface represent a condition.
connect(String, String, String) - Method in interface pedviz.loader.Database: Connects to the db with the given username, password and host.
connect(String, String, String) - Method in class pedviz.loader.HSQLDatabase
connect(String, String, String) - Method in class pedviz.loader.MultiDatabase
connect() - Method in class pedviz.loader.MultiDatabase: Connects to the db with the given
connect(String, String, String) - Method in class pedviz.loader.MySQLDatabase
connect(String, String, String) - Method in class pedviz.loader.PostgreSQLDatabase
createBox(float, float, float, float) - Static method in class pedviz.view.symbols3d.ShapeCreator3D: Returns a box.
createBox(float, float, float, float, float, float) - Static method in class pedviz.view.symbols3d.ShapeCreator3D
createBox(float, float, float, float, double) - Static method in class pedviz.view.symbols3d.ShapeCreator3D
createBox(float, float, float, float, float, float, double) - Static method in class pedviz.view.symbols3d.ShapeCreator3D
createEdgeView(Edge, DefaultEdgeView) - Method in class pedviz.algorithms.sugiyama.SugiyamaLayout
createEdgeView(Edge, DefaultEdgeView) - Method in class pedviz.graph.Layout: Factory method for creating a EdgeView object.
createGraphs(Graph, Vector<Node>, int) - Static method in class pedviz.algorithms.TestAlgo
createNodeView(Node, DefaultNodeView) - Method in class pedviz.algorithms.sugiyama.SugiyamaLayout
createNodeView(Node, DefaultNodeView) - Method in class pedviz.graph.Layout: Factory method for creating a NodeView object.
createShape(Point3f, float, Color) - Method in class pedviz.view.symbols3d.Symbol3D: Creates the GeometryArray of this symbol.
createShape(Point3f, float, Color) - Method in class pedviz.view.symbols3d.SymbolAdopted3d
createShape(Point3f, float, Color) - Method in class pedviz.view.symbols3d.SymbolDeceased3d
createShape(Point3f, float, Color) - Method in class pedviz.view.symbols3d.SymbolFamily3d
createShape(Point3f, float, Color) - Method in class pedviz.view.symbols3d.SymbolSexFemale3d
createShape(Point3f, float, Color) - Method in class pedviz.view.symbols3d.SymbolSexFemaleLow
createShape(Point3f, float, Color) - Method in class pedviz.view.symbols3d.SymbolSexMale3d
createShape(Point3f, float, Color) - Method in class pedviz.view.symbols3d.SymbolSexMaleLow
createShape(Point3f, float, Color) - Method in class pedviz.view.symbols3d.SymbolSexUndesignated3d
createShape(Point3f, float, Color) - Method in class pedviz.view.symbols3d.SymbolSexUndesignatedLow
createSphere(float, float, float, float) - Static method in class pedviz.view.symbols3d.ShapeCreator3D: Returns a sphere.
createSphere(float, float, float, float, boolean, double, int) - Static method in class pedviz.view.symbols3d.ShapeCreator3D
CsvGraphLoader - Class in pedviz.loader: This Loader class allow you to load a graph from a csv-file.
CsvGraphLoader(String, String) - Constructor for class pedviz.loader.CsvGraphLoader: Constructs a CsvGraphLoader

D

Database - Interface in pedviz.loader: Implementations of this interface represent a database. progress.
DatabaseGraphLoader - Class in pedviz.loader: This Loader class allow you to load a graph directly from a database.
DatabaseGraphLoader(Database, String) - Constructor for class pedviz.loader.DatabaseGraphLoader: Constructs a new DatabaseGraphLoader with the given connection and the table name.
DefaultEdgeView - Class in pedviz.view: This class contains all informations that are needed to draw a Edge on a GraphView.
DefaultEdgeView() - Constructor for class pedviz.view.DefaultEdgeView
DefaultNodeView - Class in pedviz.view: This class contains all informations that are needed to draw a Node on a GraphView.
DefaultNodeView() - Constructor for class pedviz.view.DefaultNodeView
deselect(Node) - Method in class pedviz.view.GraphView: Deselects the given node if it's selected.
deselect() - Method in class pedviz.view.GraphView: Deselects all nodes that are currently selected.
deselect() - Method in class pedviz.view.GraphView3D
deselect(Node) - Method in class pedviz.view.GraphView3D
DESELECTED - Static variable in class pedviz.view.NodeEvent: Node was deselected.
DOUBLE - Static variable in class pedviz.loader.ArrayGraphLoader
DOUBLE - Static variable in class pedviz.loader.CsvGraphLoader
DOUBLE - Static variable in class pedviz.loader.PedGraphLoader
DOUBLE - Static variable in class pedviz.loader.RessourceGraphLoader
drawSymbol(Graphics2D, Point2D.Float, float, Color, Color, NodeView) - Method in class pedviz.view.symbols.Symbol2D: Draws the symbol.
drawSymbol(Graphics2D, Point2D.Float, float, Color, Color, NodeView) - Method in class pedviz.view.symbols.SymbolAdopted
drawSymbol(Graphics2D, Point2D.Float, float, Color, Color, NodeView) - Method in class pedviz.view.symbols.SymbolDeceased
drawSymbol(Graphics2D, Point2D.Float, float, Color, Color, NodeView) - Method in class pedviz.view.symbols.SymbolFamily
drawSymbol(Graphics2D, Point2D.Float, float, Color, Color, NodeView) - Method in class pedviz.view.symbols.SymbolGenotypes
drawSymbol(Graphics2D, Point2D.Float, float, Color, Color, NodeView) - Method in class pedviz.view.symbols.SymbolHaplotypes
drawSymbol(Graphics2D, Point2D.Float, float, Color, Color, NodeView) - Method in class pedviz.view.symbols.SymbolQualitativeTrait
drawSymbol(Graphics2D, Point2D.Float, float, Color, Color, NodeView) - Method in class pedviz.view.symbols.SymbolSexFemale
drawSymbol(Graphics2D, Point2D.Float, float, Color, Color, NodeView) - Method in class pedviz.view.symbols.SymbolSexMale
drawSymbol(Graphics2D, Point2D.Float, float, Color, Color, NodeView) - Method in class pedviz.view.symbols.SymbolSexUndesignated
drawSymbol(Graphics2D, Point2D.Float, float, Color, Color, NodeView) - Method in class pedviz.view.symbols.SymbolText

E

Edge - Class in pedviz.graph: This class represents a connection between two nodes.
Edge(Node, Node) - Constructor for class pedviz.graph.Edge: Creates a new Edge object with the given start and end node.
EdgeView - Class in pedviz.view: This class contains all informations that are needed for drawing a Edge object in a GraphView.
EdgeView(Edge, DefaultEdgeView) - Constructor for class pedviz.view.EdgeView: Creates a EdgeView for the given Edge object with the given DefaultEdgeView as template.
Effect - Class in pedviz.view.effects: This class is the super class for effects like FishEyeEffect.
Effect() - Constructor for class pedviz.view.effects.Effect
EQUALS - Static variable in interface pedviz.algorithms.filter.Condition: Check on equal.
ErrorChecking - Class in pedviz.algorithms: The integrated method identifies the following basic errors: INVALID_SEX_DAD, INVALID_SEX_MOM, MISSING_DAD, MISSING_MOM, MULTI_PEDIGREES, SINGLETON.
ErrorChecking(Graph) - Constructor for class pedviz.algorithms.ErrorChecking: Inits ErrorChecking.
ErrorChecking(Graph, Object, Object) - Constructor for class pedviz.algorithms.ErrorChecking: Inits ErrorChecking.
ErrorChecking(Vector<Graph>, Object, Object) - Constructor for class pedviz.algorithms.ErrorChecking: Inits ErrorChecking for a collection of graphs.
ErrorChecking(Vector<Graph>) - Constructor for class pedviz.algorithms.ErrorChecking: Inits ErrorChecking for a collection of graphs.
errorMessages - Static variable in class pedviz.algorithms.GraphError
execute(Graph) - Method in class pedviz.algorithms.filter.Filter: Executes all conditions on the given graph object and returns a collection of all valid nodes.
executeQuerie(String) - Method in interface pedviz.loader.Database: Executes the given Querie.
executeQuerie(String) - Method in class pedviz.loader.HSQLDatabase
executeQuerie(String) - Method in class pedviz.loader.MultiDatabase
executeQuerie(String) - Method in class pedviz.loader.MySQLDatabase
executeQuerie(String) - Method in class pedviz.loader.PostgreSQLDatabase
exportAsCsvFile(String) - Method in class pedviz.graph.Graph: Exports the whole graph as a csv-file.
exportJPEG(String, float, boolean) - Method in class pedviz.view.GraphView: Exports the GraphView as a jpeg-file.
exportJPEG(String, float, boolean) - Method in class pedviz.view.GraphView2D
exportJPEG(String, float, boolean) - Method in class pedviz.view.GraphView3D

F

FamilySplitter - Class in pedviz.algorithms: This algorithm splits the given Graph object in single families.
FamilySplitter(Graph) - Constructor for class pedviz.algorithms.FamilySplitter: Creates the FamilySplitter algorithm with the given graph.
Filter - Class in pedviz.algorithms.filter: This class represents a collection of conditions.
Filter() - Constructor for class pedviz.algorithms.filter.Filter: Creates a new Filter object.
Filter(int) - Constructor for class pedviz.algorithms.filter.Filter: Creates a new Filter object and the conditions are combined with the given operator.
findLineOfDescents(Graph, Node, int) - Static method in class pedviz.algorithms.Highlighter: Returns a collection of nodes dependent on the given mode.
findParentsAndChilds(Node, int) - Static method in class pedviz.algorithms.Highlighter: Returns the ancestors and successors for the given node.
findParentsAndChilds(Node) - Static method in class pedviz.algorithms.Highlighter: Returns all ancestors and successor for the given node.
findPath(Node, Node) - Static method in class pedviz.algorithms.Highlighter: Checks if exists a path between nodeA and nodeB.
fireNodeEvent(NodeEvent) - Method in class pedviz.view.GraphView: Fires a NodeEvent to all listeners.
FisheyeEffect - Class in pedviz.view.effects: This class implements the FishEyeEffect.
FisheyeEffect(float, float, float) - Constructor for class pedviz.view.effects.FisheyeEffect: Creates a new FishEyeEffect with the given values.

G

getAllNodes() - Method in class pedviz.graph.Graph: Returns a collection of all nodes and subnodes.
getAllNodes() - Method in class pedviz.graph.LayoutedGraph: Returns a collection of all nodes and all subnodes.
getAlpha() - Method in class pedviz.view.DefaultEdgeView: Returns the alpha value.
getAlpha() - Method in class pedviz.view.EdgeView
getAlpha() - Method in class pedviz.view.GraphView: Returns the alpha value of hidden nodes.
getAlphaForLongLines() - Method in class pedviz.view.DefaultEdgeView: Returns the alpha value for long lines.
getAttributes() - Method in class pedviz.loader.ArrayGraphLoader: Returns a collection of all attributes.
getAttributes() - Method in class pedviz.loader.CsvGraphLoader: Returns a collection of all attributes.
getAttributes() - Method in class pedviz.loader.DatabaseGraphLoader: Returns a collection of all attributes.
getAttributes() - Method in class pedviz.loader.RessourceGraphLoader: Returns a collection of all attributes.
getBackgroundColor() - Method in class pedviz.view.GraphView: Returns the background color of this component.
getBarycentric() - Method in class pedviz.algorithms.sugiyama.SugiyamaNodeView: Returns the barycentric.
getBorderColor() - Method in class pedviz.view.DefaultNodeView: Returns the color of the node's border.
getBorderWidth() - Method in class pedviz.view.DefaultNodeView: Returns the width of the node's border.
getBounds() - Method in class pedviz.graph.LayoutedGraph
getBounds() - Method in class pedviz.view.effects.Effect: Returns the bounds.
getBounds() - Method in class pedviz.view.NodeView: Returns the bounds of the node.
getChilds() - Method in class pedviz.graph.Node: Returns a collection of all successor.
getChilds(int) - Method in class pedviz.graph.Node: Returns a collection of all successor.
getColor() - Method in class pedviz.view.DefaultEdgeView: Returns the color of the line.
getColor() - Method in class pedviz.view.DefaultNodeView: Returns the color of the node.
getColor() - Method in class pedviz.view.EdgeView
getColorArray(Color4f, int) - Static method in class pedviz.view.symbols3d.ShapeCreator3D: Creates a color array with the given color and size.
getColorDad() - Method in class pedviz.haplotype.HaplotypeItem
getColorForLongLines() - Method in class pedviz.view.DefaultEdgeView: Returns the color for long lines.
getColorMom() - Method in class pedviz.haplotype.HaplotypeItem
getColors() - Method in class pedviz.view.NodeView: Returns the Color array.
getColumns() - Method in class pedviz.loader.ArrayGraphLoader
getColumns() - Method in class pedviz.loader.CsvGraphLoader
getColumns() - Method in class pedviz.loader.DatabaseGraphLoader
getColumns() - Method in class pedviz.loader.Loader: Returns a array of all columns.
getColumns(String) - Method in class pedviz.loader.MultiDatabase: Returns a collection of all columns defined in the given table.
getColumns() - Method in class pedviz.loader.PedGraphLoader
getColumns() - Method in class pedviz.loader.RessourceGraphLoader
getComponent() - Method in class pedviz.view.GraphView: Returns the SWING/AWT component used by this instance.
getComponent() - Method in class pedviz.view.GraphView2D
getComponent() - Method in class pedviz.view.GraphView3D
getConnection() - Method in interface pedviz.loader.Database: Returns the connection.
getConnection() - Method in class pedviz.loader.HSQLDatabase
getConnection() - Method in class pedviz.loader.MultiDatabase
getConnection() - Method in class pedviz.loader.MySQLDatabase
getConnection() - Method in class pedviz.loader.PostgreSQLDatabase
getDad() - Method in class pedviz.haplotype.HaplotypeItem
getDadColumn() - Method in class pedviz.loader.Loader: Returns the field name from the dad's id
getDadId() - Method in class pedviz.haplotype.HaplotypeItem
getData(Object) - Method in class pedviz.haplotype.Haplotypes: Returns the HaplotypeItem for the node with the given id.
getData() - Method in class pedviz.view.EdgeView: Returns the stored Object.
getData() - Method in class pedviz.view.NodeView: Returns the stored Object.
getDefaultEdgeView() - Method in class pedviz.graph.LayoutedGraph: Returns the edge settings.
getDefaultNodeView() - Method in class pedviz.graph.LayoutedGraph: Returns the node settings.
getDegree() - Method in class pedviz.graph.Node: Returns the number of outgoing and ingoing edges.
getDeltaX() - Method in class pedviz.view.DefaultEdgeView
getDeltaY() - Method in class pedviz.view.DefaultEdgeView
getDeltaZ() - Method in class pedviz.view.DefaultEdgeView
getDepth() - Method in class pedviz.algorithms.RubberBands: Returns the spacing between two walls.
getEdge() - Method in class pedviz.view.EdgeView: Returns the Edge object.
getEdges() - Method in class pedviz.graph.Cluster: Returns a collection of all edges.
getEdges() - Method in class pedviz.graph.Graph: Returns a collection of all edges.
getEdges() - Method in class pedviz.graph.LayoutedGraph: Returns a collection of all edges.
getEffect() - Method in class pedviz.view.GraphView: Returns the Effect object used by this instance.
getEnd() - Method in class pedviz.graph.Edge: Returns the end node
getEnd() - Method in class pedviz.view.EdgeView: Returns the first end node.
getEndPos() - Method in class pedviz.algorithms.sugiyama.SugiyamaEdgeView: Returns the end point of the edge.
getEnds() - Method in class pedviz.view.EdgeView: Returns a collection of all end nodes.
getErrors() - Method in class pedviz.algorithms.ErrorChecking: Returns a list with all errors.
getErrors() - Method in class pedviz.haplotype.Haplotypes: Returns all errors for the node with the given id.
getErrors() - Method in class pedviz.haplotype.MerlinErrorChecking: Returns a collection of all errors.
getFamilieRank() - Method in class pedviz.graph.Node: Returns the node's familie id.
getFamilies() - Method in class pedviz.algorithms.FamilySplitter: Returns the single families as a collection of Graph objects.
getFemale() - Method in class pedviz.view.rules.AbstractionRule
getFocus() - Method in class pedviz.view.effects.Effect: Returns the focus point.
getFreeId() - Method in class pedviz.graph.Graph: Returns a free id for a node.
getGap() - Method in class pedviz.view.DefaultNodeView: Returns the gap between two children.
getGapBottom() - Method in class pedviz.view.DefaultEdgeView: Returns the gap at the bottom.
getGapTop() - Method in class pedviz.view.DefaultEdgeView: Returns the gap at the top.
getGraph() - Method in class pedviz.graph.LayoutedGraph: Returns the Graph object.
getGraph() - Method in class pedviz.view.GraphView: Returns the LayoutedGraph of which this is a view.
getGraph() - Method in class pedviz.view.NodeEvent: Returns the Graph object.
getGraphView() - Method in class pedviz.view.NodeEvent: Returns the GraphView object.
getHeight() - Method in class pedviz.view.DefaultNodeView
getHeight() - Method in class pedviz.view.Symbol
getHeight() - Method in class pedviz.view.symbols.SymbolGenotypes
getHeight() - Method in class pedviz.view.symbols.SymbolHaplotypes
getHierachiesCount() - Method in class pedviz.graph.Graph: Returns the number of hierachies.
getHierachiesDepth() - Method in class pedviz.graph.Graph: Returns the max number of nodes in a hierachy.
getHierachy(int) - Method in class pedviz.graph.Graph: Returns the hierarchie with the given id.
getHierarchy() - Method in class pedviz.graph.Node: Returns the node's hierarchy.
getHighlightedColor() - Method in class pedviz.view.DefaultEdgeView: Returns the highlighted color of the line.
getHighlightedColor() - Method in class pedviz.view.DefaultNodeView: Returns the highlighted color of the node.
getHighlightedWidth() - Method in class pedviz.view.DefaultEdgeView: Returns the width for lines that are highlighted.
getHint() - Method in class pedviz.view.NodeView: Return the hint-text.
getHint(NodeView) - Method in class pedviz.view.rules.HintRule: You can define the hint text, if you override this method.
getHorizontalGap() - Method in class pedviz.algorithms.RubberBands: Return the gap between two nodes, if they have the same parents.
getHorizontalSpacing() - Method in class pedviz.algorithms.RubberBands: Return the gap between two nodes, if they have the same parents.
getId() - Method in class pedviz.graph.Node: Returns the id.
getId() - Method in class pedviz.haplotype.MerlinError: Returns the id.
getIdColumn() - Method in class pedviz.loader.Loader: Returns the field name from the id
getIdDad() - Method in class pedviz.graph.Node: Returns the node's dad id.
getIdMom() - Method in class pedviz.graph.Node: Returns the node's mom id.
getInDegree() - Method in class pedviz.graph.Node: Returns the number of ingoing edges (parents).
getInEdges() - Method in class pedviz.graph.Node: Returns a collection of ingoing edges (parents).
getInEdges() - Method in class pedviz.view.NodeView: Returns a collection of all in-edges.
getInfo() - Method in interface pedviz.loader.Database: Returns some informations about the db.
getInfo() - Method in class pedviz.loader.HSQLDatabase
getInfo() - Method in class pedviz.loader.MultiDatabase
getInfo() - Method in class pedviz.loader.MySQLDatabase
getInfo() - Method in class pedviz.loader.PostgreSQLDatabase
getInterval() - Method in class pedviz.view.animations.Animation: Returns the interval of the timer.
getLabel() - Method in class pedviz.loader.MultiDatabase: Returns the description od the database.
getLayout() - Method in class pedviz.algorithms.Sugiyama: Returns the SugiyamaLayout object.
getLayoutedGraph() - Method in class pedviz.algorithms.Sugiyama: Returns the layouted graph.
getLayoutGraph() - Method in class pedviz.graph.Layout: Returns the layouted graph.
getLevel() - Method in class pedviz.graph.Node: Returns the node's level in hierarchy.
getLevelSize() - Method in class pedviz.graph.Hierarchy: Returns the number of different levels.
getMale() - Method in class pedviz.view.rules.AbstractionRule
getMarker() - Method in class pedviz.haplotype.MerlinError: Returns the marker.
getMarkers() - Method in class pedviz.haplotype.Haplotypes: Returns a collection of all markers in this haplotype.
getMaxIterations() - Method in class pedviz.algorithms.RubberBands: Returns the maximal number of iterations.
getMessage() - Method in interface pedviz.algorithms.Algorithm: Returns a short description of the algorithm.
getMessage() - Method in class pedviz.algorithms.ErrorChecking
getMessage() - Method in class pedviz.algorithms.FamilySplitter
getMessage() - Method in class pedviz.algorithms.RubberBands
getMessage() - Method in class pedviz.algorithms.SameParents
getMessage() - Method in class pedviz.algorithms.Sugiyama
getMessage() - Method in class pedviz.algorithms.sugiyama.SugiyamaLayout
getMessage() - Method in class pedviz.graph.Layout
getMinSize() - Method in class pedviz.view.effects.FisheyeEffect: Returns the minimum size of a node.
getMode() - Method in class pedviz.view.LODHighlighter: Returns the mode.
getMode() - Method in class pedviz.view.rules.Rule: Returns the mode.
getMom() - Method in class pedviz.haplotype.HaplotypeItem
getMomColumn() - Method in class pedviz.loader.Loader: Returns the field name from the mom's id
getMomId() - Method in class pedviz.haplotype.HaplotypeItem
getMouseOverColor() - Method in class pedviz.view.DefaultNodeView: Sets the "mouse over" color of the node.
getName() - Method in class pedviz.graph.Graph: Returns the name of the graph.
getNode(Object) - Method in class pedviz.graph.Graph: Returns the node with the given id.
getNode() - Method in class pedviz.view.NodeEvent: Returns the Node object.
getNode() - Method in class pedviz.view.NodeView: Returns the Node object for the NodeView.
getNodeCount() - Method in class pedviz.graph.Node: Returns the number of sub nodes.
getNodes() - Method in class pedviz.algorithms.GraphError: Returns a collection of all involved nodes.
getNodes() - Method in class pedviz.graph.Cluster: Returns a collection of all nodes.
getNodes() - Method in class pedviz.graph.Graph: Returns a collection of all single nodes, dummy nodes and cluster nodes.
getNodes(int) - Method in class pedviz.graph.Hierarchy: Returns a collection of all nodes from the given level.
getNodes() - Method in class pedviz.graph.Hierarchy
getNodes() - Method in class pedviz.graph.LayoutedGraph: Returns a collection of all nodes.
getNodes() - Method in class pedviz.graph.Node: Returns a collection of all subnodes.
getNodes() - Method in class pedviz.view.NodeView: Returns a collection of all subnodes.
getNodeSize() - Method in class pedviz.algorithms.RubberBands: Returns the size of a single node.
getNodeview() - Method in class pedviz.event.NodeViewEvent: Returns the NodeView object.
getNodeView(Object) - Method in class pedviz.graph.LayoutedGraph: Returns the NodeView object by the given id.
getNodeView(Node) - Method in class pedviz.graph.LayoutedGraph
getNodeView() - Method in class pedviz.view.NodeEvent: Returns the NodeView object.
getOperator() - Method in class pedviz.algorithms.filter.Filter: Returns the operator.
getOutDegree() - Method in class pedviz.graph.Node: Returns the number of outgoing edges (childrens).
getOutEdges() - Method in class pedviz.graph.Node: Returns a collection of outgoing edges (childrens)
getOutEdges() - Method in class pedviz.view.NodeView: Returns a collection of all out-edges.
getParent() - Method in class pedviz.graph.Node: Returns the cluster node, i the node is a subnode.
getParents(Graph, Node, int, int) - Static method in class pedviz.algorithms.TestAlgo
getParents() - Method in class pedviz.graph.Node: Returns a collection of all ancestors.
getParents(int) - Method in class pedviz.graph.Node: Returns a collection of all ancestors.
getParentsAndChilds(int) - Method in class pedviz.graph.Node: Returns the ancestors and successors for the given node.
getParentsAndChilds() - Method in class pedviz.graph.Node: Returns a collection of all ancestors and successor.
getPathTo(Node) - Method in class pedviz.graph.Node: Returns a collection of all Nodes on the path between this node and the given node.
getPercentComplete() - Method in interface pedviz.algorithms.Algorithm: Returns the progress in percents from 0 to 100
getPercentComplete() - Method in class pedviz.algorithms.ErrorChecking
getPercentComplete() - Method in class pedviz.algorithms.FamilySplitter
getPercentComplete() - Method in class pedviz.algorithms.RubberBands
getPercentComplete() - Method in class pedviz.algorithms.SameParents
getPercentComplete() - Method in class pedviz.algorithms.Sugiyama
getPercentComplete() - Method in class pedviz.algorithms.sugiyama.SugiyamaLayout
getPercentComplete() - Method in class pedviz.graph.Layout
getPos() - Method in class pedviz.haplotype.Haplotypes: Returns a collection of all chrom. positions.
getPosHierarchie(int) - Method in class pedviz.graph.LayoutedGraph
getPosX() - Method in class pedviz.view.NodeView: Returns the position on the X-axis.
getPosY() - Method in class pedviz.view.NodeView: Returns the position on the X-axis.
getPosZ() - Method in class pedviz.view.NodeView: Returns the position on the X-axis.
getPriority() - Method in class pedviz.view.Symbol: Returns the priority of the symbol.
getPriority() - Method in class pedviz.view.symbols.SymbolAdopted
getPriority() - Method in class pedviz.view.symbols.SymbolDeceased
getPriority() - Method in class pedviz.view.symbols.SymbolFamily
getPriority() - Method in class pedviz.view.symbols.SymbolGenotypes
getPriority() - Method in class pedviz.view.symbols.SymbolHaplotypes
getPriority() - Method in class pedviz.view.symbols.SymbolQualitativeTrait
getPriority() - Method in class pedviz.view.symbols.SymbolSexFemale
getPriority() - Method in class pedviz.view.symbols.SymbolSexMale
getPriority() - Method in class pedviz.view.symbols.SymbolSexUndesignated
getPriority() - Method in class pedviz.view.symbols.SymbolText
getPriority() - Method in class pedviz.view.symbols3d.SymbolAdopted3d
getPriority() - Method in class pedviz.view.symbols3d.SymbolDeceased3d
getPriority() - Method in class pedviz.view.symbols3d.SymbolFamily3d
getPriority() - Method in class pedviz.view.symbols3d.SymbolSexFemale3d
getPriority() - Method in class pedviz.view.symbols3d.SymbolSexFemaleLow
getPriority() - Method in class pedviz.view.symbols3d.SymbolSexMale3d
getPriority() - Method in class pedviz.view.symbols3d.SymbolSexMaleLow
getPriority() - Method in class pedviz.view.symbols3d.SymbolSexUndesignated3d
getPriority() - Method in class pedviz.view.symbols3d.SymbolSexUndesignatedLow
getRatio() - Method in class pedviz.haplotype.MerlinError: Returns the ratio.
getRubberBands() - Method in class pedviz.algorithms.Sugiyama: Returns the RubberBands object.
getRules() - Method in class pedviz.view.GraphView: Returns a vector of all rules.
getScale() - Method in class pedviz.view.GraphView: Returns the current scale factor.
getSelectedColor() - Method in class pedviz.view.DefaultNodeView: Returns the selected color of the node.
getSelection() - Method in class pedviz.view.GraphView: Returns all nodes that are currently selected.
getSelectionCount() - Method in class pedviz.view.GraphView: Returns the number of nodes that are currently selected.
getShape() - Method in class pedviz.view.rules.ShapeRule: Returns the symbol.
getSize() - Method in class pedviz.graph.Graph
getSize() - Method in class pedviz.haplotype.Haplotypes: Returns the number of all markers.
getSize() - Method in class pedviz.view.DefaultNodeView: Returns the size of the node.
getSize() - Method in class pedviz.view.symbols.SymbolText: Returns the height of the text.
getSpeed() - Method in class pedviz.view.effects.Effect: Returns the speed.
getSplitter() - Method in class pedviz.algorithms.sugiyama.SugiyamaLayout: Returns the used WallSplitter.
getStart() - Method in class pedviz.graph.Edge: Returns the start node.
getStart() - Method in class pedviz.view.EdgeView: Returns the start node.
getStyle() - Method in class pedviz.view.symbols3d.Symbol3D: Returns the style for this symbol.
getSubNodes() - Method in class pedviz.graph.LayoutedGraph: Returns a collection of all subnodes.
getSymbolMode() - Method in class pedviz.view.rules.AbstractionRule: Returns the mode.
getSymbols() - Method in class pedviz.view.DefaultNodeView: Returns a collection of all symbols for this node.
getTables() - Method in class pedviz.loader.MultiDatabase: Returns a collection of all tables in this database.
getTranslateX() - Method in class pedviz.view.GraphView: Returns the current x-translation.
getTranslateY() - Method in class pedviz.view.GraphView: Returns the current y-translation.
getType() - Method in class pedviz.algorithms.GraphError: Returns the type.
getType() - Method in class pedviz.event.NodeViewEvent: Returns the type.
getType() - Method in class pedviz.view.NodeEvent: Returns the type.
getUserData(String) - Method in class pedviz.graph.Node: Returns the trait that can be identified by the given title.
getUserdata() - Method in class pedviz.view.rules.GradientRule: Returns the trait.
getUserDataList() - Method in class pedviz.graph.Node: Returns a array of all traits.
getVerticalSpacing() - Method in class pedviz.algorithms.RubberBands: Returns the spacing between two generations.
getVisibleSize() - Method in class pedviz.haplotype.Haplotypes: Returns the number of visible markers.
getWall(Graph, Node, int) - Method in class pedviz.algorithms.sugiyama.RandomSplitter
getWall(Graph, Node, int) - Method in class pedviz.algorithms.sugiyama.SicknessSplitter
getWall(Graph, Node, int) - Method in interface pedviz.algorithms.sugiyama.Splitter: Returns the id of the wall for the given node.
getWidth() - Method in class pedviz.view.DefaultEdgeView: Returns the width of the line.
GradientRule - Class in pedviz.view.rules: This rule allow you to use the nodes color as an indicator for qualitative traits.
GradientRule(String, HashMap<Double, Color>) - Constructor for class pedviz.view.rules.GradientRule: Constructs a GradientRule with the given trait and the list of values.
Graph - Class in pedviz.graph: This class represents the pedigree as a graph.
Graph() - Constructor for class pedviz.graph.Graph: Create a new and empty graph.
Graph(Cluster) - Constructor for class pedviz.graph.Graph: Creates a new graph based on the given Cluster object.
GraphError - Class in pedviz.algorithms: Represents an error in a graph Object.
GraphError(int, Vector<Node>) - Constructor for class pedviz.algorithms.GraphError: Creates a GraphError object for a collection of nodes.
GraphError(int, Node) - Constructor for class pedviz.algorithms.GraphError: Creates a GraphError object for a single node.
GraphError(int, Node, String) - Constructor for class pedviz.algorithms.GraphError: Creates a GraphError object for a single node with a customized message.
GraphRepair - Class in pedviz.algorithms: The automatic repair method fixes problems by changing the sex or adding virtual individuals (ID starts with ##).
GraphRepair() - Constructor for class pedviz.algorithms.GraphRepair
GraphView - Class in pedviz.view: This class is the super class for components that visualize a graph.
GraphView() - Constructor for class pedviz.view.GraphView: Creates a new empty Graphview.
GraphView(LayoutedGraph) - Constructor for class pedviz.view.GraphView: Creates a new Graphview for the given LayoutedGraph object.
GraphView2D - Class in pedviz.view: This class visualizes a LayoutedGraph in a tow-dimensional environment.
GraphView2D() - Constructor for class pedviz.view.GraphView2D: Creates a new GraphView2D object.
GraphView2D(LayoutedGraph) - Constructor for class pedviz.view.GraphView2D: Creates a new GraphView2D object for the given LayoutedGraph object.
GraphView3D - Class in pedviz.view: This class visualizes a LayoutedGraph object in a three-dimensional environment.
GraphView3D() - Constructor for class pedviz.view.GraphView3D: Creates a new GraphView object.
GraphView3D(LayoutedGraph) - Constructor for class pedviz.view.GraphView3D: Creates a new GraphView object and displays the given LayoutedGaph object.
GraphView3D(GraphicsConfiguration, LayoutedGraph) - Constructor for class pedviz.view.GraphView3D: Constructs a GraphView with the given configuration and displays the given LayoutedGaph object.
GraphView3D(GraphicsConfiguration) - Constructor for class pedviz.view.GraphView3D: Constructs a GraphView with the given configuration.
GREATER - Static variable in interface pedviz.algorithms.filter.Condition: Check on greather.

H

HaplotypeItem - Class in pedviz.haplotype: Contains informations about a haplotype item.
HaplotypeItem(String, String, Color, Color) - Constructor for class pedviz.haplotype.HaplotypeItem: Creates a new HaplotypeItem with the given values.
Haplotypes - Class in pedviz.haplotype: Contains haplotypes for each node in a graph.
Haplotypes() - Constructor for class pedviz.haplotype.Haplotypes: Creates a Haplotypes object.
hasParents() - Method in class pedviz.graph.Node: Returns true, if the node has parents.
hide(Node) - Method in class pedviz.view.GraphView: Hides the given node if it's shown.
hide(Node) - Method in class pedviz.view.GraphView3D
hideAll() - Method in class pedviz.view.GraphView: Hides all nodes that are currently shown.
hideAll() - Method in class pedviz.view.GraphView3D
hideAllMarkers() - Method in class pedviz.haplotype.Haplotypes: Hides all markers.
HierarchieBuilder - Interface in pedviz.algorithms: Implementations of this interface represent an algorithm, which assigns every node a layer.
HierarchieUpDown - Class in pedviz.algorithms: This algorithm runs through the graph from top to bottom and assigns every node a layer.
HierarchieUpDown() - Constructor for class pedviz.algorithms.HierarchieUpDown: Creates a new UpDown-Hierarchy.
Hierarchy - Class in pedviz.graph: This class represents the hierarchy of a graph.
Hierarchy(Graph) - Constructor for class pedviz.graph.Hierarchy: Creates a hierarchy for the given graph.
highlight(Node) - Method in class pedviz.view.GraphView: Highlights the given node.
highlight(Collection<Node>) - Method in class pedviz.view.GraphView: Highlights a collection of nodes.
highlight(Node) - Method in class pedviz.view.GraphView3D
highlight(Collection<Node>) - Method in class pedviz.view.GraphView3D
HighlightedColorRule - Class in pedviz.view.rules: With this Rule you can define the highlighted color for a node, dependent on a given trait.
HighlightedColorRule(String, Object, Color) - Constructor for class pedviz.view.rules.HighlightedColorRule: Constructs a HighlightedColorRule with the given trait id, trait value and the given color.
Highlighter - Class in pedviz.algorithms: This class provides some generally useful methods for finding parents and children by a given node and checking if exists a path between two nodes.
Highlighter() - Constructor for class pedviz.algorithms.Highlighter
HintRule - Class in pedviz.view.rules: This abstract class is the super class for rules, which adapt the hint text.
HintRule() - Constructor for class pedviz.view.rules.HintRule
HSQLDatabase - Class in pedviz.loader: This class allows the DatabaseGraphLoader to load data from a HSQL database.
HSQLDatabase() - Constructor for class pedviz.loader.HSQLDatabase

I

insertMissingParents(Graph, Object, Object) - Static method in class pedviz.algorithms.GraphRepair: Inserts missing parents and change invalid sex.
insertMissingParents(Vector<Graph>) - Static method in class pedviz.algorithms.GraphRepair: Inserts missing parents and change invalid sex.
insertMissingParents(Vector<Graph>, Object, Object) - Static method in class pedviz.algorithms.GraphRepair: Inserts missing parents and change invalid sex.
INTEGER - Static variable in class pedviz.loader.ArrayGraphLoader
INTEGER - Static variable in class pedviz.loader.CsvGraphLoader
INTEGER - Static variable in class pedviz.loader.PedGraphLoader
INTEGER - Static variable in class pedviz.loader.RessourceGraphLoader
INVALID_SEX_DAD - Static variable in class pedviz.algorithms.GraphError
INVALID_SEX_MOM - Static variable in class pedviz.algorithms.GraphError
isAntialiasingEnabled() - Method in class pedviz.view.GraphView3D: Returns true if the visualization uses antialiasing.
isAutoUpdateOnDrag() - Method in class pedviz.view.effects.Effect: Returns true, when the focus point will be updated automatically on mouse drag.
isAutoUpdateOnMove() - Method in class pedviz.view.effects.Effect: Returns true, when the focus point will be updated automatically on mouse move.
isConnectChildren() - Method in class pedviz.view.DefaultEdgeView: Returns true, when childrens will be drawed connected.
isConnected() - Method in interface pedviz.loader.Database: Returns true, if the db is connected.
isConnected() - Method in class pedviz.loader.HSQLDatabase
isConnected() - Method in class pedviz.loader.MultiDatabase
isConnected() - Method in class pedviz.loader.MySQLDatabase
isConnected() - Method in class pedviz.loader.PostgreSQLDatabase
isDummy() - Method in class pedviz.graph.Edge: Returns true if the edge is a dummy.
isDummy() - Method in class pedviz.graph.Node: Returns true, if the node is a dummy.
isEdgeVisible() - Method in class pedviz.view.GraphView: Returns true if edges are visible.
isEnabled() - Method in class pedviz.view.LODHighlighter: Returns true, if the highlighter is enabled.
isEnabled() - Method in class pedviz.view.PathHighlighter: Returns true, if the highlighter is enabled.
isEnabled(int) - Method in class pedviz.view.rules.ColorRule: Returns true, if the rule with the given index is enabled.
isEnabled() - Method in class pedviz.view.rules.Rule: Returns true, if the rule is enabled.
isExpand() - Method in class pedviz.view.DefaultNodeView: Returns true, if the node is visible.
isHidden() - Method in class pedviz.view.EdgeView: Returns true, if the edge is hidden.
isHidden() - Method in class pedviz.view.NodeView: Returns true, if the node is hidden.
isHighlighted() - Method in class pedviz.view.EdgeView: Returns true, if the edge is highlighted.
isHighlighted() - Method in class pedviz.view.NodeView: Checks if the node is highlighted.
isLayouted() - Method in class pedviz.graph.Graph: Returns true, if the graph is layouted.
isLightEnabled() - Method in class pedviz.view.GraphView3D: Returns true if the visualization uses lights.
isMarkerVisible(int) - Method in class pedviz.haplotype.Haplotypes: Returns true, if the given marker is visible.
isMaterialEnabled() - Method in class pedviz.view.GraphView3D: Returns true if the nodes use matrials.
isMomLeft() - Method in class pedviz.view.NodeView
isMouseOver() - Method in class pedviz.view.NodeView: Checks if the mouse is over the node.
isMovingEnabled() - Method in class pedviz.view.GraphView: Returns true if moving is enabled.
isMultipleNodes() - Method in class pedviz.algorithms.GraphError: Returns true, when more nodes are involved.
isMultiselection() - Method in class pedviz.view.GraphView: Returns true if multiselection is enabled.
isSelected(Node) - Method in class pedviz.view.GraphView: Returns true if the given node is selected.
isSelected() - Method in class pedviz.view.NodeView: Checks if the node is selected.
isSelectionEnabled() - Method in class pedviz.view.GraphView: Returns true if selection is enabled.
isShowMarkers() - Method in class pedviz.view.symbols.SymbolHaplotypes
isTransparencyEnabled() - Method in class pedviz.view.GraphView3D: Returns true if the visualization uses transparency.
isVisbleSphere() - Method in class pedviz.view.GraphView3D: Returns true, if the sphere is visible.
isZoomEnabled() - Method in class pedviz.view.GraphView: Returns true if zooming is enabled.

L

Layout<N extends NodeView,E extends EdgeView> - Class in pedviz.graph
Layout(Graph, DefaultNodeView, DefaultEdgeView) - Constructor for class pedviz.graph.Layout: Creates a new Layout object for the given Graph object width the given settings.
LayoutedGraph<N extends NodeView,E extends EdgeView> - Class in pedviz.graph: This class contains all layout informations for a Graph object.
LayoutedGraph(Graph, Layout, DefaultNodeView, DefaultEdgeView) - Constructor for class pedviz.graph.LayoutedGraph: Creates a new LayoutedGaph object for the given Graph object with the given settings.
LESSER - Static variable in interface pedviz.algorithms.filter.Condition: Check on lesser.
load(Graph) - Method in class pedviz.loader.ArrayGraphLoader
load(Graph) - Method in class pedviz.loader.CsvGraphLoader
load(Graph) - Method in class pedviz.loader.DatabaseGraphLoader
load(Graph) - Method in class pedviz.loader.Loader: Loads data in the given Graph object.
load(Graph) - Method in class pedviz.loader.PedGraphLoader
load(Graph) - Method in class pedviz.loader.RessourceGraphLoader
Loader - Class in pedviz.loader: This abstract class is a super class for graph loader classes.
Loader() - Constructor for class pedviz.loader.Loader
LODHighlighter - Class in pedviz.view: This class provides methods for highlighting nodes dynamicly.
LODHighlighter() - Constructor for class pedviz.view.LODHighlighter: Creates a new LODHighlighter object.
LODHighlighter(int) - Constructor for class pedviz.view.LODHighlighter: Create a new LODHighlighter object with the given mode.

M

MATERNAL - Static variable in class pedviz.algorithms.Highlighter: Maternal lineage of a person.
MATERNAL - Static variable in class pedviz.view.LODHighlighter: Maternal lineage of a person.
MATERNAL_AND_PATERNAL - Static variable in class pedviz.algorithms.Highlighter: Maternal and paternal lineage of a person.
MATERNAL_AND_PATERNAL - Static variable in class pedviz.view.LODHighlighter: Maternal and paternal lineage of a person.
MerlinError - Class in pedviz.haplotype: Contains informations about a Error from a Merlin-Error file.
MerlinError(Object, String) - Constructor for class pedviz.haplotype.MerlinError: Creates a new MerlinError object with the given id and the given marker.
MerlinErrorChecking - Class in pedviz.haplotype: It's possible to process a Merlin error output file to highlight errors in the haplotype/genotype data.
MerlinErrorChecking(String) - Constructor for class pedviz.haplotype.MerlinErrorChecking: Loads the given Merlin-Error file.
MerlinErrorChecking(String, boolean) - Constructor for class pedviz.haplotype.MerlinErrorChecking: Loads the given Merlin-Error file.
MerlinHaplotypes - Class in pedviz.haplotype: The haplotype visualization is based on the Merlin data format .
MerlinHaplotypes(String, String) - Constructor for class pedviz.haplotype.MerlinHaplotypes: Imports the haplotype information from the given *.chr and *.map file.
MerlinHaplotypes(String, String, boolean) - Constructor for class pedviz.haplotype.MerlinHaplotypes: Imports the haplotype information from the given *.chr and *.map file.
MISSING_DAD - Static variable in class pedviz.algorithms.GraphError
MISSING_MOM - Static variable in class pedviz.algorithms.GraphError
MOUSE_ENTER - Static variable in class pedviz.view.NodeEvent: Mouse enters node.
MOUSE_LEAVE - Static variable in class pedviz.view.NodeEvent: Mouse leaves node.
moveFocus(double, double) - Method in class pedviz.view.effects.Effect: Moves the focus point by the given values.
MULTI_PEDIGREES - Static variable in class pedviz.algorithms.GraphError
MultiDatabase - Class in pedviz.loader: This class allows the DatabaseGraphLoader to load data from the database defined in the given property file.
MultiDatabase(String, String, String, String) - Constructor for class pedviz.loader.MultiDatabase: Creates a new Database object with the given username, password, host and driver.
MultiDatabase(String) - Constructor for class pedviz.loader.MultiDatabase: Creates a new Database object with the properties stored in the given file.
MySQLDatabase - Class in pedviz.loader: This class allows the DatabaseGraphLoader to load data from a MySQL database.
MySQLDatabase() - Constructor for class pedviz.loader.MySQLDatabase

N

NBETWEEN - Static variable in interface pedviz.algorithms.filter.Condition
NEQUALS - Static variable in interface pedviz.algorithms.filter.Condition: Check on not equal.
Node - Class in pedviz.graph: This class represents a individual in a pedigree (Graph).
Node(Object) - Constructor for class pedviz.graph.Node: Creates a new node with the given id.
nodeChanged(NodeViewEvent) - Method in interface pedviz.event.NodeViewListener: Change on a NodeView object.
nodeChanged(NodeViewEvent) - Method in class pedviz.graph.LayoutedGraph: Update bounds
NodeEvent - Class in pedviz.view
NodeEvent(GraphView, Node, int) - Constructor for class pedviz.view.NodeEvent: Creates a new NodeEvent with the given properties.
NodeListener - Interface in pedviz.view: Defines an object which listens for NodeEvents.
NodeView - Class in pedviz.view: This class contains all informations that are needed for drawing a Node object in a GraphView.It saves also whether the node is selected or highlighted.
NodeView(Node, DefaultNodeView) - Constructor for class pedviz.view.NodeView: Constructs a NodeView for the given Node object with the given DefaultNodeView as template.
NodeViewEvent - Class in pedviz.event: Contains informations about a NodeView Event.
NodeViewEvent(NodeView, int) - Constructor for class pedviz.event.NodeViewEvent: Creates a new NodeViewEvent with the given parameters.
NodeViewListener - Interface in pedviz.event: Interface for event handling.
NONE - Static variable in class pedviz.view.rules.AbstractionRule: Draws all children as a single node.
NUMBER - Static variable in class pedviz.view.rules.AbstractionRule: Draws all children as a single node and shows their total number.
NUMBER_2 - Static variable in class pedviz.view.rules.AbstractionRule: Draws all children as a single node and shows the number of females and males.
NumberCondition - Class in pedviz.algorithms.filter: This class represents a Condtion for a trait, which contains an integer or a double value.
NumberCondition(String, int, Double) - Constructor for class pedviz.algorithms.filter.NumberCondition: Creates a new NumberCondition for the given trait with the given mode and values.
NumberCondition(String, int, Double, Double) - Constructor for class pedviz.algorithms.filter.NumberCondition: Creates a new NumberCondition for the given trait with the given mode and values.

O

ONLY_2D - Static variable in class pedviz.view.rules.Rule: can be used only in GraphView2D.
ONLY_3D - Static variable in class pedviz.view.rules.Rule: can be used only in GraphView3D.
onNodeEvent(NodeEvent) - Method in class pedviz.view.LODHighlighter
onNodeEvent(NodeEvent) - Method in interface pedviz.view.NodeListener
onNodeEvent(NodeEvent) - Method in class pedviz.view.PathHighlighter
OR - Static variable in class pedviz.algorithms.filter.Filter: or operator.

P

PATERNAL - Static variable in class pedviz.algorithms.Highlighter: Paternal lineage of a person.
PATERNAL - Static variable in class pedviz.view.LODHighlighter: Paternal lineage of a person.
PathHighlighter - Class in pedviz.view: This class checks if exists a path between two persons and highlights it.
PathHighlighter() - Constructor for class pedviz.view.PathHighlighter: Creates a new PathHighlighter object.
PedGraphLoader - Class in pedviz.loader: This Loader class allow you to load a graph from a ped-file.
PedGraphLoader(String) - Constructor for class pedviz.loader.PedGraphLoader: Creates a new PedGraphLoader object.
pedviz.algorithms - package pedviz.algorithms: Provides differnt graph algorithms for the class graph.Graph.
pedviz.algorithms.filter - package pedviz.algorithms.filter: Provides useful filters.
pedviz.algorithms.sugiyama - package pedviz.algorithms.sugiyama: Provides classes for the Sugiyama-algorithm implementation.
pedviz.event - package pedviz.event: Provides classes for event handling.
pedviz.graph - package pedviz.graph: Provides a data structure for pedigrees.
pedviz.haplotype - package pedviz.haplotype: Provides some classes for haplotyping.
pedviz.loader - package pedviz.loader: Provides classes for loading data in a Graph object.
pedviz.rpedviz - package pedviz.rpedviz: Provides classes for the integration of Pedviz in R (http://www.r-project.org).
pedviz.view - package pedviz.view: Provides classes for visualizing a Graph object in different ways.
pedviz.view.animations - package pedviz.view.animations: Provides classes to create animations on a GaphView object.
pedviz.view.effects - package pedviz.view.effects: Provides different effects (like Fisheye) to transform a graph visualization.
pedviz.view.rules - package pedviz.view.rules: Provides classes for adapting the node's appearance.
pedviz.view.symbols - package pedviz.view.symbols: Provides classes for displaying different pedigree symbols (2D).
pedviz.view.symbols3d - package pedviz.view.symbols3d: Provides classes for displaying different pedigree symbols (3D).
plot(String, String, String[], String[], boolean) - Method in class pedviz.rpedviz.RPedviz: Plots the pedigree with hints.
plot(String, String[], boolean) - Method in class pedviz.rpedviz.RPedviz: Plots the pedigree without hints.
plot(String, String, String[], boolean) - Method in class pedviz.rpedviz.RPedviz: Plots the pedigree without hints.
plot(String, String[]) - Method in class pedviz.rpedviz.RPedviz: Plots the pedigree without hints and with the highlighter-toolbar.
plot(String, String, String[]) - Method in class pedviz.rpedviz.RPedviz: Plots the pedigree without hints and with the highlighter-toolbar.
plot(String, String[], String[]) - Method in class pedviz.rpedviz.RPedviz: Plots the pedigree with hints and with the highlighter-toolbar.
plot(String, String, String[], String[]) - Method in class pedviz.rpedviz.RPedviz: Plots the pedigree with hints and with the highlighter-toolbar.
plot(String, String, String[], String[], boolean) - Method in class pedviz.rpedviz.RPedviz2D
plot(String, String, String[], String[], boolean) - Method in class pedviz.rpedviz.RPedviz3D
POSITION_X - Static variable in class pedviz.event.NodeViewEvent
POSITION_Y - Static variable in class pedviz.event.NodeViewEvent
POSITION_Z - Static variable in class pedviz.event.NodeViewEvent
PositionZRule - Class in pedviz.view.rules: This rule can be used for changing the color, dependent on the position on the Z-axis.
PositionZRule(float, Color) - Constructor for class pedviz.view.rules.PositionZRule: Constructs the Rule with given position on the Z-axis and color.
PostgreSQLDatabase - Class in pedviz.loader: This class allows the DatabaseGraphLoader to load data from a PostgreSQL database.
PostgreSQLDatabase() - Constructor for class pedviz.loader.PostgreSQLDatabase
print() - Method in class pedviz.graph.Graph
pulse(GraphView) - Method in class pedviz.view.animations.Animation: This method will be executed when the timer is expired.
pulse(GraphView) - Method in class pedviz.view.animations.BlinkAnimation
pulse(GraphView) - Method in class pedviz.view.animations.SizeAnimation

R

RandomSplitter - Class in pedviz.algorithms.sugiyama: This class can be used as a Splitter for the SugiyamaLayout class.
RandomSplitter() - Constructor for class pedviz.algorithms.sugiyama.RandomSplitter: Creates a new RandomSplitter object.
removeAllHierachies() - Method in class pedviz.graph.Graph: Removes all hierarchies from this graph.
removeEdge(Edge) - Method in class pedviz.graph.Graph: Removes the given edge.
removeNode(Node) - Method in class pedviz.graph.Cluster: Removes the given node.
removeNode(Node) - Method in class pedviz.graph.Graph: Removes the given node.
removeNode(Node, boolean) - Method in class pedviz.graph.Graph: Removes the given node. if updateNodes is true, it updates the in-edges and out-edges from the node.
removeNode(Node) - Method in class pedviz.graph.Hierarchy: Removes the given node from the hierarchy.
removeNodeListener(NodeListener) - Method in class pedviz.view.GraphView: Removes the NodeListener object.
removeNodeViewListener(NodeViewListener) - Method in class pedviz.view.NodeView
removeRule(Rule) - Method in class pedviz.view.GraphView: Remove the given rule.
repair(Graph) - Static method in class pedviz.algorithms.GraphRepair: Inserts missing parents and change invalid sex.
rerun(LayoutedGraph) - Method in class pedviz.graph.Layout: Reruns the layoutalgorithm.
reset(DefaultNodeView) - Method in class pedviz.view.NodeView: Resets all settings do the given DefaultNodeView object.
RessourceGraphLoader - Class in pedviz.loader: This Loader class allow you to load a graph from a csv-file which is in jar-file.
RessourceGraphLoader(String, String) - Constructor for class pedviz.loader.RessourceGraphLoader: Constructs a CsvGraphLoader
RPedviz - Class in pedviz.rpedviz: This abstract class defines the interface between R and Pedviz.
RPedviz(String) - Constructor for class pedviz.rpedviz.RPedviz: Constructs a new RPedviz object.
RPedviz2D - Class in pedviz.rpedviz: This class enables a 2d visualization of pedigrees in R.
RPedviz2D() - Constructor for class pedviz.rpedviz.RPedviz2D: Constructs a new RPedviz2D object.
RPedviz3D - Class in pedviz.rpedviz: This class enables a 2.5d visualization of pedigrees in R.
RPedviz3D() - Constructor for class pedviz.rpedviz.RPedviz3D: Constructs a new RPedviz3D object.
RubberBands - Class in pedviz.algorithms: This class implements the RubberBands algorithm.
RubberBands(LayoutedGraph) - Constructor for class pedviz.algorithms.RubberBands: Creates the RubberBands algorithm for the given Graph.
Rule - Class in pedviz.view.rules: This abstract class is the super class for all rules.
Rule() - Constructor for class pedviz.view.rules.Rule
run() - Method in interface pedviz.algorithms.Algorithm: Starts the algorithm.
run() - Method in class pedviz.algorithms.ErrorChecking: Starts the error-checking.
run() - Method in class pedviz.algorithms.FamilySplitter
run() - Method in class pedviz.algorithms.RubberBands
run() - Method in class pedviz.algorithms.SameParents
run() - Method in class pedviz.algorithms.Sugiyama
run() - Method in class pedviz.algorithms.sugiyama.SugiyamaLayout
run() - Method in class pedviz.graph.Layout
run() - Method in class pedviz.view.animations.Animation

S

SameParents - Class in pedviz.algorithms: This class clusters all nodes with the same parents.
SameParents(Graph) - Constructor for class pedviz.algorithms.SameParents: Creates the SameParents algorithm with the given Graph object.
SameParents(ArrayList<Graph>) - Constructor for class pedviz.algorithms.SameParents: Creates the SameParents algorithm with the given collection of Graph objects.
select(Node) - Method in class pedviz.view.GraphView: Selects a single node.
select(ArrayList<Node>) - Method in class pedviz.view.GraphView: Selects a collection of nodes.
select(Node) - Method in class pedviz.view.GraphView3D
SELECTED - Static variable in class pedviz.view.NodeEvent: Node was selected.
SelectedColorRule - Class in pedviz.view.rules: With this Rule you can define the selected color for a node, dependent on a given trait.
SelectedColorRule(String, Object, Color) - Constructor for class pedviz.view.rules.SelectedColorRule: Constructs a SelectedColorRule with the given trait id, trait value and the given color.
setAlpha(float) - Method in class pedviz.view.DefaultEdgeView: Sets the alpha value.
setAlpha(float) - Method in class pedviz.view.GraphView: To down grade nodes of less interest their alpha value can be lowered.
setAlphaForLongLines(float) - Method in class pedviz.view.DefaultEdgeView: Sets the alpha value for long lines.
setAntialiasingEnabled(boolean) - Method in class pedviz.view.GraphView3D: Enables or disables antiliasing.
setAutoUpdateOnDrag(boolean) - Method in class pedviz.view.effects.Effect
setAutoUpdateOnMove(boolean) - Method in class pedviz.view.effects.Effect
setBackgroundColor(Color) - Method in class pedviz.view.GraphView: Sets the background color of this component.
setBackgroundColor(Color) - Method in class pedviz.view.GraphView3D
setBarycentric(float) - Method in class pedviz.algorithms.sugiyama.SugiyamaNodeView: Sets the barycentric.
setBorderColor(Color) - Method in class pedviz.view.DefaultNodeView: Sets the color of the node's border.
setBorderWidth(float) - Method in class pedviz.view.DefaultNodeView: Sets the width of the node's border.
setBounds(float, float, float, float) - Method in class pedviz.graph.LayoutedGraph
setBounds(Rectangle2D) - Method in class pedviz.view.effects.Effect: Sets the bounds.
setBounds(double, double, double) - Method in class pedviz.view.NodeView: Sets the bounds of this node.
setColor(Color) - Method in class pedviz.view.DefaultEdgeView: Sets the color of the line.
setColor(Color) - Method in class pedviz.view.DefaultNodeView: Sets the color of the node.
setColor(int, Color) - Method in class pedviz.view.rules.ColorRule: Sets the color for the rule with the given index.
setColorDad(Color) - Method in class pedviz.haplotype.HaplotypeItem
setColorForLongLines(Color) - Method in class pedviz.view.DefaultEdgeView: Sets the color for long lines.
setColorMom(Color) - Method in class pedviz.haplotype.HaplotypeItem
setColors(Color[]) - Method in class pedviz.view.NodeView: Sets the Color array.
setColors(Color[]) - Method in class pedviz.view.Symbol
setColumnType(String, int) - Method in class pedviz.loader.ArrayGraphLoader: Sets the type for the given column.
setColumnType(String, int) - Method in class pedviz.loader.CsvGraphLoader: Sets the type for the given column.
setColumnType(String, int) - Method in class pedviz.loader.PedGraphLoader: Sets the type for the given column.
setColumnType(String, int) - Method in class pedviz.loader.RessourceGraphLoader: Sets the type for the given column.
setCondition(int, String, Object) - Method in class pedviz.view.rules.ColorRule: Sets the condition for the rule width the given index.
setConnectChildren(boolean) - Method in class pedviz.view.DefaultEdgeView
setCursor(int) - Method in class pedviz.view.GraphView: Sets the cursor of the component.
setDad(String) - Method in class pedviz.haplotype.HaplotypeItem
setDadId(String) - Method in class pedviz.haplotype.HaplotypeItem
setData(Object) - Method in class pedviz.view.EdgeView: Sets the Object that will be stored.
setData(Object) - Method in class pedviz.view.NodeView: Sets the Object that will be stored.
setDefaultEdgeView(DefaultEdgeView) - Method in class pedviz.graph.LayoutedGraph: Sets the edge settings.
setDefaultNodeView(DefaultNodeView) - Method in class pedviz.graph.LayoutedGraph: Sets the node settings.
setDeltaForLongLines(float, float, float) - Method in class pedviz.view.DefaultEdgeView
setDepth(float) - Method in class pedviz.algorithms.RubberBands: Sets the spacing between two walls.
setDummy(boolean) - Method in class pedviz.graph.Edge: True, if the edge is a dummy.
setDummy(boolean) - Method in class pedviz.graph.Node: Sets
setEdgeVisible(boolean) - Method in class pedviz.view.GraphView: Displays or hides the edges.
setEdgeVisible(boolean) - Method in class pedviz.view.GraphView3D
setEffect(Effect) - Method in class pedviz.view.GraphView: Sets the given effect.
setEnabled(boolean) - Method in class pedviz.view.LODHighlighter: Enables or disables the highlighter.
setEnabled(boolean) - Method in class pedviz.view.PathHighlighter: Enables or disables the highlighter.
setEnabled(int, boolean) - Method in class pedviz.view.rules.ColorRule: Enables or disables the rule with the given index.
setEnabled(boolean) - Method in class pedviz.view.rules.Rule: Enables or disables the rule.
setEnd(Node) - Method in class pedviz.graph.Edge: Sets the end node.
setEnds(List<NodeView>) - Method in class pedviz.view.EdgeView: Sets all end node.
setErrors(HashMap<Object, MerlinError>) - Method in class pedviz.haplotype.MerlinHaplotypes: Sets a collection of errors (MerlinErrorChecking).
setExpand(boolean) - Method in class pedviz.view.DefaultNodeView: Enables and disables the visibility of the node.
setFamilieRank(int) - Method in class pedviz.graph.Node: Sets the node's familie id.
setFemale(Object) - Method in class pedviz.view.rules.AbstractionRule
setFocus(double, double) - Method in class pedviz.view.effects.Effect: Sets the focus point.
setGap(int) - Method in class pedviz.view.DefaultNodeView: Sets the gap between two children.
setGapBottom(int) - Method in class pedviz.view.DefaultEdgeView: Sets the gap at the bottom.
setGapTop(int) - Method in class pedviz.view.DefaultEdgeView: Sets the gap at the top.
setGraph(LayoutedGraph) - Method in class pedviz.view.GraphView: Sets the LayoutedGraph for this view..
setGraph(LayoutedGraph) - Method in class pedviz.view.GraphView3D
setHidden(boolean) - Method in class pedviz.view.NodeView
setHighlightedColor(Color) - Method in class pedviz.view.DefaultEdgeView: Sets the highlighted color of the line.
setHighlightedColor(Color) - Method in class pedviz.view.DefaultNodeView: Sets the highlighted color of the node.
setHighlightedWidth(float) - Method in class pedviz.view.DefaultEdgeView: Sets the width for lines that are highlighted.
setHintAttribute(String) - Method in class pedviz.view.DefaultNodeView: Sets a trait that will be displayed in the hint.
setHintText(String) - Method in class pedviz.view.DefaultNodeView: Sets the hint text.
setHorizontalGap(int) - Method in class pedviz.algorithms.RubberBands: Sets the gap between two nodes, if they have the same parents.
setHorizontalSpacing(float) - Method in class pedviz.algorithms.RubberBands: Sets the gap between two nodes, if they have the same parents.
setId(Object) - Method in class pedviz.haplotype.MerlinError: Sets the id.
setIdDad(Object) - Method in class pedviz.graph.Node: Sets the node's dad id.
setIdMom(Object) - Method in class pedviz.graph.Node: Sets the node's mom id.
setInterval(int) - Method in class pedviz.view.animations.Animation: Sets the interval of the timer.
setLayouted(boolean) - Method in class pedviz.graph.Graph: Sets
setLightEnabled(boolean) - Method in class pedviz.view.GraphView3D: Enables or disables transparency lights.
setMale(Object) - Method in class pedviz.view.rules.AbstractionRule
setMarker(String) - Method in class pedviz.haplotype.MerlinError: Sets the marker.
setMaterialEnabled(boolean) - Method in class pedviz.view.GraphView3D: Enables or disables materials.
setMaxIterations(int) - Method in class pedviz.algorithms.RubberBands: Sets the maximal number of iterations.
setMinSize(float) - Method in class pedviz.view.effects.FisheyeEffect: Sets the minimum size of a node.
setMode(int) - Method in class pedviz.view.LODHighlighter: Sets the mode.
setMode(int) - Method in class pedviz.view.rules.Rule: Sets the mode.
setMom(String) - Method in class pedviz.haplotype.HaplotypeItem
setMomId(String) - Method in class pedviz.haplotype.HaplotypeItem
setMomLeft(boolean) - Method in class pedviz.view.NodeView
setMouseOverColor(Color) - Method in class pedviz.view.DefaultNodeView: Returns the "mouse over" color of the node.
setMovingEnabled(boolean) - Method in class pedviz.view.GraphView: Enables or disables moving.
setMovingEnabled(boolean) - Method in class pedviz.view.GraphView3D
setMultiselection(boolean) - Method in class pedviz.view.GraphView: Enables or disables multiselection.
setName(String) - Method in class pedviz.graph.Graph: Sets the name of the graph.
setNodeSize(int) - Method in class pedviz.algorithms.RubberBands: Sets the size of a single node.
setNodeview(NodeView) - Method in class pedviz.event.NodeViewEvent: Sets the NodeView object.
setOperator(int) - Method in class pedviz.algorithms.filter.Filter: Sets the operator.
setPosHierarchie(int, float) - Method in class pedviz.graph.LayoutedGraph
setPosX(float) - Method in class pedviz.view.NodeView: Sets the position on the X-axis.
setPosY(float) - Method in class pedviz.view.NodeView: Sets the position on the Y-axis.
setPosZ(float) - Method in class pedviz.view.NodeView: Sets the position on the Z-axis.
setQuery(String) - Method in class pedviz.loader.DatabaseGraphLoader: Sets a query.
setRatio(double) - Method in class pedviz.haplotype.MerlinError: Sets the ratio.
setRules(Vector<Rule>) - Method in class pedviz.view.GraphView: Sets a collection of rules.
setScale(double) - Method in class pedviz.view.GraphView: Sets the scale factor.
setScale(double) - Method in class pedviz.view.GraphView2D
setScale(double) - Method in class pedviz.view.GraphView3D
setSelectedColor(Color) - Method in class pedviz.view.DefaultNodeView: Sets the selected color of the node.
setSelectionEnabled(boolean) - Method in class pedviz.view.GraphView: Enables or disables selection.
setSettings(String, String, String) - Method in class pedviz.loader.Loader: Sets the field names, in which the id, mom's id and dad's id are saved.
setShape(Symbol) - Method in class pedviz.view.rules.ShapeRule: Sets the symbol.
setShowMarkers(boolean) - Method in class pedviz.view.symbols.SymbolHaplotypes
setSize(float) - Method in class pedviz.view.DefaultNodeView: Sets the size of the node.
setSize(double) - Method in class pedviz.view.symbols.SymbolText: Sets the height of the text.
setSpeed(float) - Method in class pedviz.view.effects.Effect: Sets the speed.
setSplitter(Splitter) - Method in class pedviz.algorithms.sugiyama.SugiyamaLayout: Sets what WallSplitter will be used.
setStart(Node) - Method in class pedviz.graph.Edge: Sets the start node.
setStart(NodeView) - Method in class pedviz.view.EdgeView: Sets the start node.
setStyle(int) - Method in class pedviz.view.symbols3d.Symbol3D: Sets the style for this symbol.
setSymbolMode(int) - Method in class pedviz.view.rules.AbstractionRule: Sets the mode.
setSymbols(ArrayList<Symbol>) - Method in class pedviz.view.DefaultNodeView: Sets all symbols of the node.
setTraits(String[]) - Method in class pedviz.view.symbols.SymbolGenotypes: Collection of traits with genotype informations.
setTranslate(double, double) - Method in class pedviz.view.GraphView: Sets the x-translation and the y-translation.
setTranslateX(double) - Method in class pedviz.view.GraphView: Sets the x-translation.
setTranslateX(double) - Method in class pedviz.view.GraphView2D
setTranslateX(double) - Method in class pedviz.view.GraphView3D
setTranslateY(double) - Method in class pedviz.view.GraphView: Sets the y-translation.
setTranslateY(double) - Method in class pedviz.view.GraphView2D
setTranslateY(double) - Method in class pedviz.view.GraphView3D
setTransparencyEnabled(boolean) - Method in class pedviz.view.GraphView3D: Enables or disables transparency.
setType(int) - Method in class pedviz.event.NodeViewEvent: Sets the type.
setUserData(String, Object) - Method in class pedviz.graph.Node: Stores an trait that can be identified by the given identifier.
setUserdata(String) - Method in class pedviz.view.rules.GradientRule: Sets the trait.
setVerticalSpacing(float) - Method in class pedviz.algorithms.RubberBands: Sets the spacing between two generations.
setVisbleSphere(boolean) - Method in class pedviz.view.GraphView3D: Sets the visibilty of the sphere.
setWidth(float) - Method in class pedviz.view.DefaultEdgeView: Sets the width of the line.
setXRotatingEnabled(boolean) - Method in class pedviz.view.GraphView3D: Enables or disables rotating on the x-axis.
setYRotatingEnabled(boolean) - Method in class pedviz.view.GraphView3D: Enables or disables rotating on the y-axis..
setZoomEnabled(boolean) - Method in class pedviz.view.GraphView: Enables or disables zooming.
setZoomEnabled(boolean) - Method in class pedviz.view.GraphView3D
ShapeCreator3D - Class in pedviz.view.symbols3d: A very speedy NodeCreator implementation for about 35.000 nodes.
ShapeCreator3D() - Constructor for class pedviz.view.symbols3d.ShapeCreator3D
ShapeRule - Class in pedviz.view.rules: With this rule you can set a symbol, dependent on the given trait (UserData).
ShapeRule(String, Object, Symbol) - Constructor for class pedviz.view.rules.ShapeRule: Constructs a ShapeRule with given trait id, trait value and the symbol.
ShapeRule(Symbol) - Constructor for class pedviz.view.rules.ShapeRule: Constructs a ShapeRule with the symbol.
show(Node) - Method in class pedviz.view.GraphView: Shows the given node if it's hidden.
show(Node) - Method in class pedviz.view.GraphView3D
showAll() - Method in class pedviz.view.GraphView: Shows all nodes that are currently hidden.
showAll() - Method in class pedviz.view.GraphView3D
showAllMarkers() - Method in class pedviz.haplotype.Haplotypes: Shows all markers.
showMarker(int) - Method in class pedviz.haplotype.Haplotypes: Shows the given marker.
SicknessSplitter - Class in pedviz.algorithms.sugiyama: This class can be used as a WallSplitter for the SugiyamaLayout class.
SicknessSplitter(String[], String[]) - Constructor for class pedviz.algorithms.sugiyama.SicknessSplitter: Creates a SicknessSplitter object with the given array of traits and values.
SINGLETON - Static variable in class pedviz.algorithms.GraphError
SizeAnimation - Class in pedviz.view.animations: This animation lets a collection of nodes change their size.
SizeAnimation(GraphView, Set<Node>) - Constructor for class pedviz.view.animations.SizeAnimation: Creates a new SizeAnimation for the given GraphView object.
sortSubNodes() - Method in class pedviz.algorithms.sugiyama.SugiyamaNodeView: Sorts subnodes by their barycentric.
sortSubNodes() - Method in class pedviz.view.NodeView: Sorts all subnodes.
Splitter - Interface in pedviz.algorithms.sugiyama: This interface defines methods for an algorithm that can split the given graph in two walls.
start() - Method in class pedviz.view.animations.Animation: Starts the animation.
stateChanged(ChangeEvent) - Method in class pedviz.algorithms.Sugiyama
stop() - Method in class pedviz.view.animations.Animation: Stops the animation.
stop() - Method in class pedviz.view.animations.BlinkAnimation
STYLE_NORMAL - Static variable in class pedviz.view.symbols3d.Symbol3D
STYLE_TURM - Static variable in class pedviz.view.symbols3d.Symbol3D
SUCCESSORS - Static variable in class pedviz.algorithms.Highlighter: All successors of a person.
SUCCESSORS - Static variable in class pedviz.view.LODHighlighter: All successors of a person.
SUCCESSORS_AND_ANCESTORS - Static variable in class pedviz.algorithms.Highlighter: All successors and ancestors of a person.
SUCCESSORS_AND_ANCESTORS - Static variable in class pedviz.view.LODHighlighter: All successors and ancestors of a person.
Sugiyama - Class in pedviz.algorithms: This class combines all steps that are necessary to create a layout for a Graph object.
Sugiyama(Graph) - Constructor for class pedviz.algorithms.Sugiyama: Creates a new Sugyiama object for the given Graph object with default settings.
Sugiyama(Graph, Splitter) - Constructor for class pedviz.algorithms.Sugiyama: Creates a new Sugyiama object for the given Graph object with default settings.
Sugiyama(Graph, DefaultNodeView, DefaultEdgeView) - Constructor for class pedviz.algorithms.Sugiyama: Creates a new Sugyiama object for the given Graph object with given settings
Sugiyama(Graph, DefaultNodeView, DefaultEdgeView, Splitter) - Constructor for class pedviz.algorithms.Sugiyama: Creates a new Sugyiama object for the given Graph object with given settings and the given Splitter object.
SugiyamaEdgeView - Class in pedviz.algorithms.sugiyama: This class extends the EdgeView class by some methods used by the sugiyama algorithm.
SugiyamaEdgeView(Edge, DefaultEdgeView) - Constructor for class pedviz.algorithms.sugiyama.SugiyamaEdgeView: Creates a new SugiyamaEdgeView object for the given edge and with the given settings.
SugiyamaLayout - Class in pedviz.algorithms.sugiyama: This class applies the Sugiyama-Algorihm on the specified graph.
SugiyamaLayout(Graph, DefaultNodeView, DefaultEdgeView) - Constructor for class pedviz.algorithms.sugiyama.SugiyamaLayout: Creates the SugiyamaLayout with the given Graph object.
SugiyamaNodeView - Class in pedviz.algorithms.sugiyama: This class extends the NodeView class by a barycentric property.
SugiyamaNodeView(Node, DefaultNodeView) - Constructor for class pedviz.algorithms.sugiyama.SugiyamaNodeView
Symbol - Class in pedviz.view: This class is the super class for symbols.
Symbol() - Constructor for class pedviz.view.Symbol
Symbol2D - Class in pedviz.view.symbols: This class is the super class for all implemented symbols for the 2d visualization.
Symbol2D() - Constructor for class pedviz.view.symbols.Symbol2D
Symbol3D - Class in pedviz.view.symbols3d: This class is the super class for all implemented symbols for the 3d visualization.
Symbol3D(int) - Constructor for class pedviz.view.symbols3d.Symbol3D: Create a new Symbol object with the given style.
SymbolAdopted - Class in pedviz.view.symbols: Draws the symbol for an adopted individual.
SymbolAdopted() - Constructor for class pedviz.view.symbols.SymbolAdopted
SymbolAdopted3d - Class in pedviz.view.symbols3d: Draws the symbol for an adopted individual.
SymbolAdopted3d() - Constructor for class pedviz.view.symbols3d.SymbolAdopted3d
SymbolAdopted3d(int) - Constructor for class pedviz.view.symbols3d.SymbolAdopted3d
SymbolDeceased - Class in pedviz.view.symbols: Draws the symbol for a deceased individual.
SymbolDeceased() - Constructor for class pedviz.view.symbols.SymbolDeceased
SymbolDeceased3d - Class in pedviz.view.symbols3d: Draws the symbol for a deceased individual.
SymbolDeceased3d() - Constructor for class pedviz.view.symbols3d.SymbolDeceased3d
SymbolDeceased3d(int) - Constructor for class pedviz.view.symbols3d.SymbolDeceased3d
SymbolFamily - Class in pedviz.view.symbols: Draws the symbol for a family node.
SymbolFamily(int, Object, Object) - Constructor for class pedviz.view.symbols.SymbolFamily: Creates a new symbol for a family node.
SymbolFamily3d - Class in pedviz.view.symbols3d: Draws the symbol for a family node.
SymbolFamily3d(int, Object, Object) - Constructor for class pedviz.view.symbols3d.SymbolFamily3d: Creates a new symbol for a family node.
SymbolGenotypes - Class in pedviz.view.symbols: Draws the symbol for genotpyes.
SymbolGenotypes(String...) - Constructor for class pedviz.view.symbols.SymbolGenotypes: Creates a new GenotypeSymbol with the given collection of traits.
SymbolGenotypes(boolean, String...) - Constructor for class pedviz.view.symbols.SymbolGenotypes: Creates a new GenotypeSymbol with the given collection of traits.
SymbolHaplotypes - Class in pedviz.view.symbols: Draws the symbol for haplotypes.
SymbolHaplotypes(Haplotypes) - Constructor for class pedviz.view.symbols.SymbolHaplotypes: Creates a haplotype symbol with the given haplotypes.
SymbolHaplotypes(Haplotypes, boolean) - Constructor for class pedviz.view.symbols.SymbolHaplotypes: Creates a haplotype symbol with the given haplotypes.
SymbolPregnancy - Class in pedviz.view.symbols: Indicates a pregnancy.
SymbolPregnancy() - Constructor for class pedviz.view.symbols.SymbolPregnancy
SymbolQualitativeTrait - Class in pedviz.view.symbols: This symbols provides the possibility to display a specified trait in a bar plot with a nice color gradient.
SymbolQualitativeTrait(String, double, double, double, double) - Constructor for class pedviz.view.symbols.SymbolQualitativeTrait: Constructs a SymbolQualitativeTrait with the given values.
SymbolSexFemale - Class in pedviz.view.symbols: Draws the symbol for a female individual.
SymbolSexFemale() - Constructor for class pedviz.view.symbols.SymbolSexFemale
SymbolSexFemale3d - Class in pedviz.view.symbols3d: Draws the symbol for a female individual.
SymbolSexFemale3d() - Constructor for class pedviz.view.symbols3d.SymbolSexFemale3d
SymbolSexFemale3d(int) - Constructor for class pedviz.view.symbols3d.SymbolSexFemale3d
SymbolSexFemaleLow - Class in pedviz.view.symbols3d: Draws the symbol for a female individual.
SymbolSexFemaleLow() - Constructor for class pedviz.view.symbols3d.SymbolSexFemaleLow
SymbolSexMale - Class in pedviz.view.symbols: Draws the symbol for a male individual.
SymbolSexMale() - Constructor for class pedviz.view.symbols.SymbolSexMale
SymbolSexMale3d - Class in pedviz.view.symbols3d: Draws the symbol for a male individual.
SymbolSexMale3d() - Constructor for class pedviz.view.symbols3d.SymbolSexMale3d
SymbolSexMale3d(int) - Constructor for class pedviz.view.symbols3d.SymbolSexMale3d
SymbolSexMaleLow - Class in pedviz.view.symbols3d: Draws the symbol for a male individual.
SymbolSexMaleLow() - Constructor for class pedviz.view.symbols3d.SymbolSexMaleLow
SymbolSexUndesignated - Class in pedviz.view.symbols: Draws the symbol for a individual with unknown sex.
SymbolSexUndesignated() - Constructor for class pedviz.view.symbols.SymbolSexUndesignated
SymbolSexUndesignated3d - Class in pedviz.view.symbols3d: Draws the symbol for a individual with unknown sex.
SymbolSexUndesignated3d() - Constructor for class pedviz.view.symbols3d.SymbolSexUndesignated3d
SymbolSexUndesignated3d(int) - Constructor for class pedviz.view.symbols3d.SymbolSexUndesignated3d
SymbolSexUndesignatedLow - Class in pedviz.view.symbols3d: Draws the symbol for a individual with unknown sex.
SymbolSexUndesignatedLow() - Constructor for class pedviz.view.symbols3d.SymbolSexUndesignatedLow
SymbolText - Class in pedviz.view.symbols: This symbol allow you to display a number or a character in the symbol.
SymbolText(String) - Constructor for class pedviz.view.symbols.SymbolText: Creates a new symbol that contains the given text.

T

TestAlgo - Class in pedviz.algorithms
TestAlgo() - Constructor for class pedviz.algorithms.TestAlgo
TextCondition - Class in pedviz.algorithms.filter: This class represents a Condtion for a trait, which contains a string value.
TextCondition(String, int, String) - Constructor for class pedviz.algorithms.filter.TextCondition: Creates a new TextCondition for the given trait with the given mode and values.
TextCondition(String, int, String, String) - Constructor for class pedviz.algorithms.filter.TextCondition: Creates a new TextCondition for the given trait with the given mode and values.
toString() - Method in class pedviz.algorithms.GraphError
toString() - Method in class pedviz.graph.Edge
toString() - Method in class pedviz.graph.Graph
toString() - Method in class pedviz.graph.Node
transformPoint(float, float) - Method in class pedviz.view.effects.Effect: Transforms the given points.
transformPoint(float, float) - Method in class pedviz.view.effects.FisheyeEffect
transformSize(float, float, float, float, float) - Method in class pedviz.view.effects.Effect: Transforms the given size. x,y are untransformed and newX, newY are the transformed coordinates.
transformSize(float, float, float, float, float) - Method in class pedviz.view.effects.FisheyeEffect

U

unHighlightAll() - Method in class pedviz.view.GraphView: Clears accentuation for all nodes.
unHighlightAll() - Method in class pedviz.view.GraphView3D
updateGraphModel() - Method in class pedviz.view.GraphView: After you change the LayoutedGraph object manually run this method.
updateGraphView() - Method in class pedviz.view.GraphView: Fires an update of the GraphView manually.
updateGraphView() - Method in class pedviz.view.GraphView2D
updateModel() - Method in class pedviz.graph.LayoutedGraph: Reloads all nodes and edges from the Graph object and updates the existing model.
updateNodes(Set<Node>) - Method in class pedviz.view.GraphView: Redraws the given nodes.
updateNodes(Set<Node>) - Method in class pedviz.view.GraphView2D
updateNodes(Set<Node>) - Method in class pedviz.view.GraphView3D
updateRules() - Method in class pedviz.view.GraphView: Reapplies all rules.
updateRules() - Method in class pedviz.view.GraphView2D
updateRules() - Method in class pedviz.view.GraphView3D
updateYPosition() - Method in class pedviz.algorithms.RubberBands

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