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

A

actionPerformed(ActionEvent) - Method in class sonia.SoniaInterface
 
actionPerformed(ActionEvent) - Method in class sonia.LogWindow
 
actionPerformed(ActionEvent) - Method in class sonia.LayoutWindow
Queries the event to determine which button was clicked, and calls the corresponding method.
actionPerformed(ActionEvent) - Method in class sonia.LayoutSettingsDialog
 
actionPerformed(ActionEvent) - Method in class sonia.DotNetParser
Action listener for getting the OK from the parser options dialog.
actionPerformed(ActionEvent) - Method in class sonia.CoolingSchedule
Checks which button is pressed and takes the appropriate action.
actionPerformed(ActionEvent) - Method in class sonia.ApplySettingsDialog
figures out what user did and calls apropriate method
addArc(int, int, double) - Method in class sonia.LayoutSlice
Adds an arc to the slice, summing the passed weight with the weight already listed for that relation.
addArcEvent(ArcAttribute) - Method in class sonia.RenderSlice
 
addArcEvents(Vector) - Method in class sonia.NetDataStructure
 
addLayoutProperty(String, double) - Method in class sonia.ApplySettingsDialog
called by the layout algorithm during setup so that it can add parameters to the dilog box.
addNodeEvent(NodeAttribute) - Method in class sonia.RenderSlice
 
addNodeEvent(NodeAttribute) - Method in class sonia.LayoutSlice
Adds the passed node event to the collection of node events in this slice.
addNodeEvents(Vector) - Method in class sonia.NetDataStructure
 
addPresentNode(int) - Method in class sonia.LayoutSlice
Puts the passed index in the list of nodes which are present in this slice.
addStabilityEstimate(StabilityEstimate) - Method in class sonia.LayoutSlice
 
applyCoordsToSlice(double[], double[], LayoutSlice) - Static method in class sonia.LayoutUtils
Sets the coordinates of the LayoutSlice to the coordinates of the passed arrays.
applyLayoutTo(LayoutSlice) - Method in class sonia.SoniaLayoutEngine
Applies a layout algorithm to the passed slice.
applyLayoutTo(LayoutSlice, int, int, ApplySettingsDialog) - Method in class sonia.RubBandFRLayout
 
applyLayoutTo(LayoutSlice, int, int, ApplySettingsDialog) - Method in class sonia.RandomFRLayout
 
applyLayoutTo(LayoutSlice, int, int, ApplySettingsDialog) - Method in class sonia.PILayout
 
applyLayoutTo(LayoutSlice, int, int, ApplySettingsDialog) - Method in class sonia.OrigCoordLayout
 
applyLayoutTo(LayoutSlice, int, int, ApplySettingsDialog) - Method in interface sonia.NetLayout
 
applyLayoutTo(LayoutSlice, int, int, ApplySettingsDialog) - Method in class sonia.MultiCompKKLayout
Gets a few settings and starts the layoutRunner thread.
applyLayoutTo(LayoutSlice, int, int, ApplySettingsDialog) - Method in class sonia.MetricMDSLayout
 
applyLayoutTo(LayoutSlice, int, int, ApplySettingsDialog) - Method in class sonia.KKLayout
 
applyLayoutTo(LayoutSlice, int, int, ApplySettingsDialog) - Method in class sonia.FRLayout
 
applyLayoutTo(LayoutSlice, int, int, ApplySettingsDialog) - Method in class sonia.CircleLayout
applies the circular layout to the passed slice, using the passed with and height, and the settings from the passed settings dialog.
applyLayoutToCurrent() - Method in class sonia.SoniaLayoutEngine
Applies the layout to the current slice.
applyLayoutToRemaining() - Method in class sonia.SoniaLayoutEngine
Starts an independent thread to run the layout algorithms, this allows screen redraws and events (like pause) to take place.
applySettings() - Method in class sonia.GraphicsSettingsDialog
Transfers the settings from the display checkboxes to the Canvas.
ApplySettingsDialog - class sonia.ApplySettingsDialog.
Provides the controls for specifing layout parameters and how the layots will be applied.
ApplySettingsDialog(SoniaController, SoniaLayoutEngine, Frame, NetLayout) - Constructor for class sonia.ApplySettingsDialog
Creates a dilog box with settings to control the various stages of the layout process, including some algorithm specific parameters, which it adds to the window by communicating with the layout algorithm.
ArcAttribute - class sonia.ArcAttribute.
Holds the attributes which describe an arc event, starting, ending, colors, original coords, labels, etc.
ArcAttribute() - Constructor for class sonia.ArcAttribute
instantiates an arc attribute with defualt values and no from or to
ArcAttribute(double, double, int, int, double, double) - Constructor for class sonia.ArcAttribute
instantiate an arc attribute with some of the basic parameters
AVG_TIE_VALS - Static variable in class sonia.NetDataStructure
 

B

barycenterLayout(LayoutSlice, int, int, boolean) - Static method in class sonia.LayoutUtils
Recenters nodes so that the average position (bary center) is in the middle of the window.
barycenterLayout(LayoutSlice, int, int, double[], double[], boolean) - Static method in class sonia.LayoutUtils
Recenters nodes so that the average position (bary center) is in the middle of the window.

C

calcAllSliceAvg() - Method in class sonia.StressInfo
 
calcDiameter(DenseDoubleMatrix2D) - Static method in class sonia.NetUtils
 
calcDiameter(LayoutSlice) - Static method in class sonia.NetUtils
Returns a double equal to the graph-theoretic diameter of the passed network (the length of the longest shortest path).
calcStability() - Method in class sonia.StabilityEstimate
 
calcStability() - Method in class sonia.SoniaLayoutEngine
 
calcStress() - Method in class sonia.SoniaLayoutEngine
Does stability and stress (modified version of Kruskal's stress, for comparing screen distances to desired matrix distances) calculations for current slice, displays them as a shepard's plot in the stress window.
captureImage() - Method in class sonia.SoniaMovieMaker
Records the currently displayed image to the movie file.
centerLayout(LayoutSlice, int, int, boolean) - Static method in class sonia.LayoutUtils
Recenters nodes so that center of layout is in the center of the window.
centerLayout(LayoutSlice, int, int, double[], double[], boolean) - Static method in class sonia.LayoutUtils
Centers nodes so that center of layout is in the center of the window.
changeToSliceNum(int) - Method in class sonia.SoniaLayoutEngine
Checks if the passed slice number exists, then changes the current slice number.
CIRCLE - Static variable in class sonia.ApplySettingsDialog
 
CircleLayout - class sonia.CircleLayout.
CircleLayout is one of the most boring network layouts, it just puts all nodes in a circle in the middle of the screen.
circleLayout(LayoutSlice, int, int) - Static method in class sonia.LayoutUtils
Positions nodes in a circle which fits within the rectangle defined by width and height.
CircleLayout(SoniaController, SoniaLayoutEngine) - Constructor for class sonia.CircleLayout
CircleLayout is one of the most boring network layouts, it just puts all nodes in a circle in the middle of the screen.
compareTo(Object) - Method in class sonia.NodeAttribute
compares start times for list sorting.
compareTo(Object) - Method in interface sonia.NetworkEvent
 
compareTo(Object) - Method in class sonia.ArcAttribute
compares start times for list sorting.
CoolingSchedule - class sonia.CoolingSchedule.
CoolingSchedule is both the data structure for controlling the cooling of a "simulated anealing" processes layout, methods for providing acesses to the processes, and the UI for the user, and feedback from the layout process.
CoolingSchedule(int) - Constructor for class sonia.CoolingSchedule
Creates a cooling schedule (and gui) withe the specified number of control points
CoordInterpolator - interface sonia.CoordInterpolator.
Interface for interpolation schemes to be used in generating coordinates for nodes when rendering slices between slice layouts.
copyLayout(LayoutSlice, LayoutSlice) - Static method in class sonia.LayoutUtils
Sets the coordinates in fromSlice to match those in toSlice.
CosineInterpolation - class sonia.CosineInterpolation.
CoosineInterpolation calculates a slow-in, slow-out sinusoidal interpolation between the node coordinates of the current slice and the coordinates in the destination slice.
CosineInterpolation() - Constructor for class sonia.CosineInterpolation
Instantiates the consine interpolator.
createLayout() - Method in class sonia.SoniaController
Checks that a file has been loaded, then creates a layout engien for the most recently loaded file.
CURRENT - Static variable in class sonia.ApplySettingsDialog
 

D

disposeEngine() - Method in class sonia.SoniaLayoutEngine
Gives the engine a chance to do any clean up (like asking layouts to dispose of schedules..
disposeEngine(SoniaLayoutEngine) - Method in class sonia.SoniaController
Removes the passed layout engine from the list of layouts
disposeLayout() - Method in class sonia.RubBandFRLayout
 
disposeLayout() - Method in class sonia.RandomFRLayout
 
disposeLayout() - Method in class sonia.PILayout
 
disposeLayout() - Method in class sonia.OrigCoordLayout
 
disposeLayout() - Method in interface sonia.NetLayout
gives the layout a chance to dispose of any associate objects or windows (such as the cooling schedule)
disposeLayout() - Method in class sonia.MultiCompKKLayout
 
disposeLayout() - Method in class sonia.MetricMDSLayout
 
disposeLayout() - Method in class sonia.KKLayout
 
disposeLayout() - Method in class sonia.FRLayout
Kills of the cooling schedule and nulls itself
disposeLayout() - Method in class sonia.CircleLayout
 
disposeNetwork(NetDataStructure) - Method in class sonia.SoniaController
Removes the passed Network from the list of stored networks
disposePhasePlot() - Method in class sonia.SoniaLayoutEngine
Hides and then nullifies the PhasePlot (if it exists)so that it will not take proccessing time.
disposeStressPlot() - Method in class sonia.SoniaLayoutEngine
 
DotNetParser - class sonia.DotNetParser.
Class for constructing networks from text files in Pajek's *.net Arc/Edge list file format.
DotNetParser() - Constructor for class sonia.DotNetParser
Instantiates a parser for importing network data in files folowing the .net format.
DotSonParser - class sonia.DotSonParser.
The idea for the .son parser is that it reads an edgelist format, but one that is "column based" rather than "token based" like the .net parser.
DotSonParser() - Constructor for class sonia.DotSonParser
Parser for .son files, list based network format which allows column variable assignment and a bit more flexiblity than the pajek .net format

E

endMoveNodes() - Method in class sonia.NodeMover
 
exportMatricies() - Method in class sonia.SoniaController
Brings up a dialog to chose which layout to export, then a save dialog, and then saves out a text file containing a set of matricies corresponding to each slice in the layout.
exportMovie() - Method in class sonia.SoniaController
Brings up a dialog to pick which of the layouts to export as a movie, then makes a movie exporter and passes it to the layout engine.

F

fillRenderSlice(RenderSlice) - Method in class sonia.NetDataStructure
 
finishLayout(NetLayout, LayoutSlice, double, double) - Method in class sonia.SoniaLayoutEngine
Does any final repositioning (rescaling, recentering, Isolate repositioning, etc) of the nodes, logs layout settings and results, and sets the slice to "finished" status, updates the display.
finishMovie() - Method in class sonia.SoniaMovieMaker
 
FRLayout - class sonia.FRLayout.
Positions nodes in layout according to a modified implementation of the Fruchterman-Reingold graph layout algorithm.
FRLayout(SoniaController, SoniaLayoutEngine) - Constructor for class sonia.FRLayout
Configures the layout, displays a cooling schedule with default control points.

G

get(int, int) - Method in class sonia.Subnet
 
getAllShortPathMatrix(DoubleMatrix2D) - Static method in class sonia.NetUtils
returns an adjacency matrix in which each entry is the "All-Pairs shortest path: distance between the nodes, calculated with Dijkstra's algorithm
getAllShortPathMatrix(LayoutSlice) - Static method in class sonia.NetUtils
returns an adjacency matrix in which each entry is the "All-Pairs shortest path: distance between the nodes, calculated with Dijkstra's algorithm
getAllSliceMaxMin(ArrayList) - Static method in class sonia.NetUtils
loops over all the slices in engine and returns the max and min value
getArcColor() - Method in class sonia.ArcAttribute
returns the color of the arc
getArcCount(int, int) - Method in class sonia.LayoutSlice
returns the number of arcsEvents relating i and j.
getArcEvents() - Method in class sonia.RenderSlice
 
getArcLabel() - Method in class sonia.ArcAttribute
returns the string of the arc label
getArcList() - Method in interface sonia.Parser
Returns a vector containing all the parsed ArcEvents
getArcList() - Method in class sonia.DotSonParser
 
getArcList() - Method in class sonia.DotNetParser
Returns a Vector containing all the ArcAttributes parsed from the file.
getArcTransVal() - Method in class sonia.SoniaCanvas
 
getArcWeight() - Method in class sonia.ArcAttribute
returns the double weight of the arc
getArcWeight(int, int) - Method in class sonia.LayoutSlice
returns the weight of the relation between i and j (the value of the arcs matrix)
getArcWidth() - Method in class sonia.ArcAttribute
the double value giving the number of pixels wide to draw the arc
getArcWidthFact() - Method in class sonia.SoniaCanvas
 
getBorderColor() - Method in class sonia.NodeAttribute
 
getBorderWidth() - Method in class sonia.NodeAttribute
 
getBottomPad() - Method in class sonia.SoniaLayoutEngine
returns the pixel height of the bottom pad (the area at the bottom of the layout window where the buttons and text fields are)
getComponents(SparseDoubleMatrix2D, boolean) - Static method in class sonia.NetUtils
Returns an array list containing a set of Subnets correspondig to the strong components of the network.
getCtlValString() - Method in class sonia.CoolingSchedule
Returns a string giving the control points in a form suitable for editing or logging, and reparseing.
getCtlValues() - Method in class sonia.CoolingSchedule
Returns an array of doubles containing the screen coordinates for the control points.
getCurrentPath() - Method in class sonia.SoniaController
Returns the path to the last used file.
getCurrentSlice() - Method in class sonia.SoniaLayoutEngine
returns the current LayoutSlice
getCurrentSliceNum() - Method in class sonia.SoniaLayoutEngine
returns the index number of the currently selected slice
getCurrentXCoords() - Method in class sonia.SoniaLayoutEngine
Returns a double array of the current x coords for the current slice.
getCurrentYCoords() - Method in class sonia.SoniaLayoutEngine
Returns a double array of the current y coords for the current slice.
getDisplayHeight() - Method in class sonia.SoniaLayoutEngine
Asks the display for the height of the frame using getHeight().
getDisplayWidth() - Method in class sonia.SoniaLayoutEngine
Asks the display for the width of the frame using getWidth().
getEndTime() - Method in class sonia.NodeAttribute
 
getEndTime() - Method in interface sonia.NetworkEvent
 
getEndTime() - Method in class sonia.ArcAttribute
returns the double end time for the arc.
getErrorSlices() - Method in class sonia.SoniaLayoutEngine
returns an array of booleans corresponding to each slice, true if there are errors.
getEventsFromTo(double, double) - Method in class sonia.NetDataStructure
returns a list containing all the nodes and arcs within the passed time bounds
getFileName() - Method in class sonia.SoniaController
Returns fileName, but with any extension after "." removed
getFirstTime() - Method in class sonia.NetDataStructure
 
getFont() - Method in class sonia.SoniaController
Returns the UI font for consistancy across layouts.
getFromNodeId() - Method in class sonia.ArcAttribute
returns the int corresponding to the starting node
getInputFile(String, String) - Method in class sonia.SoniaController
Asks the interface to throw up an open file dialog, gets file name and returns it.
getInputFileName(String, String) - Method in class sonia.SoniaInterface
throws up an open file dialog for choosing files to load.
getInterpFrames() - Method in class sonia.SoniaLayoutEngine
Returns the current number of intermediary interpolation ("tweening") frames to be drawn while animating transitions between slices.
getIsolates() - Method in class sonia.LayoutSlice
Returns a list of indecies cooresponding to the nodes with no in or out connections
getIsolatesCode() - Method in class sonia.ApplySettingsDialog
returns an int indicating the setting for how to handle the position of isolated nodes.
getLabelColor() - Method in class sonia.ArcAttribute
returns the color of the arc's label
getLabelSize() - Method in class sonia.NodeAttribute
 
getLabelSize() - Method in class sonia.ArcAttribute
returns the size (font size?) to draw the label
getLastTime() - Method in class sonia.NetDataStructure
 
getLayoutHeight() - Method in class sonia.SoniaLayoutEngine
Returns the pixel hieght of the area availible for laying out the network.
getLayoutInfo() - Method in class sonia.SoniaLayoutEngine
Gives a string describing the layout.
getLayoutInfo() - Method in class sonia.RubBandFRLayout
 
getLayoutInfo() - Method in class sonia.RandomFRLayout
 
getLayoutInfo() - Method in class sonia.PILayout
 
getLayoutInfo() - Method in class sonia.OrigCoordLayout
 
getLayoutInfo() - Method in interface sonia.NetLayout
Returns a string with several lines of text describing the layout settings.
getLayoutInfo() - Method in class sonia.MultiCompKKLayout
Returns the layout info string for the log, which may contain information about starting and stopping values, etc.
getLayoutInfo() - Method in class sonia.MetricMDSLayout
 
getLayoutInfo() - Method in class sonia.KKLayout
 
getLayoutInfo() - Method in class sonia.FRLayout
 
getLayoutInfo() - Method in class sonia.CircleLayout
returns information about the layout, in this case the radius
getLayoutProperty(String) - Method in class sonia.ApplySettingsDialog
gets the user entered value of the algorithm specific layout property, if name matches one of the previously setup parameters.
getLayoutSlices(double, double, double, double, int) - Method in class sonia.NetDataStructure
creates layoutSlices (bins for events) all in one go and sorts events into them.
getLayoutType() - Method in class sonia.RubBandFRLayout
 
getLayoutType() - Method in class sonia.RandomFRLayout
 
getLayoutType() - Method in class sonia.PILayout
 
getLayoutType() - Method in class sonia.OrigCoordLayout
 
getLayoutType() - Method in interface sonia.NetLayout
Returns a string giving the name of the kind of layout.
getLayoutType() - Method in class sonia.MultiCompKKLayout
Returns a String with the name of the kind of the layout
getLayoutType() - Method in class sonia.MetricMDSLayout
 
getLayoutType() - Method in class sonia.KKLayout
 
getLayoutType() - Method in class sonia.FRLayout
 
getLayoutType() - Method in class sonia.CircleLayout
returns the name of the layout, in this case "Circle Layout"
getLayoutWidth() - Method in class sonia.SoniaLayoutEngine
Returns the pixel width of the area availible for laying out the network.
getLayoutWindow() - Method in class sonia.SoniaLayoutEngine
 
getLeftPad() - Method in class sonia.SoniaLayoutEngine
how far from the left edge of the window to start the layout coordinate origin.
getMatrix() - Method in class sonia.Subnet
 
getMatrix(LayoutSlice) - Static method in class sonia.NetUtils
creates and returns the adjacency matrix of arc weights in the passed slice
getMatrixMaxMin(DoubleMatrix2D) - Static method in class sonia.NetUtils
returns the max and min values of a matrix, assumes no negitive values
getMaxMatrixVal() - Method in class sonia.SoniaLayoutEngine
returns the stored maximum value of a cell in the network matricies, calc'd by setupLayout().
getMaxNumNodes() - Method in interface sonia.Parser
Returns the maximum number of unique nodes (not NodeEvents) so that the size of the network matricies can be determined
getMaxNumNodes() - Method in class sonia.LayoutSlice
 
getMaxNumNodes() - Method in class sonia.DotSonParser
 
getMaxNumNodes() - Method in class sonia.DotNetParser
Returns the largest possible number of nodes (NOT node events) which can be in existance at once - the number of unique node ids.
getMaxUsrPasses() - Method in class sonia.CoolingSchedule
Returns the user-specified maximum number of passes for the layout algorithm, as defined by the the horisonal position of the last control point.
getMaxYvalue() - Method in class sonia.CoolingSchedule
Returns the maximum y value of the plot, which all data will be scaled to.
getMinMatrixValue() - Method in class sonia.SoniaLayoutEngine
returns the stored minmum value of a cell in the network matricies, calc'd by setupLayout().
getNetIndex(int) - Method in class sonia.Subnet
 
getNetIndexList() - Method in class sonia.Subnet
 
getNetInfo() - Method in interface sonia.Parser
Returns a string containing any additional info about the parsed file, such as comments (if supported)
getNetInfo() - Method in class sonia.NetDataStructure
 
getNetInfo() - Method in class sonia.DotSonParser
 
getNetInfo() - Method in class sonia.DotNetParser
Returns the info string from the network, this will include anything included in the "* Network" tag at the start of the file.
getNodeColor() - Method in class sonia.NodeAttribute
 
getNodeEvent(int) - Method in class sonia.LayoutSlice
Returns a node event corresponding to the passed index.
getNodeEvents() - Method in class sonia.RenderSlice
 
getNodeId() - Method in class sonia.NodeAttribute
 
getNodeIdLookup() - Method in class sonia.DotNetParser
Returns hash table for geting the internal id numbers of nodes from their name or pajekID
getNodeLabel() - Method in class sonia.NodeAttribute
 
getNodeList() - Method in interface sonia.Parser
Returns a vector containing all the parsed NodeEvents
getNodeList() - Method in class sonia.DotSonParser
 
getNodeList() - Method in class sonia.DotNetParser
Returns a Vector containing all the NodeAttributes parsed from the file.
getNodeScaleFact() - Method in class sonia.SoniaCanvas
 
getNodeShape() - Method in class sonia.NodeAttribute
 
getNodeSize() - Method in class sonia.NodeAttribute
 
getNumArcEvents() - Method in interface sonia.Parser
Returns the total number of ArcEvents parsed and created
getNumArcEvents() - Method in class sonia.DotSonParser
 
getNumArcEvents() - Method in class sonia.DotNetParser
Returns the number of arc events parsed.
getNumNodeEvents() - Method in interface sonia.Parser
Returns the total number of NodeEvents parsed and created
getNumNodeEvents() - Method in class sonia.DotSonParser
 
getNumNodeEvents() - Method in class sonia.DotNetParser
Returns the number of node events parsed.
getNumNodes() - Method in class sonia.Subnet
 
getNumSlices() - Method in class sonia.SoniaLayoutEngine
returns the number of slices in the slice vector
getObsTime() - Method in class sonia.NodeAttribute
 
getObsTime() - Method in interface sonia.NetworkEvent
 
getObsTime() - Method in class sonia.ArcAttribute
returns the double starting time for the arc, controls which slice it will appear in
getObsXCoord() - Method in class sonia.NodeAttribute
Returns the x coordinate originaly specified by the parser (or set later), this is NOT the node's layout coordinate which is stored in the slice.
getObsYCoord() - Method in class sonia.NodeAttribute
Returns the y coordinate originaly specified by the parser (or set later), this is NOT the node's layout coordinate which is stored in the slice.
getOutputFile(String, String) - Method in class sonia.SoniaController
Asks the interface to throw up a save file dialog, gets file name and returns it.
getOutputFileName(String, String) - Method in class sonia.SoniaInterface
Throws up a save file dialog and, returns a string with path and filename for saving files
getPad() - Method in class sonia.SoniaLayoutEngine
the desired margin between the nodes and the edge of the window
getParser() - Method in class sonia.NetDataStructure
 
getParserInfo() - Method in interface sonia.Parser
Returns a string with the name of the parser
getParserInfo() - Method in class sonia.DotSonParser
gives the name of the parser.
getParserInfo() - Method in class sonia.DotNetParser
Returns the name of the parser, in this case "DotNetParser".
getPearsons(SparseDoubleMatrix2D) - Static method in class sonia.NetUtils
 
getPhasePlot() - Method in class sonia.SoniaLayoutEngine
if there is already a phase plot for this engine, it will be returned, Otherwise null will be returned.
getPickedObject() - Method in class sonia.ListPicker
 
getPresentNodes() - Method in class sonia.LayoutSlice
returns a list containing the indcies of all the nodes present in the slice
getRenderSlice(double, double) - Method in class sonia.SoniaLayoutEngine
Creates a new RenderSlice, passes it to the NetDataStructure to get filled with the node and arc attributes that land in its range.
getRepaintN() - Method in class sonia.ApplySettingsDialog
returns an integer which controls how frequently the network will be redrawn while the layout is in process (redraw every Nth pass)
getResult() - Method in class sonia.OptionPrompter
returns the boolean describing the choice made (true for OK)
getReverse(SparseDoubleMatrix2D, double, double) - Static method in class sonia.NetUtils
reterns a new matrix which is the reverse similarity->disimilairty, disimilarity->similart of the passed matrix.
getRow(int) - Method in class sonia.LayoutSlice
returns an array of weights corresponding to the out relations of the node
getSlice(int) - Method in class sonia.SoniaLayoutEngine
returns the LayoutSlice with the corresponding index.
getSliceDelta() - Method in class sonia.LayoutSettingsDialog
 
getSliceDuration() - Method in class sonia.LayoutSettingsDialog
 
getSliceEnd() - Method in class sonia.RenderSlice
 
getSliceEnd() - Method in class sonia.LayoutSlice
 
getSliceEnd() - Method in class sonia.LayoutSettingsDialog
 
getSliceMatricies() - Method in class sonia.SoniaLayoutEngine
Returns a Vector of matricies corresponding to each of the slices stored in the engine.
getSliceStart() - Method in class sonia.RenderSlice
 
getSliceStart() - Method in class sonia.LayoutSlice
 
getSliceStart() - Method in class sonia.LayoutSettingsDialog
 
getStartCoordCode() - Method in class sonia.ApplySettingsDialog
returns the int corresponding to the setting for the starting coordinates (where nodes are positioned before algorithm runs).
getStress(LayoutSlice) - Static method in class sonia.NetUtils
 
getSubnetMatrix(SparseDoubleMatrix2D, IntArrayList) - Static method in class sonia.NetUtils
creates a new matrix with dimensions equal to number of nodes in intArrayList and containing only the relationships between the listed elements and of the same type (sparse, dense) as the passed matrix
getSubsetArray(double[]) - Method in class sonia.Subnet
 
getSummaryString() - Method in class sonia.ApplySettingsDialog
returns a string summarizing the layout settings to record in the log
getSymAvgArcWeight(int, int) - Method in class sonia.LayoutSlice
return2 the average of the i -> j and j -> i tie
getSymMaxArcWeight(int, int) - Method in class sonia.LayoutSlice
returns the max of the i -> j and j -> i ties
getSymMaxMatrix(LayoutSlice) - Static method in class sonia.NetUtils
returns a matrix which is the symetrized (i->j and j->i = Max((i->j,j->i))) version of the passed LayoutSlice.
getSymMaxMatrix(SparseDoubleMatrix2D) - Static method in class sonia.NetUtils
returns a matrix which is the symetrized (i->j and j->i = Max((i->j,j->i))) version of the passed adjacency matrix.
getSymMinArcWeight(int, int) - Method in class sonia.LayoutSlice
returns the min of the i -> j and j -> i ties
getTempFactor(int) - Method in class sonia.CoolingSchedule
Calculates and returns the "simulated aneeling" control value apropriate for the pass value.
getToNodeId() - Method in class sonia.ArcAttribute
returns the int corresponding to the ending node
getTopInset() - Method in class sonia.SoniaLayoutEngine
how much of the top is coverd by title bar
getTopPad() - Method in class sonia.SoniaLayoutEngine
Returns the number of pixels from the top to start the coordinate origin.
getTotalSliceArcs() - Method in class sonia.LayoutSlice
returns the number of entries that are not null or zero in the arcs matrix
getType() - Method in class sonia.NoInterpolation
 
getType() - Method in class sonia.CosineInterpolation
Returns a string giving the name of the interpolation.
getType() - Method in interface sonia.CoordInterpolator
Returns a String with the name of the layout
getUniformRand(double, double) - Method in class sonia.SoniaController
Returns a random double drawn with a uniform probability from the spcified range.
getUniformRand(int, int) - Method in class sonia.SoniaController
Returns a random integer drawn with a uniform probability from the spcified range.
getUpdatesN() - Method in class sonia.SoniaLayoutEngine
 
getUserString() - Method in class sonia.TextPrompter
Returns the string entered in the text field by the user
getXCoords() - Method in class sonia.LayoutSlice
 
getYCoords() - Method in class sonia.LayoutSlice
 
goToSlice(int) - Method in class sonia.LayoutWindow
Changes the layout to the specified slice (both in the layout engine and graphically) directly without an animated transition.
GraphicsSettingsDialog - class sonia.GraphicsSettingsDialog.
Displays settings for configuring and modifying the display of the networks in the LayoutWindow.
GraphicsSettingsDialog(SoniaController, SoniaLayoutEngine, Frame, SoniaCanvas) - Constructor for class sonia.GraphicsSettingsDialog
Creates the graphic settings components and sets up the display.

I

IGNORE - Static variable in class sonia.ApplySettingsDialog
 
inDegree(int) - Method in class sonia.LayoutSlice
returns the indegree of the node with the corresponding index.
interpCoords(LayoutSlice, LayoutSlice, double) - Method in class sonia.SoniaLayoutEngine
Givin a start and end slice (with their layout coordinates) and a time (within the range of those slices) calculates new intermediate coordinates according to the current interpolation scheme, and stores them as the current x and y coords to be used when drawing the network to the screen.
interpXCoords(LayoutSlice, LayoutSlice, double) - Method in class sonia.NoInterpolation
 
interpXCoords(LayoutSlice, LayoutSlice, double) - Method in class sonia.CosineInterpolation
Returns an array of coordinates corresponding to the x coords of each node, interpolated between the coordinates of the startSlice and the nextSlice.
interpXCoords(LayoutSlice, LayoutSlice, double) - Method in interface sonia.CoordInterpolator
Returns an array of values for the x coordinates, interpolating between the coordinates of currentSlice and nextSlices based on the value of time.
interpYCoords(LayoutSlice, LayoutSlice, double) - Method in class sonia.NoInterpolation
 
interpYCoords(LayoutSlice, LayoutSlice, double) - Method in class sonia.CosineInterpolation
Returns an array of coordinates corresponding to the y coords of each node, interpolated between the coordinates of the startSlice and the nextSlice.
interpYCoords(LayoutSlice, LayoutSlice, double) - Method in interface sonia.CoordInterpolator
Returns an array of values for the x coordinates, interpolating between the coordinates of currentSlice and nextSlices based on the value of time.
isAntiAlias() - Method in class sonia.SoniaCanvas
 
isArcTrans() - Method in class sonia.SoniaCanvas
 
isCircleRestrict() - Method in class sonia.ApplySettingsDialog
restrict nodes to a bounding circle? (only works with FR, and not very well)
isEndBarycenter() - Method in class sonia.ApplySettingsDialog
recenter the layout the average of the nodes' coordinates when finished?
isEndRecenter() - Method in class sonia.ApplySettingsDialog
recenter the layout (max, min) when the algorithm is finished?
isError() - Method in class sonia.LayoutSlice
returns flag indicating if layout has an error
isGhostSlice() - Method in class sonia.SoniaCanvas
 
isHideArcs() - Method in class sonia.SoniaCanvas
 
isHideNodes() - Method in class sonia.SoniaCanvas
 
isIsolateExclude() - Method in class sonia.ApplySettingsDialog
should isolates be excluded when rescaling? (often used if the isolates are being positioned seperately)
isLayoutFinished() - Method in class sonia.LayoutSlice
checks flag to see if layout is in use by an algorithm
isPaused() - Method in class sonia.SoniaController
Checks is the controler is in paused mode.
isRecenter() - Method in class sonia.ApplySettingsDialog
recenter the layout after each pass of the algorithm (so that it won't drift off screen if you are watching the redraws)
isRepaint() - Method in class sonia.ApplySettingsDialog
true if the layout is going to be redrawn while algorithm is running
isRescale() - Method in class sonia.ApplySettingsDialog
should the layout be rescaled when finsihed?
isShowArcLabels() - Method in class sonia.SoniaCanvas
 
isShowArcWeights() - Method in class sonia.SoniaCanvas
 
isShowArrows() - Method in class sonia.SoniaCanvas
 
isShowId() - Method in class sonia.SoniaCanvas
 
isShowLabels() - Method in class sonia.SoniaCanvas
 
isShowStats() - Method in class sonia.SoniaCanvas
 
isShowUpdates() - Method in class sonia.SoniaLayoutEngine
 
isStopOnError() - Method in class sonia.ApplySettingsDialog
if true, the "apply to remaining" thread will stop if a layout has an erorr, other wise it will just go on to the next layout

K

KKLayout - class sonia.KKLayout.
An early implementation of the Kamada-Kawai "spring-embedder" layout algrorithm.
KKLayout(SoniaController) - Constructor for class sonia.KKLayout
 

L

layoutComplete(double[], double[]) - Method in class sonia.StabilityEstimate
 
LayoutSettingsDialog - class sonia.LayoutSettingsDialog.
Displays the controls and parameters for specifying the range of the network data, how to bin it into slices, the aggregation and interpolation techniques, and choosing which layout algorithm will be used.
LayoutSettingsDialog(SoniaController, SoniaLayoutEngine, Frame) - Constructor for class sonia.LayoutSettingsDialog
 
LayoutSlice - class sonia.LayoutSlice.
 
LayoutSlice(int, double, double) - Constructor for class sonia.LayoutSlice
each LayoutSlice is a bin holding all of the events that are to be included within the same layout.
LayoutUtils - class sonia.LayoutUtils.
Provides a set of static utility methods which can be called by the LayoutEngine for comonly used layout functions.
LayoutUtils() - Constructor for class sonia.LayoutUtils
 
LayoutWindow - class sonia.LayoutWindow.
LayoutWindow does the drawing of the networks to screen, and provides controls for moving through time slice bins.
LayoutWindow(SoniaController, SoniaLayoutEngine, int, int) - Constructor for class sonia.LayoutWindow
Creates the layout window which functions as a view into the network data with controls for steping through the data slice by slice, adjusting graphics parameters, applying the layout algorithms, etc.
ListPicker - class sonia.ListPicker.
Takes a list, creates a dialog presenting the user with a list view of all the objects on it, and returns the one chosen by the user
ListPicker(Frame, ArrayList, String) - Constructor for class sonia.ListPicker
 
loadNetFromFile() - Method in class sonia.SoniaController
Brings up a file dialog, if a file is chosen it looks at the extension (.net or .son) to determine which parser to use, passes the text to the parser, and gets and stores the resulting network.
log(String) - Method in class sonia.SoniaController
Asks the log to append the passed text.
log(String) - Method in class sonia.LogWindow
Appends the passed string into the log buffer for display or output to a text file.
LogWindow - class sonia.LogWindow.
Semi-independent window that logs all actions of a session for repeatability includes ability to write contents out to text file independently
LogWindow(SoniaController) - Constructor for class sonia.LogWindow
 

M

main(String[]) - Static method in class sonia.SoniaController
Instantiates the main controller class, with optional arguments.
makeLayoutSlice(double, double, int) - Method in class sonia.NetDataStructure
creates a layout slice and loops over all the events, including them if they land within the slice.
makeMovie(SoniaMovieMaker) - Method in class sonia.SoniaLayoutEngine
Asks the display to start making a movie with the passed SoniaMovieMaker by callinging makeMovie(exporter) on the LayoutWindow
makeMovie(SoniaMovieMaker) - Method in class sonia.LayoutWindow
Attaches the passed MovieMaker to the layout, and then launches the movie recording thread, which will call the record movie method to step through the layouts transitioning and recording each frame.
matchLayouts(double[], double[], double[], double[]) - Method in class sonia.StabilityEstimate
 
MetricMDSLayout - class sonia.MetricMDSLayout.
Metric Multi-Dimensional Scaling Layout attempts to position the nodes by doing an eigenvalue calculation on the distance matrix to determine the optimal projection.
MetricMDSLayout(SoniaController, SoniaLayoutEngine) - Constructor for class sonia.MetricMDSLayout
 
mouseClicked(MouseEvent) - Method in class sonia.PhasePlot
Determines which slice was clicked, and asks the layout to change to it, if it is ready
mouseClicked(MouseEvent) - Method in class sonia.NodeMover
 
mouseClicked(MouseEvent) - Method in class sonia.CoolingSchedule
 
mouseDragged(MouseEvent) - Method in class sonia.PhasePlot
 
mouseDragged(MouseEvent) - Method in class sonia.NodeMover
 
mouseDragged(MouseEvent) - Method in class sonia.CoolingSchedule
If there is a point selected (from the mouse pressed event), drags the control point around on the screen, adjusting the control values in real time.
mouseEntered(MouseEvent) - Method in class sonia.PhasePlot
 
mouseEntered(MouseEvent) - Method in class sonia.NodeMover
 
mouseEntered(MouseEvent) - Method in class sonia.CoolingSchedule
 
mouseExited(MouseEvent) - Method in class sonia.PhasePlot
 
mouseExited(MouseEvent) - Method in class sonia.NodeMover
 
mouseExited(MouseEvent) - Method in class sonia.CoolingSchedule
 
mouseMoved(MouseEvent) - Method in class sonia.PhasePlot
Shows the time coordinates of the mouse in the plot window
mouseMoved(MouseEvent) - Method in class sonia.NodeMover
 
mouseMoved(MouseEvent) - Method in class sonia.CoolingSchedule
 
mousePressed(MouseEvent) - Method in class sonia.PhasePlot
 
mousePressed(MouseEvent) - Method in class sonia.NodeMover
 
mousePressed(MouseEvent) - Method in class sonia.CoolingSchedule
Checks if mouse is over a control point, and sents the slected index
mouseReleased(MouseEvent) - Method in class sonia.PhasePlot
 
mouseReleased(MouseEvent) - Method in class sonia.NodeMover
 
mouseReleased(MouseEvent) - Method in class sonia.CoolingSchedule
 
MultiCompKKLayout - class sonia.MultiCompKKLayout.
Implements a modified version of the Kamada-Kawai spring-embedder layout algorithm.
MultiCompKKLayout(SoniaController, SoniaLayoutEngine) - Constructor for class sonia.MultiCompKKLayout
Instantiates the layout with reference to the main SoniaController and the the SoniaLayoutEngine connected to this layout

N

NetDataStructure - class sonia.NetDataStructure.
Title:SoNIA (Social Network Image Animator)
NetDataStructure(SoniaController, String, int, int, int) - Constructor for class sonia.NetDataStructure
Holds the time and space coordinates and attributes for the nodes and edges as they were read from input files.
NetLayout - interface sonia.NetLayout.
Interface for layout algorithms which allows them to be interchangeable.
NetUtils - class sonia.NetUtils.
Contains a set of static utility methods for performing network calculations and matrix operations used in sonia.
NetUtils() - Constructor for class sonia.NetUtils
 
NetworkEvent - interface sonia.NetworkEvent.
Interface for making Node- and Arc-events comparable (by their start times)
NodeAttribute - class sonia.NodeAttribute.
Stores all the data pertaining to a specific time or period of time, with the ability to draw itself.
NodeAttribute(int) - Constructor for class sonia.NodeAttribute
 
NodeAttribute(int, String, double, double, double, double, String) - Constructor for class sonia.NodeAttribute
 
NodeMover - class sonia.NodeMover.
Temporarily added to the LayoutWindow to allow the user to reposition nodes by dragging them on the screen.
NodeMover(SoniaController, SoniaLayoutEngine, Frame) - Constructor for class sonia.NodeMover
 
NoInterpolation - class sonia.NoInterpolation.
NoInterpolation just returns the coords of the layout which the time lies within.
NoInterpolation() - Constructor for class sonia.NoInterpolation
 
NUM_TIES - Static variable in class sonia.NetDataStructure
 

O

OptionPrompter - class sonia.OptionPrompter.
Takes a suggestion string, shows it to the user, and returns input via get method, also has prompt string for window title
OptionPrompter(Frame, String, String) - Constructor for class sonia.OptionPrompter
Creates and displays a dialog with promptString as the window title and messageString as the message above the buttons.
ORIG_FILE - Static variable in class sonia.ApplySettingsDialog
 
OrigCoordLayout - class sonia.OrigCoordLayout.
OrigCoordLayout does nothing, since the idea is to use the original coordinates from the parsed file, but the rescale and isolate options do work
OrigCoordLayout(SoniaController, SoniaLayoutEngine) - Constructor for class sonia.OrigCoordLayout
 
outDegree(int) - Method in class sonia.LayoutSlice
returns the outdegree of the node with the corresponding index.

P

paint(Graphics) - Method in class sonia.StressInfo
 
paint(Graphics) - Method in class sonia.StabilityEstimate
 
paint(Graphics) - Method in class sonia.SoniaCanvas
Redraws the previously drawn off-screen image (buffer) to the passed Graphics from the window.
paint(Graphics) - Method in class sonia.PhasePlot
 
paint(Graphics) - Method in class sonia.LayoutWindow
repaints the cached image of the last time the network was drawn to the screen and hopefully the rest of the gui components
paint(Graphics) - Method in class sonia.CoolingSchedule
Paints the plot data and information to the passed graphics context.
paint(Graphics2D, SoniaCanvas) - Method in class sonia.RenderSlice
 
paint(Graphics2D, SoniaCanvas, double, double) - Method in class sonia.NodeAttribute
Paints the node onto the passed graphics at the passed coords, using the graphics settings of the canvas.
paint(Graphics2D, SoniaCanvas, double, double, double, double) - Method in class sonia.ArcAttribute
draws the arc to the passed graphics, using the passed coordinates (from the current coords in the layout engine) the arcs internal values can be modified by settings at the canvas level.
parseCtlValueString(String) - Method in class sonia.CoolingSchedule
Parses a delimited string and sets the control points accordingly, ask to have them painted on the screen.
parseNetwork(String) - Method in interface sonia.Parser
Asks the parser to read a network from the file indicated by the passed string
parseNetwork(String) - Method in class sonia.DotSonParser
attempts to open a connection to the passed file and path, read in text and parse it to create a set of nodes and arcs.
parseNetwork(String) - Method in class sonia.DotNetParser
Opens a connection to the .net file and attempts to parse a network from it.
Parser - interface sonia.Parser.
There are multiple data formats available for storing and exchanging network data, with varying degrees of use, human code-ability, features, flexibility, etc.
pause() - Method in class sonia.SoniaLayoutEngine
Asks the current layout to pause
pause() - Method in class sonia.RubBandFRLayout
 
pause() - Method in class sonia.RandomFRLayout
 
pause() - Method in class sonia.PILayout
 
pause() - Method in class sonia.OrigCoordLayout
 
pause() - Method in interface sonia.NetLayout
Interupts the layout if it is running.
pause() - Method in class sonia.MultiCompKKLayout
Sets a flag to break the layout loop.
pause() - Method in class sonia.MetricMDSLayout
 
pause() - Method in class sonia.KKLayout
 
pause() - Method in class sonia.FRLayout
 
pause() - Method in class sonia.CircleLayout
should pause the layout, but for circle layout it does nothing, since there is only one very fast pass anyway
PhasePlot - class sonia.PhasePlot.
Gives a "phase-space" graphical representation of the network data and the settings selected in the layoutSettings dialog, indicates the current slice and render window, allows navigation by clicking on slices.
PhasePlot(SoniaLayoutEngine, NetDataStructure, LayoutSettingsDialog) - Constructor for class sonia.PhasePlot
 
PILayout - class sonia.PILayout.
Moody's Peer Influence
PILayout(SoniaController, SoniaLayoutEngine) - Constructor for class sonia.PILayout
 
PIN_CIRCLE - Static variable in class sonia.ApplySettingsDialog
 
PIN_EDGE - Static variable in class sonia.ApplySettingsDialog
 
PIN_ORIG - Static variable in class sonia.ApplySettingsDialog
 
PIN_PREVIOUS - Static variable in class sonia.ApplySettingsDialog
 
pinIsolatesBottom(LayoutSlice, int, int) - Static method in class sonia.LayoutUtils
positions all the isolates in a row along the bottom of the layout
pinIsolatesCircle(LayoutSlice, int, int) - Static method in class sonia.LayoutUtils
positions all the isolates in a circle independent of the rest of the layout
pinIsolatesOrig(LayoutSlice) - Static method in class sonia.LayoutUtils
 
plotData(Graphics2D) - Method in class sonia.PhasePlot
 
PREV_SLICE - Static variable in class sonia.ApplySettingsDialog
 

R

RandomFRLayout - class sonia.RandomFRLayout.
Random FR is based on the same concept as FRLayout, but uses a differnt procedure for getting to its results.
RandomFRLayout(SoniaController, SoniaLayoutEngine) - Constructor for class sonia.RandomFRLayout
 
RANDOMIZE - Static variable in class sonia.ApplySettingsDialog
 
randomizeLayout(SoniaController, LayoutSlice, int, int) - Static method in class sonia.LayoutUtils
Randomly positions nodes on layout.
removeStabilityEstimate() - Method in class sonia.LayoutSlice
 
renderCurrentSettings() - Method in class sonia.LayoutWindow
Creates a render slice network with the current settings for render parameters displayed on the controlls.
RenderSlice - class sonia.RenderSlice.
A bin or container for the node and arc events meeting its criteria, it draws them to the screen when asked.
RenderSlice(SoniaLayoutEngine, double, double) - Constructor for class sonia.RenderSlice
 
RenderSlice(SoniaLayoutEngine, double, double, Vector, Vector) - Constructor for class sonia.RenderSlice
Render slice is a bin holding all the objects to be renderd at a given time.
rescalePositions(LayoutSlice, int, int, double[], double[], boolean) - Static method in class sonia.LayoutUtils
Rescales the node coordinates so that the layout will fit within the layout window.
reset() - Method in class sonia.CoolingSchedule
Resents the plots stored values to the default initial values
resume() - Method in class sonia.SoniaLayoutEngine
Ask the current layout to un-pause (set pause flag to false)
resume() - Method in class sonia.RubBandFRLayout
 
resume() - Method in class sonia.RandomFRLayout
 
resume() - Method in class sonia.PILayout
 
resume() - Method in class sonia.OrigCoordLayout
 
resume() - Method in interface sonia.NetLayout
Un-sets the interput flag, but does not actually restart he layout
resume() - Method in class sonia.MultiCompKKLayout
un-pauses the layout by setting the break flag to false, but doesn't actually restart the layout.
resume() - Method in class sonia.MetricMDSLayout
 
resume() - Method in class sonia.KKLayout
 
resume() - Method in class sonia.FRLayout
 
resume() - Method in class sonia.CircleLayout
should resume the layout, but for circle layout it does nothing, since there is only one very fast pass anyway
RubBandFRLayout - class sonia.RubBandFRLayout.
Positions nodes in layout according to iterations of an implementation of the Fruchmen-Reingold graph layout algorithm, except that nodes also maintain a phatom tie or "rubber band" tugging them close to their location in the previous layout.
RubBandFRLayout(SoniaController, SoniaLayoutEngine) - Constructor for class sonia.RubBandFRLayout
 
run() - Method in class sonia.RubBandFRLayout
 
run() - Method in class sonia.RandomFRLayout
 
run() - Method in class sonia.PILayout
 
run() - Method in class sonia.MultiCompKKLayout
Runs the KK layout algorithm.
run() - Method in class sonia.MetricMDSLayout
 
run() - Method in class sonia.KKLayout
 
run() - Method in class sonia.FRLayout
called by the layout thread, should only be called internally by the layout

S

saveImageForGhost() - Method in class sonia.SoniaCanvas
Takes the current off-screen image (of the soon-to-be-previous frame) and stores it to be drawn underneath the picture of the curret network.
setAntiAlias(boolean) - Method in class sonia.SoniaCanvas
 
setArcColor(Color) - Method in class sonia.ArcAttribute
sets the color of the arc to the passed Color
setArcLabel(String) - Method in class sonia.ArcAttribute
sets the label of the arc to the string
setArcTrans(boolean) - Method in class sonia.SoniaCanvas
 
setArcTransVal(float) - Method in class sonia.SoniaCanvas
 
setArcWeight(double) - Method in class sonia.ArcAttribute
sets weight of the arc to the passed double.
setArcWeight(int, int, double) - Method in class sonia.LayoutSlice
Sets the i,jth entry in the arc's matrix, replacing its value.
setArcWidth(double) - Method in class sonia.ArcAttribute
sets the width of the arc to the absolute value of the passed double (prevents negitive widths)
setArcWidthFact(float) - Method in class sonia.SoniaCanvas
 
setBorderColor(Color) - Method in class sonia.NodeAttribute
 
setBorderWidth(double) - Method in class sonia.NodeAttribute
 
setCoords(int, double, double) - Method in class sonia.LayoutSlice
Sets the stored coordinates for the node at index to the passed values.
setCoordsToSlice(int) - Method in class sonia.SoniaLayoutEngine
Sets the current x and y screen coordinates for the nodes to the coordinates stored in the slice corresponding to the passed slice number.
setCurrentPath(String) - Method in class sonia.SoniaController
 
setDataEndDefault(double) - Method in class sonia.LayoutSettingsDialog
Sets the default value to be shown in the layout end field, should be set to the largest time value in the data.
setDataStartDefault(double) - Method in class sonia.LayoutSettingsDialog
Sets the default value to be shown in the layout start field, should be set to the smallest time value in the data.
setDisplayHeight(int) - Method in class sonia.SoniaLayoutEngine
Checks if the passed value is > 0, sets the width of the display (layoutWindow) to the value (adding the bottomPad to make room for the buttons), sets the height to its current value.
setDisplayWidth(int) - Method in class sonia.SoniaLayoutEngine
Checks if the passed value is > 0, sets the with of the display (layoutWindow) to the value, sets the height to its current value.
setEndTime(double) - Method in class sonia.NodeAttribute
 
setEndTime(double) - Method in interface sonia.NetworkEvent
 
setEndTime(double) - Method in class sonia.ArcAttribute
sets the ending time for the arc to the passed double
setError(boolean) - Method in class sonia.LayoutSlice
set flag to say that there are problems with the layout
setFileName(String) - Method in class sonia.SoniaController
Sets the file name to the passed string
setFromNodeId(int) - Method in class sonia.ArcAttribute
sets the int corresponding to the starting node
setGhostSlice(boolean) - Method in class sonia.SoniaCanvas
 
setHideArcs(boolean) - Method in class sonia.SoniaCanvas
 
setHideNodes(boolean) - Method in class sonia.SoniaCanvas
 
setInterpFrames(int) - Method in class sonia.SoniaLayoutEngine
Sets the number intermediary interpolation ("tweening") frames to be drawn while animating transitions between slices.
setLabelColor(Color) - Method in class sonia.NodeAttribute
 
setLabelColor(Color) - Method in class sonia.ArcAttribute
sets the color of the arc's label
setLabelSize(float) - Method in class sonia.NodeAttribute
 
setLabelSize(float) - Method in class sonia.ArcAttribute
sets the size (font size?) to draw the arc label
setLayoutFinished(boolean) - Method in class sonia.LayoutSlice
sets flag so that other layouts won't access this slice at the same time
setLayoutProperty(String, double) - Method in class sonia.ApplySettingsDialog
sets the algorithm specific layout pramter to the passed value, after checking that there is a parameter corresponding to name.
setMaxNetSize(int) - Method in class sonia.NetDataStructure
 
setMaxPasses(int) - Method in class sonia.CoolingSchedule
Sets the maximum number of passes permited.
setMaxYvalue(double) - Method in class sonia.CoolingSchedule
Sets the maximum y value for the plot, essentialy sets the vertical scale.
setNetInfo(String) - Method in class sonia.NetDataStructure
 
setNodeColor(Color) - Method in class sonia.NodeAttribute
 
setNodeLabel(String) - Method in class sonia.NodeAttribute
 
setNodeScaleFact(float) - Method in class sonia.SoniaCanvas
 
setNodeShape(RectangularShape) - Method in class sonia.NodeAttribute
 
setNodeSize(double) - Method in class sonia.NodeAttribute
 
setObsTime(double) - Method in class sonia.NodeAttribute
 
setObsTime(double) - Method in interface sonia.NetworkEvent
 
setObsTime(double) - Method in class sonia.ArcAttribute
sets the starting time for the arc to the passed double
setObsXCoord(double) - Method in class sonia.NodeAttribute
Sets the stord x coordinate, this is NOT the node's layout coordinate which is stored in the slice, but is a default coordinate, generally set by the parser to match the orginal observation in the file.
setObsYCoord(double) - Method in class sonia.NodeAttribute
Sets the stord y coordinate, this is NOT the node's layout coordinate which is stored in the slice, but is a default coordinate, generally set by the parser to match the orginal observation in the file.
setParser(DotNetParser) - Method in class sonia.NetDataStructure
 
setPaused(boolean) - Method in class sonia.SoniaController
Sets paused mode the passed state, and asks the current engine to pause or resume.
setRenderSlice(RenderSlice) - Method in class sonia.SoniaCanvas
 
setShowArcLabels(boolean) - Method in class sonia.SoniaCanvas
 
setShowArcWeights(boolean) - Method in class sonia.SoniaCanvas
 
setShowArrows(boolean) - Method in class sonia.SoniaCanvas
 
setShowId(boolean) - Method in class sonia.SoniaCanvas
 
setShowLabels(boolean) - Method in class sonia.SoniaCanvas
 
setShowStats(boolean) - Method in class sonia.SoniaCanvas
 
setShowUpdates(boolean) - Method in class sonia.SoniaLayoutEngine
Sets wether or not individual updates from the layout algorithms will be drawn to the screen during the layout process.
setSliceEnd(double) - Method in class sonia.LayoutSlice
 
setSliceStart(double) - Method in class sonia.LayoutSlice
 
setToNodeId(int) - Method in class sonia.ArcAttribute
sets the int corresponding to the ending node
setUpdatesN(int) - Method in class sonia.SoniaLayoutEngine
Sets how often the layouts will be drawn to the screen while the algorithm is optimizing.
setupLayout(double, double, double, double, int, NetLayout, CoordInterpolator) - Method in class sonia.SoniaLayoutEngine
Sets up the layout and data sctructures, asking netData to generate a vector of slices from the given range, finding max values (to be used in converting similarity to disimilarity matrix), shows slice, etc.
setupLayoutProperties(ApplySettingsDialog) - Method in class sonia.RubBandFRLayout
 
setupLayoutProperties(ApplySettingsDialog) - Method in class sonia.RandomFRLayout
 
setupLayoutProperties(ApplySettingsDialog) - Method in class sonia.PILayout
 
setupLayoutProperties(ApplySettingsDialog) - Method in class sonia.OrigCoordLayout
 
setupLayoutProperties(ApplySettingsDialog) - Method in interface sonia.NetLayout
Asks the layout to add layout specific propertyName/defaultValue pairs to the dialog to the layout settings dialog.
setupLayoutProperties(ApplySettingsDialog) - Method in class sonia.MultiCompKKLayout
Attaches algorithm-specific parameter names and default values to the ApplySettingsDialog box.
setupLayoutProperties(ApplySettingsDialog) - Method in class sonia.MetricMDSLayout
 
setupLayoutProperties(ApplySettingsDialog) - Method in class sonia.KKLayout
 
setupLayoutProperties(ApplySettingsDialog) - Method in class sonia.FRLayout
Adds the FR layout parameters to the applySettingsDialog.
setupLayoutProperties(ApplySettingsDialog) - Method in class sonia.CircleLayout
adds the layout specific "radius" paramter to the passed settings dialog.
setupMovie(SoniaCanvas, int) - Method in class sonia.SoniaMovieMaker
opens a file dialog asking where to save the movie, opens a "QuickTime session" throws up a new window with the same size as the layout, and plays the layout, recording each frame to the new window, and into the movie file.
setValues() - Method in class sonia.CoolingSchedule
Calls TextPropmter with a string of control values from getCtlValString() to let the user modify or record them, parses the result and sents the points accordingly.
setValuesFromDialog() - Method in class sonia.ApplySettingsDialog
gets all the parameters from the settings dialog and sets them in the LayoutEngine
shepardPlot(LayoutSlice) - Method in class sonia.StressInfo
 
showApplyLayoutSettings() - Method in class sonia.SoniaLayoutEngine
Throws up the ApplySettingsDialog for the user to specify the details of how the chosen layout algorithm will run.
showConvergance(int, double) - Method in class sonia.CoolingSchedule
Plots a point to show the convergance of the algorithm, the difference between the value at the previous time and the ccurrent value.
showCurrentSlice() - Method in class sonia.LayoutWindow
Updates the display to show the slice currently selected in the layout engine
showDialog() - Method in class sonia.LayoutSettingsDialog
 
showDialog() - Method in class sonia.GraphicsSettingsDialog
 
showDialog() - Method in class sonia.ApplySettingsDialog
displays the dialog on screen
showError(String) - Method in class sonia.SoniaInterface
Displays the passed text as an error message in the status window, may beep and/or turn red/
showError(String) - Method in class sonia.SoniaController
Asks the UI to display text in the status window of the controller interface as an error (red text, will beep)
showPassValue(int) - Method in class sonia.CoolingSchedule
Draws a virtical line on the plot to indicate the current pass value
showPhasePlot() - Method in class sonia.SoniaLayoutEngine
Creates and displays a PhasePlot showing the location of each arc and node event in time, and how the slices land.
showRenderSliceTimes(double, double) - Method in class sonia.PhasePlot
records the start and end time so the render slice can be drawn on the plot
showStatus(String) - Method in class sonia.SoniaInterface
Displays the passed text as a message in the status window
showStatus(String) - Method in class sonia.SoniaController
Asks the UI to display text in the status window of the controller interface
showYValue(double) - Method in class sonia.CoolingSchedule
Draws a horisontal line on the plot at a height corresponding to the passed double value when scaled to the plot.
sonia - package sonia
SoNIA is a Java-based package for visualizing dynamic or longitudinal "network" data.
SoniaCanvas - class sonia.SoniaCanvas.
Title:SoNIA (Social Network Image Animator)
SoniaCanvas(SoniaLayoutEngine, LayoutWindow) - Constructor for class sonia.SoniaCanvas
Does the actual job of rendering the network, and maintains the graphics settings.
SoniaController - class sonia.SoniaController.
Main controlling class for SoNIA.
SoniaController(int) - Constructor for class sonia.SoniaController
Instantiates the controller class, sets up data structures, fonts, starts log.
SoniaInterface - class sonia.SoniaInterface.
Handles gui and UI for SoniaControler and and calls all methods via controller.
SoniaInterface(SoniaController) - Constructor for class sonia.SoniaInterface
 
SoniaLayoutEngine - class sonia.SoniaLayoutEngine.
The main controlling class for a layout.
SoniaLayoutEngine(SoniaController, NetDataStructure, String) - Constructor for class sonia.SoniaLayoutEngine
Class responsible for maintaining data structures for layouts, coordinating layout algorithms, suppling graphics to consumers, etc
SoniaMovieMaker - class sonia.SoniaMovieMaker.
Sets up connection to QuickTime for Java libraries to export the network animation as a movie.
SoniaMovieMaker(SoniaController, SoniaLayoutEngine) - Constructor for class sonia.SoniaMovieMaker
 
StabilityEstimate - class sonia.StabilityEstimate.
This class is not yet functioning.
StabilityEstimate(SoniaController, SoniaLayoutEngine) - Constructor for class sonia.StabilityEstimate
 
StressInfo - class sonia.StressInfo.
The stress measure in SoNIA essentially an adaptation from Kruskal Multidimensional Scaling stress measure.
StressInfo(SoniaController, SoniaLayoutEngine) - Constructor for class sonia.StressInfo
 
Subnet - class sonia.Subnet.
Subnet contains a matrix describing a subset of the relationships of the overall network, and remaps its indicies to those for the original net
Subnet(SparseDoubleMatrix2D, IntArrayList) - Constructor for class sonia.Subnet
 
SUM_TIE_VALS - Static variable in class sonia.NetDataStructure
 

T

TextPrompter - class sonia.TextPrompter.
Tages a suggestion string, shows it to the user, and returns input via get method, also has prompt string for window title
TextPrompter(Frame, String, String) - Constructor for class sonia.TextPrompter
Tages a suggestion string, shows it to the user, and returns input via get method, also has prompt string for window title
toString() - Method in class sonia.Subnet
 
toString() - Method in class sonia.SoniaLayoutEngine
returns the name of this layout engine and some info;
toString() - Method in class sonia.RenderSlice
 
transitionToSlice(int) - Method in class sonia.LayoutWindow
Creates a smoothly animated transition from the current slice to the specified slice number.

U

update(Graphics) - Method in class sonia.SoniaCanvas
override update to *not* erase the background before painting
updateDisplay() - Method in class sonia.LayoutWindow
update display actually redraws the network to an Image, stores the image for later repaints.
updateDisplay(Graphics, boolean) - Method in class sonia.SoniaCanvas
Redraws the entire network on the buffer image, and then draws this image to the passed graphics object.
updateDisplays() - Method in class sonia.SoniaLayoutEngine
Asks the LayoutWindow to update its display by calling updateDisplay() on it.
updateDisplays() - Method in class sonia.SoniaController
If not paused, iterates over all the layout engines and asks them to update their displays.

W

windowActivated(WindowEvent) - Method in class sonia.StressInfo
 
windowActivated(WindowEvent) - Method in class sonia.StabilityEstimate
 
windowActivated(WindowEvent) - Method in class sonia.SoniaInterface
 
windowActivated(WindowEvent) - Method in class sonia.PhasePlot
 
windowActivated(WindowEvent) - Method in class sonia.LogWindow
 
windowActivated(WindowEvent) - Method in class sonia.LayoutWindow
 
windowActivated(WindowEvent) - Method in class sonia.CoolingSchedule
 
windowClosed(WindowEvent) - Method in class sonia.StressInfo
 
windowClosed(WindowEvent) - Method in class sonia.StabilityEstimate
 
windowClosed(WindowEvent) - Method in class sonia.SoniaInterface
 
windowClosed(WindowEvent) - Method in class sonia.PhasePlot
 
windowClosed(WindowEvent) - Method in class sonia.LogWindow
 
windowClosed(WindowEvent) - Method in class sonia.LayoutWindow
 
windowClosed(WindowEvent) - Method in class sonia.CoolingSchedule
 
windowClosing(WindowEvent) - Method in class sonia.StressInfo
 
windowClosing(WindowEvent) - Method in class sonia.StabilityEstimate
 
windowClosing(WindowEvent) - Method in class sonia.SoniaInterface
Prompts with an "are you sure" dialog before exiting sonia.
windowClosing(WindowEvent) - Method in class sonia.PhasePlot
 
windowClosing(WindowEvent) - Method in class sonia.LogWindow
 
windowClosing(WindowEvent) - Method in class sonia.LayoutWindow
 
windowClosing(WindowEvent) - Method in class sonia.CoolingSchedule
 
windowDeactivated(WindowEvent) - Method in class sonia.StressInfo
 
windowDeactivated(WindowEvent) - Method in class sonia.StabilityEstimate
 
windowDeactivated(WindowEvent) - Method in class sonia.SoniaInterface
 
windowDeactivated(WindowEvent) - Method in class sonia.PhasePlot
 
windowDeactivated(WindowEvent) - Method in class sonia.LogWindow
 
windowDeactivated(WindowEvent) - Method in class sonia.LayoutWindow
 
windowDeactivated(WindowEvent) - Method in class sonia.CoolingSchedule
 
windowDeiconified(WindowEvent) - Method in class sonia.StressInfo
 
windowDeiconified(WindowEvent) - Method in class sonia.StabilityEstimate
 
windowDeiconified(WindowEvent) - Method in class sonia.SoniaInterface
 
windowDeiconified(WindowEvent) - Method in class sonia.PhasePlot
 
windowDeiconified(WindowEvent) - Method in class sonia.LogWindow
 
windowDeiconified(WindowEvent) - Method in class sonia.LayoutWindow
 
windowDeiconified(WindowEvent) - Method in class sonia.CoolingSchedule
 
windowIconified(WindowEvent) - Method in class sonia.StressInfo
 
windowIconified(WindowEvent) - Method in class sonia.StabilityEstimate
 
windowIconified(WindowEvent) - Method in class sonia.SoniaInterface
 
windowIconified(WindowEvent) - Method in class sonia.PhasePlot
 
windowIconified(WindowEvent) - Method in class sonia.LogWindow
 
windowIconified(WindowEvent) - Method in class sonia.LayoutWindow
 
windowIconified(WindowEvent) - Method in class sonia.CoolingSchedule
 
windowOpened(WindowEvent) - Method in class sonia.StressInfo
 
windowOpened(WindowEvent) - Method in class sonia.StabilityEstimate
 
windowOpened(WindowEvent) - Method in class sonia.SoniaInterface
 
windowOpened(WindowEvent) - Method in class sonia.PhasePlot
 
windowOpened(WindowEvent) - Method in class sonia.LogWindow
 
windowOpened(WindowEvent) - Method in class sonia.LayoutWindow
 
windowOpened(WindowEvent) - Method in class sonia.CoolingSchedule
 
writeLogToFile() - Method in class sonia.LogWindow
Displays a save file dialog, opens an ouput stream, and writes out the contents of the log window to a text file with the name and location acquired from the file dialog.

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