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

A

addNode(int, float[], float) - Method in class ccvisu.MinimizerBarnesHut.OctTree
Adds a graph node to the octtree.
addNode2(int, float[], float) - Method in class ccvisu.MinimizerBarnesHut.OctTree
Adds a graph node to the octtree, without changing the position and weight of the root.
addRepulsionDir(int, MinimizerBarnesHut.OctTree, float[]) - Method in class ccvisu.MinimizerBarnesHut
Computes the direction of the repulsion force from the tree on the specified node.
analyzeDistances() - Method in class ccvisu.MinimizerBarnesHut
Computes and outputs some statistics.
area - Variable in class ccvisu.WriterDataGraphicsDISP
 
attrExponent - Variable in class ccvisu.MinimizerBarnesHut
Exponent of the Euclidean distance in the attraction energy.
attrIndexes - Variable in class ccvisu.MinimizerBarnesHut
Node indexes of the similarity lists.
attrValues - Variable in class ccvisu.MinimizerBarnesHut
Similarity values of the similarity lists.

B

backColor - Variable in class ccvisu.WriterDataGraphics
 
baryCenter - Variable in class ccvisu.MinimizerBarnesHut
Position of the barycenter of the nodes.
blackCircle - Variable in class ccvisu.WriterDataGraphics
 
buildOctTree() - Method in class ccvisu.MinimizerBarnesHut
Builds the octtree.

C

CCVisu - class ccvisu.CCVisu.
Main class of the CCVisu package.
CCVisu() - Constructor for class ccvisu.CCVisu
 
CVS - Static variable in class ccvisu.CCVisu
CVS log format (only input).
canvas - Variable in class ccvisu.ScreenDisplay
Canvas for graphics.
ccvisu - package ccvisu
 
children - Variable in class ccvisu.MinimizerBarnesHut.OctTree
Children of this tree node.
chkAvail(String[], int) - Static method in class ccvisu.CCVisu
Checks whether the command line argument at index i has a follower argument.
color - Variable in class ccvisu.GraphVertex
 
computeBaryCenter() - Method in class ccvisu.MinimizerBarnesHut
Computes the position of the barycenter baryCenter of all nodes.
computeLayout(GraphData, int, int, boolean, boolean, float) - Static method in class ccvisu.CCVisu
Compute layout for a given graph.
computeRepuFactor() - Method in class ccvisu.MinimizerBarnesHut
Computes the factor for repulsion forces repuFactor such that in the energy minimum the average Euclidean distance between pairs of nodes with similarity 1.0 is approximately 1.

D

DISP - Static variable in class ccvisu.CCVisu
Display gaph layout on screen (only output).
degree - Variable in class ccvisu.GraphVertex
(Weighted) Edge degree of the vertex.
display - Variable in class ccvisu.WriterDataGraphicsDISP
 

E

edges - Variable in class ccvisu.GraphData
Edges of type GraphEdgeInt.
endl - Static variable in class ccvisu.CCVisu
End of line.
endl - Static variable in class ccvisu.ReaderDataGraph
End of line.
endl - Static variable in class ccvisu.WriterData
End of line.

F

filename - Variable in class ccvisu.ReaderDataGraphCVS.Revision
 
fixedPos - Variable in class ccvisu.MinimizerBarnesHut
The minimizer does not change the position for nodes with entry true.
fontSize - Variable in class ccvisu.WriterDataGraphics
 

G

GraphData - class ccvisu.GraphData.
Contains the representation of a graph.
GraphData() - Constructor for class ccvisu.GraphData
Constructor.
GraphEdgeInt - class ccvisu.GraphEdgeInt.
Represents an edge between two vertices x and y (given as vertex ids) of weight w.
GraphEdgeInt() - Constructor for class ccvisu.GraphEdgeInt
 
GraphEdgeString - class ccvisu.GraphEdgeString.
Represents an edge between two vertices x and y (given as vertex names) of weight w (also String).
GraphEdgeString() - Constructor for class ccvisu.GraphEdgeString
 
GraphVertex - class ccvisu.GraphVertex.
Represents a vertex of the graph, including name, id, and several attributes.
GraphVertex() - Constructor for class ccvisu.GraphVertex
Constructor.
getDirection(int, float[]) - Method in class ccvisu.MinimizerBarnesHut
Computes the direction of the total force acting on the specified node.
getDist(float[], float[]) - Method in class ccvisu.MinimizerBarnesHut
Returns the Euclidean distance between the specified positions.
getDistToBaryCenter(int) - Method in class ccvisu.MinimizerBarnesHut
Returns the Euclidean distance between node i and the baryCenter.
getEnergy(int) - Method in class ccvisu.MinimizerBarnesHut
Returns the energy of the specified node.
getFormat(String) - Static method in class ccvisu.CCVisu
Transforms the format given as a string into the appropriate integer value.
getRepulsionEnergy(int, MinimizerBarnesHut.OctTree) - Method in class ccvisu.MinimizerBarnesHut
Returns the repulsion energy between the node with the specified index and the nodes in the octtree.
getVertexNames(int, int) - Method in class ccvisu.WriterDataGraphicsDISP
Compute list of names of the vertices at the given position.
graph - Variable in class ccvisu.WriterData
Graph representation.
gravitationFactor - Variable in class ccvisu.MinimizerBarnesHut
Factor for the gravitation energy (attraction to the barycenter), 0.0f for no gravitation.

H

hideSource - Variable in class ccvisu.WriterDataGraphics
 
hideSource - Variable in class ccvisu.WriterDataLAY
 

I

id - Variable in class ccvisu.GraphVertex
 
in - Variable in class ccvisu.ReaderData
Input stream reader object.
index - Variable in class ccvisu.MinimizerBarnesHut.OctTree
For leafs, the unique index of the graph node; for non-leafs -1.
initializeLayout(GraphData, int) - Static method in class ccvisu.CCVisu
Compute randomized initial layout for a given graph with the given number of dimensions.
insetleft - Variable in class ccvisu.WriterDataGraphicsDISP
 
isSource - Variable in class ccvisu.GraphVertex
True if the vertex is the source vertex of an edge.

L

LAY - Static variable in class ccvisu.CCVisu
Graph layout in textual format.
level - Static variable in class ccvisu.Verbosity
 
logmsg - Variable in class ccvisu.ReaderDataGraphCVS.Revision
 

M

Minimizer - class ccvisu.Minimizer.
Minimizer for a given energy model, which is set by the constructor of the concrete minimizer implementation.
Minimizer() - Constructor for class ccvisu.Minimizer
 
MinimizerBarnesHut - class ccvisu.MinimizerBarnesHut.
Minimizer for the (weighted) (edge-repulsion) LinLog energy model, based on the Barnes-Hut algorithm.
MinimizerBarnesHut(int, int[][], float[][], float[], float[][], boolean[], float, float) - Constructor for class ccvisu.MinimizerBarnesHut
Sets the number of nodes, the similarity matrices (edge weights), and the position matrix.
MinimizerBarnesHut.OctTree - class ccvisu.MinimizerBarnesHut.OctTree.
Octtree for graph nodes with positions in 3D space.
MinimizerBarnesHut.OctTree(int, float[], float, float[], float[]) - Constructor for class ccvisu.MinimizerBarnesHut.OctTree
Creates an octtree containing one graph node.
main(String[]) - Static method in class ccvisu.CCVisu
Main program.
markSpecial(GraphData) - Static method in class ccvisu.CCVisu
Special marking for certain vertices by setting attributes of the vertex, e.g., color and showName.
maxPos - Variable in class ccvisu.MinimizerBarnesHut.OctTree
Maximum coordinates of the cuboid in each of the 3 dimensions.
minPos - Variable in class ccvisu.MinimizerBarnesHut.OctTree
Minimum coordinates of the cuboid in each of the 3 dimensions.
minVert - Variable in class ccvisu.WriterDataGraphics
 
minimizeEnergy(int) - Method in class ccvisu.Minimizer
Minimizes iteratively the energy using the Barnes-Hut algorithm.
minimizeEnergy(int) - Method in class ccvisu.MinimizerBarnesHut
Iteratively minimizes energy using the Barnes-Hut algorithm.
moveNode(float[], float[], float) - Method in class ccvisu.MinimizerBarnesHut.OctTree
Updates the positions of the octtree nodes when the position of a graph node has changed.

N

name - Variable in class ccvisu.GraphVertex
 
nameToVertex - Variable in class ccvisu.GraphData
Maps a vertex name to a GraphVertex.
nodeNr - Variable in class ccvisu.MinimizerBarnesHut
Number of nodes.

O

octTree - Variable in class ccvisu.MinimizerBarnesHut
Octtree for repulsion computation.
out - Variable in class ccvisu.WriterDataGraphicsSVG
 
out - Variable in class ccvisu.WriterDataGraphicsVRML
 
out - Variable in class ccvisu.WriterDataLAY
 
out - Variable in class ccvisu.WriterDataRSF
 

P

paint(Graphics) - Method in class ccvisu.ScreenDisplay.MyCanvas
Draws the layout layout on the screen.
parent - Variable in class ccvisu.ScreenDisplay.MyCanvas
 
parseDate(String) - Method in class ccvisu.ReaderDataGraphCVS
Parses the date entry.
pos - Variable in class ccvisu.GraphData
Layout.
pos - Variable in class ccvisu.MinimizerBarnesHut
Position in 3-dimensional space for every node.
pos - Variable in class ccvisu.ReaderDataLAY.LayoutEntry
 
position - Variable in class ccvisu.MinimizerBarnesHut.OctTree
Barycenter of the contained graph nodes.
printHelp() - Static method in class ccvisu.CCVisu
Prints usage information.
printVersion() - Static method in class ccvisu.CCVisu
Prints version information.

R

RSF - Static variable in class ccvisu.CCVisu
Graph (relation) in relational standard format.
ReaderData - class ccvisu.ReaderData.
Reader for input data.
ReaderData(BufferedReader) - Constructor for class ccvisu.ReaderData
Constructor.
ReaderDataGraph - class ccvisu.ReaderDataGraph.
Reader for input graphs.
ReaderDataGraph(BufferedReader) - Constructor for class ccvisu.ReaderDataGraph
Constructor.
ReaderDataGraphCVS - class ccvisu.ReaderDataGraphCVS.
Reader for CVS log files.
ReaderDataGraphCVS(BufferedReader, int) - Constructor for class ccvisu.ReaderDataGraphCVS
Constructor.
ReaderDataGraphCVS.Revision - class ccvisu.ReaderDataGraphCVS.Revision.
Represents a CVS revision entry (an abstraction of it).
ReaderDataGraphCVS.Revision() - Constructor for class ccvisu.ReaderDataGraphCVS.Revision
 
ReaderDataGraphRSF - class ccvisu.ReaderDataGraphRSF.
Reader for co-change graphs in RSF format.
ReaderDataGraphRSF(BufferedReader) - Constructor for class ccvisu.ReaderDataGraphRSF
Constructor.
ReaderDataLAY - class ccvisu.ReaderDataLAY.
Reader for layouts in text format.
ReaderDataLAY(BufferedReader) - Constructor for class ccvisu.ReaderDataLAY
Constructor.
ReaderDataLAY.LayoutEntry - class ccvisu.ReaderDataLAY.LayoutEntry.
 
ReaderDataLAY.LayoutEntry() - Constructor for class ccvisu.ReaderDataLAY.LayoutEntry
 
read() - Method in class ccvisu.ReaderData
Reads the graph or layout data from stream reader in.
read() - Method in class ccvisu.ReaderDataGraph
Reads the graph data from stream reader in.
read() - Method in class ccvisu.ReaderDataLAY
Reads the layout data from stream reader in, in text format LAY.
readEdges() - Method in class ccvisu.ReaderDataGraph
Reads the edges of a graph from stream reader in, and stores them in a list (of GraphEdgeString elements).
readEdges() - Method in class ccvisu.ReaderDataGraphCVS
Reads the edges of a graph in CVS log format from stream reader in, and stores them in a list (of GraphEdgeString elements).
readEdges() - Method in class ccvisu.ReaderDataGraphRSF
Reads the edges of a graph in RSF (relational standard format) from stream reader in, and stores them in a list (of GraphEdgeString elements).
readGraph(Vector) - Static method in class ccvisu.ReaderDataGraph
Reads the graph data from list of string edges (see class comment).
readRevisionList() - Method in class ccvisu.ReaderDataGraphCVS
Parses the CVS log data and extracts revisions.
recoverTransactions(Vector) - Method in class ccvisu.ReaderDataGraphCVS
Recovers the change transactions for the co-change graph from the revision information, i.e., it assignes the transaction ids for the revisions.
repaint() - Method in class ccvisu.ScreenDisplay
Repaint the drawing on the frame, i.e., deligate to canvas.
repu - Variable in class ccvisu.MinimizerBarnesHut
Repulsion vector.
repuFactor - Variable in class ccvisu.MinimizerBarnesHut
Factor for repulsion energy that normalizes average distance between pairs of nodes with maximum similarity to (roughly) 1.
repuStrategy - Static variable in class ccvisu.MinimizerBarnesHut
Factors for the repulsion force for pulsing.

S

SVG - Static variable in class ccvisu.CCVisu
Graph layout in SVG format (only output).
ScreenDisplay - class ccvisu.ScreenDisplay.
Frame implementation for displaying the layout on the screen device.
ScreenDisplay(WriterDataGraphicsDISP, Color, boolean) - Constructor for class ccvisu.ScreenDisplay
Constructor.
ScreenDisplay.MyCanvas - class ccvisu.ScreenDisplay.MyCanvas.
Canvas implementation for displaying the layout on the screen.
ScreenDisplay.MyCanvas(ScreenDisplay, WriterDataGraphicsDISP) - Constructor for class ccvisu.ScreenDisplay.MyCanvas
Constructor.
scalePos - Variable in class ccvisu.WriterDataGraphicsSVG
 
scalePos - Variable in class ccvisu.WriterDataGraphicsVRML
 
showName - Variable in class ccvisu.GraphVertex
True if the name shall be annotated in the visualization.

T

time - Variable in class ccvisu.ReaderDataGraphCVS.Revision
 
timeWindow - Variable in class ccvisu.ReaderDataGraphCVS
Time-window constant for transaction recovery, in milli-seconds.
toggleVertexNames(int, int) - Method in class ccvisu.WriterDataGraphicsDISP
Toggle the showName flag of the vertices at the given position.
toggle_showName() - Method in class ccvisu.GraphVertex
Toggles the annotation of the vertex.
transaction - Variable in class ccvisu.ReaderDataGraphCVS.Revision
An artificially created number.

U

user - Variable in class ccvisu.ReaderDataGraphCVS.Revision
 

V

VRML - Static variable in class ccvisu.CCVisu
Graph layout in VRML format (only output).
Verbosity - class ccvisu.Verbosity.
Represents the verbosity level.
Verbosity() - Constructor for class ccvisu.Verbosity
 
vertex - Variable in class ccvisu.ReaderDataLAY.LayoutEntry
 
vertexName - Variable in class ccvisu.ScreenDisplay.MyCanvas
 
vertices - Variable in class ccvisu.GraphData
Maps a vertex id to a GraphVertex.

W

WriterData - class ccvisu.WriterData.
Writer for output data.
WriterData(GraphData) - Constructor for class ccvisu.WriterData
Constructor.
WriterDataGraphics - class ccvisu.WriterDataGraphics.
Writer for graphical output of layout data.
WriterDataGraphics(GraphData, boolean, float, int, Color, boolean) - Constructor for class ccvisu.WriterDataGraphics
Constructor.
WriterDataGraphicsDISP - class ccvisu.WriterDataGraphicsDISP.
Writer for displaying the layout on the screen device.
WriterDataGraphicsDISP(GraphData, boolean, float, int, Color, boolean, boolean) - Constructor for class ccvisu.WriterDataGraphicsDISP
Constructor.
WriterDataGraphicsSVG - class ccvisu.WriterDataGraphicsSVG.
Writer for layouts in SVG format (Scalable Vector Graphs, XML, W3C).
WriterDataGraphicsSVG(GraphData, PrintWriter, boolean, float, int, Color, boolean, float) - Constructor for class ccvisu.WriterDataGraphicsSVG
Constructor.
WriterDataGraphicsVRML - class ccvisu.WriterDataGraphicsVRML.
Writer for layouts in VRML format.
WriterDataGraphicsVRML(GraphData, PrintWriter, boolean, float, int, Color, boolean, float) - Constructor for class ccvisu.WriterDataGraphicsVRML
Constructor.
WriterDataLAY - class ccvisu.WriterDataLAY.
Writer for layouts in text format.
WriterDataLAY(GraphData, PrintWriter, boolean) - Constructor for class ccvisu.WriterDataLAY
 
WriterDataRSF - class ccvisu.WriterDataRSF.
Writer for co-change graphs in RSF format.
WriterDataRSF(GraphData, PrintWriter) - Constructor for class ccvisu.WriterDataRSF
 
w - Variable in class ccvisu.GraphEdgeInt
Edge weight.
w - Variable in class ccvisu.GraphEdgeString
 
weight - Variable in class ccvisu.MinimizerBarnesHut.OctTree
Total weight of the contained graph nodes.
width() - Method in class ccvisu.MinimizerBarnesHut.OctTree
Returns the maximum extension of the octtree.
write() - Method in class ccvisu.WriterData
Writes the graph or layout data.
write() - Method in class ccvisu.WriterDataGraphics
Writes the layout data in a graphics format.
write() - Method in class ccvisu.WriterDataGraphicsDISP
Nothing to do here.
write() - Method in class ccvisu.WriterDataGraphicsSVG
Writes the layout in graphics format SVG.
write() - Method in class ccvisu.WriterDataGraphicsVRML
Writes the layout in graphics format VRML.
write() - Method in class ccvisu.WriterDataLAY
Writes the layout data in text format LAY.
write() - Method in class ccvisu.WriterDataRSF
Writes the graph data in RSF (relational standard format).
writeDISP(int, Graphics, int, int, int) - Method in class ccvisu.WriterDataGraphicsDISP
Writes the layout on the screen device (DISP output format).
writeGraphicsLayout(int) - Method in class ccvisu.WriterDataGraphics
Write graphics layout.
writeLAY(String) - Method in class ccvisu.WriterDataGraphicsDISP
Writes layout to file using class WriterDataLAY.
writeVertex(GraphVertex, int, int, int, int) - Method in class ccvisu.WriterDataGraphics
Writes a vertex.
writeVertex(GraphVertex, int, int, int, int) - Method in class ccvisu.WriterDataGraphicsDISP
Writes a vertex on screen.
writeVertex(GraphVertex, int, int, int, int) - Method in class ccvisu.WriterDataGraphicsSVG
Writes a vertex in SVG format.
writeVertex(GraphVertex, int, int, int, int) - Method in class ccvisu.WriterDataGraphicsVRML
Writes a vertex in VRML format.
writer - Variable in class ccvisu.ScreenDisplay.MyCanvas
 

X

x - Variable in class ccvisu.GraphEdgeInt
Source vertex of edge.
x - Variable in class ccvisu.GraphEdgeString
 
xMap - Variable in class ccvisu.WriterDataGraphicsDISP
 

Y

y - Variable in class ccvisu.GraphEdgeInt
Target vertex of edge.
y - Variable in class ccvisu.GraphEdgeString
 
yMap - Variable in class ccvisu.WriterDataGraphicsDISP
 

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