/**
* Basis analysis of a graph
*
* @param tg graph to analyse
*/
public static void analyse(timgraph tg) {
basicroot = tg.inputName.getNameRoot();
tg.calcStrength();
FileOutput fo = new FileOutput(tg);
boolean vertexListOn = true;
boolean printTriangles = true;
boolean printSquares = true;
boolean printNearestNeighbours = false;
boolean edgeListOn = true;
boolean graphMLOn = false;
fo.informationGeneral(
"",
SEP,
vertexListOn,
printTriangles,
printSquares,
printNearestNeighbours,
edgeListOn,
graphMLOn,
tg.outputControl);
// fo.informationGeneral("", SEP);
// fo.edgeListSimple();
// if (tg.isVertexLabelled()) fo.printEdges(true, false, false, false, false);
}
/**
* Basic routine to analyse a given graph.
*
* <p>BasicAnalysis arguments are just the usual <tt>timgraph</tt> arguments. Specify input file
* name and graph characteristics using timgraph arguments and the outputs will be those defined
* by the <tt>OutputControl</tt> class.
*
* @param args <tt>timgraph</tt> the command line arguments
* @see TimGraph.timgraph#printUsage
* @see TimGraph.OutputMode
*/
public static void main(String[] args) {
System.out.println(
"BasicAnalysis Arguments: just specify file name and characteristics using timgraph arguments alone");
System.out.println(" Output is controled by OutputMode argument -oNNN");
OutputMode o = new OutputMode(255);
o.printUsage(System.out, "");
// String basicFileName="TGCGn1x6y6t108p0";
// String basicFileName="aegean39S1L3a_v1_3e-1.0j0.0m0.5k1.0l4.5b1.2D100.0MC_r4_edgeweight";
// String basicFileName="MSC-2010classbygroup";
// String basicFileName="MSC-2010subclassbygroup";
// String [] aList = { "-fir"+basicFileName, "-fieinputBVNLS.dat", "-o511"};
// String basicFileName="RAEmanAuthorPaper";
// String [] aList = { "-fin"+basicFileName+"inputBVNLS.dat", "-o511"};
// String basicFileName="karateTSE";
// String [] aList = { "-fin"+basicFileName, "-fieinputEL.dat", "-o511"};
// String basicFileName="UKHEI08";
// String [] aList = { "-fin"+basicFileName, "-fieinputLAM.dat", "-gn99", "-e0", "-o255",
// "-xi0"};
// String basicFileName="BiTest";
// String [] aList = { "-fin"+basicFileName, "-fieinputBVNLS.dat", "-gn99", "-e0", "-o255",
// "-xi0"};
// String basicFileName="burtinputELS.dat";
// String [] aList = { "-fin"+basicFileName,"-fisinput/burt","-fosoutput/burt","-o511"};
// String basicFileName="vaneshtestinput.net";
// String [] aList = { "-fin"+basicFileName,"-fisinput/vanesh","-fosoutput/vanesh","-o511",
// "-xv10", "-xe20"};
// String basicFileName="testinputELS.dat";
// String [] aList = { "-fin"+basicFileName,"-fisinput/Test","-fosoutput/Test","-o7",
// "-xv10", "-xe20"};
String basicFileName = "UKwardsSEJDinputELS.dat";
String[] aList = {"-fin" + basicFileName, "-fisinput/UKwards", "-fosoutput/UKwards", "-o511"};
if (args.length > 0) aList = args;
tg = new timgraph();
tg.parseParam(aList);
tg.outputControl.printMode(System.out, " ");
tg.setNameRoot(tg.inputName.getNameRoot());
// tg.setNetworkFromManyInputFiles(); // this will read in the network
// tg.printParametersBasic();
int xColumn = 1;
int yColumn = 2;
boolean headerOn = false;
boolean infoOn = false;
int nameColumn = 1;
tg.setNetworkFromInputFiles();
// tg.setNetworkFromManyInputFiles(xColumn, yColumn, nameColumn, headerOn, infoOn); // this will
// read in the network
tg.printParametersBasic();
System.out.println("Output: " + tg.outputControl.getModeString(" "));
if (tg.getNumberVertices() < 20) tg.printNetwork(true);
analyse(tg);
}
/** @param args the command line arguments */
public static void main(String[] args) {
SetUpNetwork setnet = new SetUpNetwork(infoLevel);
// String name="SFWANPDFV05bright3cons025";
// int n=0;
String name = "SFWANPDFV05cons025";
int ano = 0;
if (args.length > ano)
if (args[ano].charAt(0) == '*') {
name = args[ano].substring(1, args[ano].length());
}
String wordName = "bright";
ano++;
if (args.length > ano)
if (args[ano].charAt(0) == '*') {
wordName = args[ano].substring(1, args[ano].length());
}
// set cutoff for strength within community in final graph, if less than one using fractional,
// otherwise aboslute
double min = 0.9;
ano++;
if (args.length > ano)
if (args[ano].charAt(0) == '*') {
min = Double.parseDouble(args[ano].substring(1, args[ano].length()));
}
boolean normaliseOn;
if (min < 1.0) normaliseOn = true;
else normaliseOn = false;
System.out.println(
"--- Looking at file name "
+ name
+ " for subgraph centred on word "
+ wordName
+ ", "
+ (normaliseOn ? "fractional " : "absolute ")
+ "cutoff "
+ min);
String[] aList = {
"-gvet",
"-gdf",
"-gewt",
"-gelt",
"-gvlt",
"-fin" + name,
"-fieinputELS.dat",
"-gn99",
"-e0",
"-o11",
"-xi0"
};
timgraph big = setnet.setUpNetwork(name, aList, infoLevel);
if ((infoLevel > 0) && big.getNumberVertices() < 20) big.printNetwork(true);
TreeSet labelSet = big.getEdgeLabelSet();
int numberLabelsBig = labelSet.size();
System.out.println(
"Network " + big.inputName.getNameRoot() + " has " + numberLabelsBig + " distinct labels");
FileOutput fobig = new FileOutput(big);
fobig.printEdges(true, false, false, false, true);
fobig.graphMLEdgePartition(numberLabelsBig);
// String epname="LouvainQSWLGEP_";
//
// VertexPartition ep = new VertexPartition(epname,big.getNumberStubs()/2);
// ep.readIntPartition(big.inputName.getNameRootFullPath()+"inputEP.dat", 1, 2, false);
//
// big.setEdgeLabels(ep);
// need edge weights on as labels carry the partition
tg =
big.makeEdgeSubGraph(
wordName, false, true, big.isVertexLabelled(), big.isVertexEdgeListOn());
// tg.setNameRoot(epname+wordName+"V_");
tg.printParametersBasic();
if ((infoLevel > 0) && tg.getNumberVertices() < 20) tg.printNetwork(true);
int numberLabels = tg.relabelEdges(wordName);
System.out.println(
"Network "
+ tg.inputName.getNameRoot()
+ " has "
+ numberLabels
+ " distinct labels around word "
+ wordName);
labelSet = tg.getEdgeLabelSet();
int numberLabelsTotal = labelSet.size();
System.out.println(
"Network "
+ tg.inputName.getNameRoot()
+ " has "
+ numberLabelsTotal
+ " distinct labels ");
// output graph as is.
// tg.setNameRoot(name+"edgeSG");
FileOutput fo = new FileOutput(tg);
fo.informationGeneral("", SEP);
fo.printEdges(true, false, false, false, true);
fo.graphMLEdgePartition(numberLabels);
boolean splitBipartite = false;
boolean outputType1 = false;
fo.printEdgeCommunityStats(true, true, splitBipartite, outputType1);
// min value set as third parameter double min=0.9;
int imin = (int) (min * 1000);
TreeSet<Integer> sgvertexList = tg.edgeLabelToVertexSet(min, normaliseOn, false);
int vvv = tg.getVertexFromName(wordName);
sgvertexList.add(vvv);
timgraph newgraph =
tg.projectSubgraph(
"",
sgvertexList,
tg.isDirected(),
tg.isVertexLabelled(),
tg.isWeighted(),
tg.isVertexEdgeListOn(),
tg.isBipartite());
String ending; // ="f"+((int)(min*1000));
if (normaliseOn) ending = "f" + ((int) (min * 1000));
else ending = "a" + min;
newgraph.setNameRoot(newgraph.inputName.getNameRoot() + "_" + "EP2VC" + ending);
labelSet = newgraph.getEdgeLabelSet();
numberLabelsTotal = labelSet.size();
System.out.println(
"Network "
+ newgraph.inputName.getNameRoot()
+ " has "
+ numberLabelsTotal
+ " distinct labels ");
FileOutput fon = new FileOutput(newgraph);
fon.informationGeneral("", SEP);
fon.graphMLEdgePartition(numberLabels);
splitBipartite = false;
outputType1 = false;
fon.printEdgeCommunityStats(true, true, splitBipartite, outputType1);
}
