private void writeAttributes(XMLStreamWriter xmlWriter, AttributeTable table) throws Exception {
List<AttributeColumn> staticCols = new ArrayList<AttributeColumn>();
List<AttributeColumn> dynamicCols = new ArrayList<AttributeColumn>();
String attClass = table == attributeModel.getNodeTable() ? "node" : "edge";
for (AttributeColumn col : table.getColumns()) {
if (!col.getOrigin().equals(AttributeOrigin.PROPERTY)) {
if (exportDynamic && col.getType().isDynamicType()) {
dynamicCols.add(col);
} else {
staticCols.add(col);
}
} else if (exportDynamic
&& col.getType().isDynamicType()
&& col.getType() != AttributeType.TIME_INTERVAL
&& col.getOrigin().equals(AttributeOrigin.PROPERTY)
&& col.getIndex() == PropertiesColumn.EDGE_WEIGHT.getIndex()) {
dynamicCols.add(col);
}
}
if (!staticCols.isEmpty()) {
writeAttributes(xmlWriter, staticCols.toArray(new AttributeColumn[0]), "static", attClass);
}
if (!dynamicCols.isEmpty()) {
writeAttributes(xmlWriter, dynamicCols.toArray(new AttributeColumn[0]), "dynamic", attClass);
}
}
@Override
public void execute(GraphModel graphModel, AttributeModel attributeModel) {
// Graph graph = graphModel.getGraphVisible();
HierarchicalGraph graph = null;
// get visible graph
if (directed) {
graph = graphModel.getHierarchicalDirectedGraphVisible();
} else {
graph = graphModel.getHierarchicalUndirectedGraphVisible();
}
// lock graph
graph.readLock();
try {
Progress.start(progressTicket, graph.getNodeCount());
// all coefficients
nodeCoefficients = new double[graph.getNodeCount()];
// attribute column
AttributeTable nodeTable = attributeModel.getNodeTable();
AttributeColumn clusteringColumn = nodeTable.getColumn("newClusteringCoefficient");
if (clusteringColumn == null) {
clusteringColumn =
nodeTable.addColumn(
"newClusteringCoefficient",
"Local Clustering Coefficient",
AttributeType.DOUBLE,
AttributeOrigin.COMPUTED,
0.0);
}
int i = 0;
// for each node
for (Node e : graph.getNodes()) {
// compute coefficient
double coeficient = 0.0;
double denominator = (graph.getDegree(e) * (graph.getDegree(e) - 1));
if (!directed) {
denominator /= 2;
}
double numerator = 0.0;
// get neighbors as list
List<Node> n2 = Arrays.asList(graph.getNeighbors(e).toArray());
List<Node> neighbors2 = new ArrayList<Node>(n2);
for (Node neighbor1 : graph.getNeighbors(e)) {
neighbors2.remove(neighbor1);
// count edges betwwen neighbors
for (Node neighbor2 : neighbors2) {
if (graph.getEdge(neighbor1, neighbor2) != null
|| graph.getEdge(neighbor2, neighbor1) != null) {
numerator++;
}
}
}
// compute coefficient
if (denominator > 0) {
coeficient = numerator / denominator;
} else {
coeficient = 0.0;
}
averageCoefficient += coeficient;
nodeCoefficients[i] = coeficient;
i++;
// set attribute
AttributeRow row = (AttributeRow) e.getNodeData().getAttributes();
row.setValue(clusteringColumn, coeficient);
Progress.progress(progressTicket);
if (cancel) {
break;
}
}
if (graph.getNodeCount() > 0) {
averageCoefficient = averageCoefficient / graph.getNodeCount();
}
graph.readUnlockAll();
} catch (Exception e) {
e.printStackTrace();
// Unlock graph
graph.readUnlockAll();
}
}
public void convertToNetwork() throws IOException, InvalidFormatException {
container = MyFileImporter.container;
container.setEdgeDefault(EdgeDefault.UNDIRECTED);
String firstDelimiter;
String secondDelimiter;
firstDelimiter = Utils.getCharacter(MyFileImporter.firstConnectorDelimiter);
secondDelimiter = Utils.getCharacter(MyFileImporter.secondConnectorDelimiter);
boolean oneTypeOfAgent =
MyFileImporter.getFirstConnectedAgent().equals(MyFileImporter.getSecondConnectedAgent());
nbColumnFirstAgent = MyFileImporter.firstConnectedAgentIndex;
nbColumnSecondAgent = MyFileImporter.secondConnectedAgentIndex;
Integer lineCounter = 0;
InputStream inp;
inp = new FileInputStream(fileName);
Workbook wb = WorkbookFactory.create(inp);
Row row;
Sheet sheet = wb.getSheet(sheetName);
int startingRow;
if (MyFileImporter.headersPresent) {
startingRow = 1;
} else {
startingRow = 0;
}
Set<String> linesFirstAgent = new HashSet();
Set<String> linesSecondAgent = new HashSet();
for (int i = startingRow; i <= sheet.getLastRowNum(); i++) {
row = sheet.getRow(i);
if (row == null) {
break;
}
Cell cell = row.getCell(nbColumnFirstAgent);
if (cell == null) {
Issue issue =
new Issue(
"problem with line "
+ lineCounter
+ " (empty column "
+ MyFileImporter.getFirstConnectedAgent()
+ "). It was skipped in the conversion",
Issue.Level.WARNING);
MyFileImporter.getStaticReport().logIssue(issue);
continue;
}
String firstAgent = row.getCell(nbColumnFirstAgent).getStringCellValue();
if (firstAgent == null || firstAgent.isEmpty()) {
Issue issue =
new Issue(
"problem with line "
+ lineCounter
+ " (empty column "
+ MyFileImporter.getFirstConnectedAgent()
+ "). It was skipped in the conversion",
Issue.Level.WARNING);
MyFileImporter.getStaticReport().logIssue(issue);
continue;
}
if (MyFileImporter.removeDuplicates) {
boolean newLine = linesFirstAgent.add(firstAgent);
if (!newLine) {
continue;
}
}
String secondAgent = null;
if (!oneTypeOfAgent) {
cell = row.getCell(nbColumnSecondAgent);
if (cell == null) {
Issue issue =
new Issue(
"problem with line "
+ lineCounter
+ " (empty column "
+ MyFileImporter.getFirstConnectedAgent()
+ "). It was skipped in the conversion",
Issue.Level.WARNING);
MyFileImporter.getStaticReport().logIssue(issue);
continue;
}
secondAgent = row.getCell(nbColumnSecondAgent).getStringCellValue();
if (secondAgent == null || secondAgent.isEmpty()) {
Issue issue =
new Issue(
"problem with line "
+ lineCounter
+ " (empty column "
+ MyFileImporter.getSecondConnectedAgent()
+ "). It was skipped in the conversion",
Issue.Level.WARNING);
MyFileImporter.getStaticReport().logIssue(issue);
continue;
}
if (MyFileImporter.removeDuplicates) {
boolean newLine = linesFirstAgent.add(firstAgent);
if (!newLine) {
continue;
}
}
}
lineCounter++;
String[] firstAgentSplit;
String[] secondAgentSplit;
if (firstDelimiter != null) {
firstAgentSplit = firstAgent.trim().split(firstDelimiter);
} else {
firstAgentSplit = new String[1];
firstAgentSplit[0] = firstAgent;
}
for (String node : firstAgentSplit) {
nodesFirst.add(node.trim());
}
if (!oneTypeOfAgent) {
if (secondDelimiter != null) {
secondAgentSplit = secondAgent.trim().split(secondDelimiter);
} else {
secondAgentSplit = new String[1];
secondAgentSplit[0] = secondAgent;
}
for (String node : secondAgentSplit) {
nodesSecond.add(node.trim());
}
} else {
secondAgentSplit = null;
}
String[] both = ArrayUtils.addAll(firstAgentSplit, secondAgentSplit);
// let's find all connections between all the tags for this picture
Utils usefulTools = new Utils();
List<String> connections = usefulTools.getListOfLinks(both, MyFileImporter.removeSelfLoops);
edges.addAll(connections);
}
NodeDraft node;
AttributeTable atNodes = container.getAttributeModel().getNodeTable();
AttributeColumn acFrequency = atNodes.addColumn("frequency", AttributeType.INT);
AttributeColumn acType = atNodes.addColumn("type", AttributeType.STRING);
for (String n : nodesFirst.elementSet()) {
node = container.factory().newNodeDraft();
node.setId(n);
node.setLabel(n);
node.addAttributeValue(acFrequency, nodesFirst.count(n));
node.addAttributeValue(acType, MyFileImporter.getFirstConnectedAgent());
container.addNode(node);
}
for (String n : nodesSecond.elementSet()) {
node = container.factory().newNodeDraft();
node.setId(n);
node.setLabel(n);
node.addAttributeValue(acFrequency, nodesSecond.count(n));
node.addAttributeValue(acType, MyFileImporter.getSecondConnectedAgent());
container.addNode(node);
}
// loop for edges
Integer idEdge = 0;
EdgeDraft edge;
for (String e : edges.elementSet()) {
System.out.println("edge: " + e);
String sourceNode = e.split("\\|")[0];
String targetNode = e.split("\\|")[1];
if (!MyFileImporter.innerLinksIncluded) {
if ((nodesFirst.contains(sourceNode) & nodesFirst.contains(targetNode))
|| (nodesSecond.contains(sourceNode) & nodesSecond.contains(targetNode))) {
continue;
}
}
edge = container.factory().newEdgeDraft();
idEdge = idEdge + 1;
edge.setSource(container.getNode(sourceNode));
edge.setTarget(container.getNode(targetNode));
edge.setWeight((float) edges.count(e));
edge.setId(String.valueOf(idEdge));
edge.setType(EdgeDraft.EdgeType.UNDIRECTED);
container.addEdge(edge);
}
}
