private void writeNodes(XMLStreamWriter xmlWriter, HierarchicalGraph graph) throws Exception {
if (cancel) {
return;
}
xmlWriter.writeStartElement(NODES);
AttributeColumn dynamicCol =
dynamicCol = attributeModel.getNodeTable().getColumn(DynamicModel.TIMEINTERVAL_COLUMN);
NodeIterable nodeIterable = exportHierarchy ? graph.getNodesTree() : graph.getNodes();
for (Node node : nodeIterable) {
xmlWriter.writeStartElement(NODE);
String id = node.getNodeData().getId();
xmlWriter.writeAttribute(NODE_ID, id);
if (node.getNodeData().getLabel() != null && !node.getNodeData().getLabel().isEmpty()) {
xmlWriter.writeAttribute(NODE_LABEL, node.getNodeData().getLabel());
}
if (exportHierarchy) {
Node parent = graph.getParent(node);
if (parent != null) {
xmlWriter.writeAttribute(NODE_PID, parent.getNodeData().getId());
}
}
if (exportDynamic && dynamicCol != null && visibleInterval != null) {
TimeInterval timeInterval =
(TimeInterval) node.getNodeData().getAttributes().getValue(dynamicCol.getIndex());
if (timeInterval != null) {
writeTimeInterval(xmlWriter, timeInterval);
}
}
if (exportAttributes && node.getNodeData().getAttributes() != null) {
AttributeRow attributeRow = (AttributeRow) node.getNodeData().getAttributes();
writeAttValues(xmlWriter, attributeRow, visibleInterval);
}
if (exportSize) {
writeNodeSize(xmlWriter, node);
}
if (exportPosition) {
writeNodePosition(xmlWriter, node);
}
if (exportColors) {
writeNodeColor(xmlWriter, node);
}
xmlWriter.writeEndElement();
Progress.progress(progress);
if (cancel) {
break;
}
}
xmlWriter.writeEndElement();
}
public void script() {
// Init a project - and therefore a workspace
ProjectController pc = Lookup.getDefault().lookup(ProjectController.class);
pc.newProject();
Workspace workspace = pc.getCurrentWorkspace();
// Get controllers and models
ImportController importController = Lookup.getDefault().lookup(ImportController.class);
// Import file
Container container;
try {
File file =
new File(
getClass().getResource("/org/gephi/toolkit/demos/resources/polblogs.gml").toURI());
container = importController.importFile(file);
container.getLoader().setEdgeDefault(EdgeDefault.DIRECTED); // Force DIRECTED
container.setAllowAutoNode(false); // Don't create missing nodes
} catch (Exception ex) {
ex.printStackTrace();
return;
}
// Append imported data to GraphAPI
importController.process(container, new DefaultProcessor(), workspace);
// List node columns
AttributeController ac = Lookup.getDefault().lookup(AttributeController.class);
AttributeModel model = ac.getModel();
for (AttributeColumn col : model.getNodeTable().getColumns()) {
System.out.println(col);
}
// Add boolean column
AttributeColumn testCol = model.getNodeTable().addColumn("test", AttributeType.BOOLEAN);
// Write values to nodes
GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getModel();
for (Node n : graphModel.getGraph().getNodes()) {
n.getNodeData().getAttributes().setValue(testCol.getIndex(), Boolean.TRUE);
}
// Iterate values - fastest
AttributeColumn sourceCol = model.getNodeTable().getColumn("source");
for (Node n : graphModel.getGraph().getNodes()) {
System.out.println(n.getNodeData().getAttributes().getValue(sourceCol.getIndex()));
}
// Iterate values - normal
for (Node n : graphModel.getGraph().getNodes()) {
System.out.println(n.getNodeData().getAttributes().getValue("source"));
}
}
public void setValue(AttributeValue value) {
AttributeColumn column = value.getColumn();
if (attributeTable.getColumn(column.getIndex()) != column) {
column = attributeTable.getColumn(column);
if (column == null) {
throw new IllegalArgumentException(
"The "
+ attributeTable.getName()
+ " value column "
+ value.getColumn().getId()
+ " with index "
+ value.getColumn().getIndex()
+ " doesn't exist");
}
value = attributeTable.getFactory().newValue(column, value.getValue());
}
setValue(column.getIndex(), (AttributeValueImpl) value, true);
}
@Override
public void selectColumn(final AttributeColumn column) {
if (model != null) {
if (!(model.getChart() == null && column == null)
|| (model.getChart() != null && !model.getChart().getColumn().equals(column))) {
if (column != null && !attributeModel.getGraphTable().hasColumn(column.getId())) {
throw new IllegalArgumentException("Not a graph column");
}
Thread thread =
new Thread(
new Runnable() {
@Override
public void run() {
TimelineChart chart = null;
Graph graph =
Lookup.getDefault()
.lookup(GraphController.class)
.getModel()
.getGraphVisible();
if (column != null) {
DynamicType type =
(DynamicType) graph.getAttributes().getValue(column.getIndex());
if (type != null) {
List<Interval> intervals =
type.getIntervals(model.getCustomMin(), model.getCustomMax());
Number[] xs = new Number[intervals.size() * 2];
Number[] ys = new Number[intervals.size() * 2];
int i = 0;
for (Interval interval : intervals) {
Number x = (Double) interval.getLow();
Number y = (Number) interval.getValue();
xs[i] = x;
ys[i] = y;
i++;
xs[i] = (Double) interval.getHigh();
ys[i] = y;
i++;
}
if (xs.length > 0) {
chart = new TimelineChartImpl(column, xs, ys);
}
}
}
model.setChart(chart);
fireTimelineModelEvent(
new TimelineModelEvent(TimelineModelEvent.EventType.CHART, model, chart));
}
},
"Timeline Chart");
thread.start();
}
}
}
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);
}
}
private void writeColumns(Clusterer clusterer) {
Cluster[] clusters = clusterer.getClusters();
if (clusters != null && clusters.length > 0) {
ClustererBuilder builder = getBuilder(clusterer);
AttributeModel am = Lookup.getDefault().lookup(AttributeController.class).getModel();
String id = "clustering_" + builder.getName();
String title = "Clustering (" + builder.getName() + ")";
AttributeColumn col = am.getNodeTable().getColumn(id);
if (col == null) {
col =
am.getNodeTable()
.addColumn(id, title, AttributeType.INT, AttributeOrigin.COMPUTED, null);
StatusDisplayer.getDefault()
.setStatusText("A new column \"" + title + "\" has been created");
}
for (int i = 0; i < clusters.length; i++) {
Integer clusterId = new Integer(i);
for (Node n : clusters[i].getNodes()) {
n.getNodeData().getAttributes().setValue(col.getIndex(), clusterId);
}
}
}
}
public Object getValue(AttributeColumn column) {
if (column == null) {
throw new NullPointerException();
}
updateColumns();
int index = column.getIndex();
if (checkIndexRange(index)) {
AttributeValue val = values[index];
if (val.getColumn() == column) {
return val.getValue();
}
}
return null;
}
private void writeEdges(XMLStreamWriter xmlWriter, HierarchicalGraph graph) throws Exception {
if (cancel) {
return;
}
xmlWriter.writeStartElement(EDGES);
AttributeColumn dynamicCol =
dynamicCol = attributeModel.getEdgeTable().getColumn(DynamicModel.TIMEINTERVAL_COLUMN);
EdgeIterable edgeIterable =
exportHierarchy ? graph.getEdgesTree() : graph.getEdgesAndMetaEdges();
for (Edge edge : edgeIterable) {
xmlWriter.writeStartElement(EDGE);
if (edge.getEdgeData().getId() != null
&& !edge.getEdgeData().getId().equals(Integer.toString(edge.getId()))) {
xmlWriter.writeAttribute(EDGE_ID, edge.getEdgeData().getId());
}
xmlWriter.writeAttribute(EDGE_SOURCE, edge.getSource().getNodeData().getId());
xmlWriter.writeAttribute(EDGE_TARGET, edge.getTarget().getNodeData().getId());
if (edge.isDirected() && graphModel.isMixed()) {
xmlWriter.writeAttribute(EDGE_TYPE, "directed");
} else if (!edge.isDirected() && graphModel.isMixed()) {
xmlWriter.writeAttribute(EDGE_TYPE, "undirected");
}
String label = edge.getEdgeData().getLabel();
if (label != null && !label.isEmpty()) {
xmlWriter.writeAttribute(EDGE_LABEL, label);
}
float weight = edge.getWeight();
if (weight != 1f) {
xmlWriter.writeAttribute(EDGE_WEIGHT, "" + weight);
}
if (exportDynamic && dynamicCol != null && visibleInterval != null) {
TimeInterval timeInterval =
(TimeInterval) edge.getEdgeData().getAttributes().getValue(dynamicCol.getIndex());
if (timeInterval != null) {
writeTimeInterval(xmlWriter, timeInterval);
}
}
if (exportColors) {
writeEdgeColor(xmlWriter, edge);
}
if (exportAttributes && edge.getEdgeData().getAttributes() != null) {
AttributeRow attributeRow = (AttributeRow) edge.getEdgeData().getAttributes();
writeAttValues(xmlWriter, attributeRow, visibleInterval);
}
xmlWriter.writeEndElement();
Progress.progress(progress);
if (cancel) {
break;
}
}
xmlWriter.writeEndElement();
}
private void writeAttValues(
XMLStreamWriter xmlWriter, AttributeRow row, TimeInterval visibleInterval) throws Exception {
xmlWriter.writeStartElement(ATTVALUES);
for (AttributeValue val : row.getValues()) {
AttributeColumn col = val.getColumn();
if (!col.getOrigin().equals(AttributeOrigin.PROPERTY)
|| (exportDynamic
&& col.getOrigin().equals(AttributeOrigin.PROPERTY)
&& col.getIndex() == PropertiesColumn.EDGE_WEIGHT.getIndex())) {
AttributeType type = col.getType();
if (type.isDynamicType()) {
DynamicType dynamicValue = (DynamicType) val.getValue();
if (dynamicValue != null && visibleInterval != null && exportDynamic) {
List<Interval<?>> intervals =
dynamicValue.getIntervals(visibleInterval.getLow(), visibleInterval.getHigh());
for (Interval<?> interval : intervals) {
Object value = interval.getValue();
if (value != null) {
xmlWriter.writeStartElement(ATTVALUE);
xmlWriter.writeAttribute(ATTVALUE_FOR, col.getId());
xmlWriter.writeAttribute(ATTVALUE_VALUE, value.toString());
if (!Double.isInfinite(interval.getLow())) {
String intervalLow = formatTime(interval.getLow());
xmlWriter.writeAttribute(
interval.isLowExcluded() ? START_OPEN : START, intervalLow);
}
if (!Double.isInfinite(interval.getHigh())) {
String intervalHigh = formatTime(interval.getHigh());
xmlWriter.writeAttribute(
interval.isHighExcluded() ? END_OPEN : END, intervalHigh);
}
xmlWriter.writeEndElement();
}
}
} else if (dynamicValue != null) {
TimeInterval interval = visibleInterval;
if (interval == null) {
interval = new TimeInterval();
}
Object value =
DynamicUtilities.getDynamicValue(
dynamicValue, interval.getLow(), interval.getHigh());
if (value != null) {
xmlWriter.writeStartElement(ATTVALUE);
xmlWriter.writeAttribute(ATTVALUE_FOR, val.getColumn().getId());
xmlWriter.writeAttribute(ATTVALUE_VALUE, value.toString());
xmlWriter.writeEndElement();
}
}
} else {
if (val.getValue() != null) {
xmlWriter.writeStartElement(ATTVALUE);
xmlWriter.writeAttribute(ATTVALUE_FOR, col.getId());
xmlWriter.writeAttribute(ATTVALUE_VALUE, val.getValue().toString());
xmlWriter.writeEndElement();
}
}
}
}
xmlWriter.writeEndElement();
}
private void writeAttributes(
XMLStreamWriter xmlWriter, AttributeColumn[] cols, String mode, String attClass)
throws Exception {
if (exportAttributes) {
xmlWriter.writeStartElement(ATTRIBUTES);
xmlWriter.writeAttribute(ATTRIBUTES_CLASS, attClass);
xmlWriter.writeAttribute(ATTRIBUTES_MODE, mode);
for (AttributeColumn col : cols) {
if (!col.getOrigin().equals(AttributeOrigin.PROPERTY)
|| (exportDynamic
&& col.getOrigin().equals(AttributeOrigin.PROPERTY)
&& col.getIndex() == PropertiesColumn.EDGE_WEIGHT.getIndex())) {
xmlWriter.writeStartElement(ATTRIBUTE);
xmlWriter.writeAttribute(ATTRIBUTE_ID, col.getId());
xmlWriter.writeAttribute(ATTRIBUTE_TITLE, col.getTitle());
if (col.getType().equals(AttributeType.INT)) {
xmlWriter.writeAttribute(ATTRIBUTE_TYPE, "integer");
} else if (col.getType().isListType()) {
if (col.getType().equals(AttributeType.LIST_INTEGER)) {
xmlWriter.writeAttribute(ATTRIBUTE_TYPE, "listint");
} else if (col.getType().equals(AttributeType.LIST_CHARACTER)) {
xmlWriter.writeAttribute(ATTRIBUTE_TYPE, "listchar");
} else {
xmlWriter.writeAttribute(
ATTRIBUTE_TYPE, col.getType().getTypeString().toLowerCase().replace("_", ""));
}
} else if (col.getType().isDynamicType()) {
AttributeType staticType = TypeConvertor.getStaticType(col.getType());
if (staticType.equals(AttributeType.INT)) {
xmlWriter.writeAttribute(ATTRIBUTE_TYPE, "integer");
} else {
xmlWriter.writeAttribute(ATTRIBUTE_TYPE, staticType.getTypeString().toLowerCase());
}
} else {
xmlWriter.writeAttribute(ATTRIBUTE_TYPE, col.getType().getTypeString().toLowerCase());
}
if (col.getDefaultValue() != null) {
xmlWriter.writeStartElement(ATTRIBUTE_DEFAULT);
xmlWriter.writeCharacters(col.getDefaultValue().toString());
xmlWriter.writeEndElement();
}
xmlWriter.writeEndElement();
}
}
xmlWriter.writeEndElement();
}
}