Java CyTable类代码示例

import org.cytoscape.model.CyTable; //导入依赖的package包/类
private void setColumnIndicesForNewSeriesMapping(CyTable table, DataSeries<?,?> sourceSeries, String sourceColumn, DataSeries<?,?> smoothedSeries, String targetColumn, Map<Integer, Integer> rowMapping)
{
	if(rowMapping != null)
	{
		table.getAllRows().forEach(
				row -> 
					row.set(targetColumn, rowMapping.get(row.get(sourceColumn, DataSeriesMappingManager.MAPPING_COLUMN_CLASS)))
			);
	}
	else
	{
		table.getAllRows().forEach(
				row -> 
					row.set(targetColumn, row.get(sourceColumn, DataSeriesMappingManager.MAPPING_COLUMN_CLASS))
			);			
	}
}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
@Override
public void replaceMapping(DataSeries<?,?> sourceTimeSeries, DataSeries<?,?> targetTimeSeries, Map<String, List<Integer>> rowGrouping) {
	final DataSeriesMappingManager mappingManager = registrar.getService(DataSeriesMappingManager.class);
	List<MappingDescriptor<DataSeries<?,?>>> allDescriptors = mappingManager.getMappingDescriptorsForSeries(sourceTimeSeries);
	
	Map<Integer, Integer> rowMapping = rowMappingFromRowGrouping(rowGrouping, targetTimeSeries);
	
	allDescriptors.forEach(descriptor -> {
		mappingManager.unmap(descriptor);

		//No need to write anything if rows were not grouped
		if(rowGrouping != null)
		{
			CyTable table = mappingManager.getMappingTable(descriptor.getNetwork(), descriptor.getTargetClass());
			setColumnIndicesForNewSeriesMapping(table, sourceTimeSeries, descriptor.getColumnName(), targetTimeSeries, descriptor.getColumnName(), rowMapping);
		}
		
		mappingManager.mapDataSeriesRowsToTableColumn(descriptor.getNetwork(), descriptor.getTargetClass(), descriptor.getColumnName(), targetTimeSeries);
	});
}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
@Override
public void copyMapping(DataSeries<?,?> sourceTimeSeries, DataSeries<?,?> targetTimeSeries, Map<String, List<Integer>> rowGrouping, String mappingSuffix)
   {
	final DataSeriesMappingManager mappingManager = registrar.getService(DataSeriesMappingManager.class);
	List<MappingDescriptor<DataSeries<?,?>>> allDescriptors = mappingManager.getMappingDescriptorsForSeries(sourceTimeSeries);
	
	Map<Integer, Integer> rowMapping = rowMappingFromRowGrouping(rowGrouping, targetTimeSeries);
			allDescriptors.forEach(descriptor -> {
				String newColumnName = descriptor.getColumnName() + mappingSuffix;
				CyTable table = mappingManager.getMappingTable(descriptor.getNetwork(), descriptor.getTargetClass());
				if (table.getColumn(newColumnName) == null)
				{
					table.createColumn(newColumnName, DataSeriesMappingManager.MAPPING_COLUMN_CLASS, false);
				}
				setColumnIndicesForNewSeriesMapping(table, sourceTimeSeries, descriptor.getColumnName(), targetTimeSeries, newColumnName, rowMapping);
				mappingManager.mapDataSeriesRowsToTableColumn(descriptor.getNetwork(), descriptor.getTargetClass(), newColumnName, targetTimeSeries);
			});				
}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
private void updateEdgeWeightColumnList() {
    weightColumnModel.removeAllElements();

    if (session == null) {
        return;
    }

    CyNetworkView view = session.getNetworkView();
    CyNetwork model = view.getModel();
    CyTable table = model.getDefaultEdgeTable();
    table.getColumns()
         .stream()
         .filter(c -> !CyIdentifiable.SUID.equals(c.getName()) && Number.class.isAssignableFrom(c.getType()))
         .map(c -> c.getName())
         .sorted(String.CASE_INSENSITIVE_ORDER)
         .forEach(name -> weightColumnModel.addElement(name));

    weightColumn.setSelectedItem(session.getWeightColumn());

    if (weightColumn.getSelectedIndex() == -1 && weightColumnModel.getSize() > 0) {
        weightColumn.setSelectedIndex(0);
    }
}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
void updateColumnList(SafeSession session) {
    lastAnnotationPath = null;
    this.session = session;

    nodeIdsModel.removeAllElements();

    if (session == null) {
        return;
    }

    CyNetworkView view = session.getNetworkView();
    CyNetwork model = view.getModel();
    CyTable table = model.getDefaultNodeTable();
    SafeUtil.getStringColumnNames(table)
            .forEach(name -> {
                nodeIdsModel.addElement(name);
            });

    nodeIds.setSelectedItem(session.getIdColumn());
}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
void setNetworkView(CyNetworkView view) {
    if (view == null) {
        setSession(null);
        return;
    }

    long suid = view.getSUID();
    synchronized (sessionMutex) {
        SafeSession session = sessionsBySuid.get(suid);
        if (session == null) {
            session = createNewSession(view);
            sessionsBySuid.put(suid, session);

            CyNetwork network = view.getModel();
            CyTable nodeTable = network.getDefaultNodeTable();
            sessionsBySuid.put(nodeTable.getSUID(), session);
        }
        setSession(session);
    }
}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
public static void checkSafeColumns(CyTable table) {
    CyColumn column = table.getColumn(StyleFactory.HIGHLIGHT_COLUMN);
    if (column == null) {
        table.createColumn(StyleFactory.HIGHLIGHT_COLUMN, Double.class, false, 0D);
    }

    column = table.getColumn(StyleFactory.COLOR_COLUMN);
    if (column == null) {
        table.createColumn(StyleFactory.COLOR_COLUMN, String.class, false, null);
    }

    column = table.getColumn(StyleFactory.BRIGHTNESSS_COLUMN);
    if (column == null) {
        table.createColumn(StyleFactory.BRIGHTNESSS_COLUMN, Double.class, false, 0D);
    }
}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
public void saveToSession(SafeSession[] sessions) {
    deleteExistingTables();

    CyTable dataTable = getSafeDataTable();
    checkColumn(dataTable, SAFE_DATA_COLUMN, String.class);

    Arrays.stream(sessions)
          .forEach(session -> {
              try {
                  serializeSession(dataTable, session);
              } catch (Throwable t) {
                  t.printStackTrace();
              }
          });

    tableManager.addTable(dataTable);
}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
void serializeSession(CyTable dataTable,
                      SafeSession session) {
    CyNetworkView networkView = session.getNetworkView();
    CyNetwork network = networkView.getModel();
    CyTable networkTable = network.getDefaultNetworkTable();
    CyRow row = networkTable.getRow(network.getSUID());

    checkColumn(networkTable, DATA_TABLE_COLUMN, Long.class);
    Long suid = dataTable.getSUID();
    row.set(DATA_TABLE_COLUMN, suid);

    CyRow viewRow = dataTable.getRow(networkView.getSUID());
    try (StringWriter writer = new StringWriter()) {
        toJson(session, writer);
        String json = writer.toString();
        viewRow.set(SAFE_DATA_COLUMN, json);
    } catch (IOException e) {
        e.printStackTrace();
    }
}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
public LongObjectMap<SafeSession> loadFromSession(CySession cySession) throws IOException {

        CyTable dataTable = cySession.getTables()
                                     .stream()
                                     .map(metadata -> metadata.getTable())
                                     .filter(table -> DATA_TABLE_TITLE.equals(table.getTitle()))
                                     .findFirst()
                                     .orElse(null);

        LongObjectMap<SafeSession> sessions = new LongObjectHashMap<>();
        if (dataTable == null) {
            return sessions;
        }

        for (CyRow row : dataTable.getAllRows()) {
            String json = row.get(SAFE_DATA_COLUMN, String.class);
            SafeSession session = parseSession(json);

            Long oldSuid = row.get(CyIdentifiable.SUID, Long.class);
            CyNetworkView view = cySession.getObject(oldSuid, CyNetworkView.class);
            session.setNetworkView(view);
            sessions.put(view.getSUID(), session);
        }
        return sessions;
    }
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
public void exportModel() {
	for(CyNetwork network: networkManager.getNetworkSet()) {
		CyTable asTable = createAnnotationSetTable(network);
		CyTable clusterTable = createClusterTable(network);
		
		Ids ids = new Ids();
		
		Collection<CyNetworkView> networkViews = networkViewManager.getNetworkViews(network);
		for(CyNetworkView networkView : networkViews) {
			Optional<NetworkViewSet> nvs = modelManagerProvider.get().getExistingNetworkViewSet(networkView);
			if(nvs.isPresent()) {
				try {
					exportModel(nvs.get(), asTable, clusterTable, ids);
				}catch(Exception ex) {
					ex.printStackTrace();
				}
				continue;
			}
		}
	}
}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
private CyTable createAnnotationSetTable(CyNetwork network) {
	CyTable table = createTable(network, ANNOTATION_SET_TABLE, ANNOTATION_SET_ID);
	createColumn(table, NAME, String.class);
	createColumn(table, NETWORK_VIEW_SUID, Long.class);
	createListColumn(table, LABEL_COLUMN, String.class);
	createColumn(table, ACTIVE, Boolean.class);
	createColumn(table, SHAPE_TYPE, String.class);
	createColumn(table, SHOW_CLUSTERS, Boolean.class);
	createColumn(table, SHOW_LABELS, Boolean.class);
	createColumn(table, USE_CONSTANT_FONT_SIZE, Boolean.class);
	createColumn(table, FONT_SCALE, Integer.class);
	createColumn(table, FONT_SIZE, Integer.class);
	createColumn(table, OPACITY, Integer.class);
	createColumn(table, BORDER_WIDTH, Integer.class);
	createColumn(table, FILL_COLOR, Integer.class); // store as RGB int value
	createColumn(table, BORDER_COLOR, Integer.class);
	createColumn(table, FONT_COLOR, Integer.class);
	createColumn(table, LABEL_MAKER_ID, String.class);
	createColumn(table, LABEL_MAKER_CONTEXT, String.class);
	createColumn(table, CREATION_PARAMS, String.class);
	return table;
}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
public static void set(CyNetwork network, CyIdentifiable entry, String tableName, String name, Object value, Class<?> type) {
	CyRow row = network.getRow(entry, tableName);
	CyTable table = row.getTable();
	CyColumn column = table.getColumn(name);
	if (value != null) {
		if (column == null) {
			if (value instanceof List) {
				table.createListColumn(name, type, false);
			}
			else if (value instanceof Collection) {
				throw new IllegalArgumentException("Arrt. values collection is not a List: "
						+ value.getClass().getSimpleName());
			}
			else {
				table.createColumn(name, type, false);
			}
		}
		row.set(name, value);
	}
}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
@Override
protected void setEdgeAttribute(CyEdge edge, String colName, Object value) 
{
	if (value == null) return; //ignore
	if (value instanceof RdfNode) { value = value.toString(); }
	
	CyTable table = myNet.getDefaultEdgeTable();
	if (table.getColumn(colName) == null)
	{
		table.createColumn(colName, value.getClass(), true);
	}
	
	try
	{
		table.getRow(edge.getSUID()).set(colName, value);
	}
	catch (IllegalStateException e)
	{
		// class cast problem when sparql result does not match column class.
		// TODO...
		e.printStackTrace();
	}

}
 

import org.cytoscape.model.CyTable; //导入依赖的package包/类
public void selectEdges(String n1, String n2) {
    CyTable nodeTable = network.getDefaultNodeTable();
    List<CyEdge> edges = network.getEdgeList();
    
    for(CyRow row : nodeTable.getAllRows()) {
        row.set(CyNetwork.SELECTED, false);
    }
    
    for(CyEdge edge : edges) {
        if((network.getRow(edge.getSource()).get(CyNetwork.NAME, String.class).equalsIgnoreCase(n1) && network.getRow(edge.getTarget()).get(CyNetwork.NAME, String.class).equalsIgnoreCase(n2)) ||
                (network.getRow(edge.getSource()).get(CyNetwork.NAME, String.class).equalsIgnoreCase(n2) && network.getRow(edge.getTarget()).get(CyNetwork.NAME, String.class).equalsIgnoreCase(n1))) {
            network.getRow(edge).set(CyNetwork.SELECTED, true);
        }
        else{
            network.getRow(edge).set(CyNetwork.SELECTED, false);
        }
    }
    
    if (networkView != null) {
        networkView.updateView();
        applicationManager.setCurrentNetworkView(networkView);
    }
}