Java CyColumn类代码示例

import org.cytoscape.model.CyColumn; //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.CyColumn; //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.CyColumn; //导入依赖的package包/类
/**
 * Adds a column to the current network settings.
 * 
 * @param network
 * @param addedColumnName
 */
public void addColumnName(CyNetwork network, String addedColumnName) {
	CyColumn c = network.getDefaultNodeTable().getColumn(addedColumnName);
	if (c == null)
		return;
	
	if (existsColumn(addedColumnName) && c != null)
		return;

	columnNamesSet.add(addedColumnName);
	columnNames.add(addedColumnName);
	int i = columnNames.size() - 1;

	if (c.getListElementType() == String.class) {
		allGroupColumns.add(i);
		allGroupColumnSizes.add(Constants.CATEGORY_MAX_SIZE);
	} else if (c.getType() == String.class) {
		allStringColumns.add(i);
	} else if (c.getType() == Double.class) {
		allDoubleColumns.add(i);
	}
}
 

import org.cytoscape.model.CyColumn; //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("Attribute value is a Collection and not List: "
						+ value.getClass().getSimpleName());
			}
			else {
				table.createColumn(name, type, false);
			}
		}
		row.set(name, value);
	}
}
 

import org.cytoscape.model.CyColumn; //导入依赖的package包/类
private ListSingleSelection<String> getTargetColumns() 
{
	final CyTable table = network.getTable(CyNode.class, CyNetwork.DEFAULT_ATTRS);
	final List<String> colNames = new ArrayList<String>();
	
	for (final CyColumn col : table.getColumns()) {
		// Exclude list, numerical, boolean type columns
		if (String.class.isAssignableFrom(col.getType())) {
			colNames.add(col.getName());
		}
	}

	ListSingleSelection<String> toReturn = 
			new ListSingleSelection<String>(colNames);
	
	if(colNames.contains("UNIPROT"))
		toReturn.setSelectedValue("UNIPROT");
	else if(colNames.contains("GENE SYMBOL"))
		toReturn.setSelectedValue("GENE SYMBOL");
	else if(colNames.contains("URI"))
		toReturn.setSelectedValue("URI");
	else if(colNames.contains(CyRootNetwork.SHARED_NAME))
		toReturn.setSelectedValue(CyRootNetwork.SHARED_NAME); //less desired
	
	return toReturn;
}
 

import org.cytoscape.model.CyColumn; //导入依赖的package包/类
private void showColumnsForClass(Class<?> columnType, ListSingleSelection<String> selection, Class<? extends CyIdentifiable> targetClass)
{
	CyNetwork network = targetNetwork.getSelectedValue();
	List<CyColumn> candidateColumns = new ArrayList<>(mappingManager.getMappingTable(network, targetClass).getColumns());
	List<String> filteredCandidateColumnsNames = candidateColumns.stream()
			.filter(col -> col.getType() == columnType && !col.isPrimaryKey())
			.map(col -> col.getName())
			.collect(Collectors.toList());
	
	filteredCandidateColumnsNames.sort(new AlphanumComparator<>());
	
	selection.setPossibleValues(filteredCandidateColumnsNames);
	
}
 

import org.cytoscape.model.CyColumn; //导入依赖的package包/类
static boolean isStringColumn(CyColumn column) {
    Class<?> type = column.getType();
    if (type.equals(String.class)) {
        return true;
    }
    if (type.equals(List.class) && column.getListElementType()
                                         .equals(String.class)) {
        return true;
    }
    return false;
}
 

import org.cytoscape.model.CyColumn; //导入依赖的package包/类
private void checkColumn(CyTable table,
                         String name,
                         Class<?> type) {
    CyColumn column = table.getColumn(name);
    if (column == null) {
        table.createColumn(name, type, false);
    }
}
 

import org.cytoscape.model.CyColumn; //导入依赖的package包/类
public static List<String> getColumnsOfType(CyNetwork network, Class<?> type, boolean node, boolean addNone, boolean allowList) {
	List<String> columns = new LinkedList<>();
	
	CyTable table;
	if(node)
		table = network.getDefaultNodeTable();
	else 
		table = network.getDefaultEdgeTable();
	
	for(CyColumn column : table.getColumns()) {
		if(column.getName().equalsIgnoreCase("suid")) {
			continue;
		}
		
		if(type.isAssignableFrom(column.getType())) {
			columns.add(column.getName());
		}
		else if(allowList && List.class.equals(column.getType()) && type.isAssignableFrom(column.getListElementType())) {
			columns.add(column.getName());
		}
	}
	
	columns.sort(Comparator.naturalOrder());
	if(addNone) {
		columns.add(0, NONE);
	}
	return columns;
}
 

import org.cytoscape.model.CyColumn; //导入依赖的package包/类
private String getLabelColumn() {
	Collection<CyColumn> columns = networkView.getModel().getDefaultNodeTable().getColumns();
	for(CyColumn column : columns) {
		String name = column.getName();
		if(name.endsWith("GS_DESCR")) {
			return name;
		}
	}
	return CyNetwork.NAME;
}
 

import org.cytoscape.model.CyColumn; //导入依赖的package包/类
private void aggregateAttributes(CyNetwork originNetwork, SummaryNetwork summaryNetwork) {
	CyTable originNodeTable = originNetwork.getDefaultNodeTable();
	
	CyTable summaryNodeTable = summaryNetwork.network.getDefaultNodeTable();
	summaryNodeTable.createColumn("cluster node count", Integer.class, false);
	
	List<String> columnsToAggregate = new ArrayList<>();
	for(CyColumn column : originNodeTable.getColumns()) {
		String name = column.getName();
		if(summaryNodeTable.getColumn(name) == null) {
			columnsToAggregate.add(name);
			Class<?> listElementType = column.getListElementType();
			if(listElementType == null) {
				summaryNodeTable.createColumn(name, column.getType(), false);
			}
			else {
				summaryNodeTable.createListColumn(name, listElementType, false);
			}
		}
	}
	
	for(SummaryCluster cluster : summaryNetwork.getClusters()) {
		CyNode summaryNode = summaryNetwork.getNodeFor(cluster);
		CyRow row = summaryNodeTable.getRow(summaryNode.getSUID());
		
		row.set("name", cluster.getLabel());
		row.set("cluster node count", cluster.getNodes().size());
		
		for(String columnName : columnsToAggregate) {
			Object result = aggregate(originNetwork, cluster, columnName);
			row.set(columnName, result);
		}
	}
}
 

import org.cytoscape.model.CyColumn; //导入依赖的package包/类
@Override
public void run(TaskMonitor taskMonitor) {
	taskMonitor.setTitle(BuildProperties.APP_NAME);
	taskMonitor.setStatusMessage("Calculating clusterMaker edgeCutOff attribute.");
	
	CyTable table = network.getDefaultEdgeTable();
	CyColumn column = table.getColumn(edgeAttribute);
	
	double min = Double.MAX_VALUE;
	boolean updated = false;
	
	if(column != null) {
		Class<?> type = column.getType();
		if(Number.class.isAssignableFrom(type)) {
			for(CyRow row : table.getAllRows()) {
				Number value = (Number) row.get(edgeAttribute, type);
				if(value != null) {
					double doubleValue = value.doubleValue();
					if(Double.isFinite(doubleValue)) {
						min = Math.min(doubleValue, min);
						updated = true;
					}
				}
			}
		}
	}
	
	result = updated ? min : null;
}
 

import org.cytoscape.model.CyColumn; //导入依赖的package包/类
private void addVirtualColumn (CyColumn col, CyTable subTable){
	VirtualColumnInfo colInfo = col.getVirtualColumnInfo();
	CyColumn checkCol= subTable.getColumn(col.getName());
	
	if (checkCol == null)
		subTable.addVirtualColumn(col.getName(), colInfo.getSourceColumn(), colInfo.getSourceTable(), 
				colInfo.getTargetJoinKey(), col.isImmutable());

	else
		if (!checkCol.getVirtualColumnInfo().isVirtual() ||
				!checkCol.getVirtualColumnInfo().getSourceTable().equals(colInfo.getSourceTable()) ||
				!checkCol.getVirtualColumnInfo().getSourceColumn().equals(colInfo.getSourceColumn()))
			subTable.addVirtualColumn(col.getName(), colInfo.getSourceColumn(), colInfo.getSourceTable(), 
					colInfo.getTargetJoinKey(), col.isImmutable());
}
 

import org.cytoscape.model.CyColumn; //导入依赖的package包/类
public static CyColumn getOrCreateColumnByPrototype(String name, Object prototype,
                                    boolean immutable, CyTable table) {
    if (name == null) throw new NullPointerException("name cannot be null");
    if (table == null) throw new NullPointerException("table cannot be null");

    Class<?> type = (prototype == null) ? String.class : prototype.getClass();
    if (!SUPPORTED_TYPES.contains(type)) {
        type = String.class;
    }

    return getOrCreateColumn(name, type, immutable, table);
}
 

import org.cytoscape.model.CyColumn; //导入依赖的package包/类
public static CyColumn getOrCreateListColumn(String name, Class<?> type, boolean immutable, CyTable table) {
    if (name == null) throw new NullPointerException("name cannot be null");
    if (type == null) throw new NullPointerException("type cannot be null");
    if (table == null) throw new NullPointerException("table cannot be null");

    CyColumn column = table.getColumn(name);
    if (column == null) {
        table.createListColumn(name, type, immutable);
        column = table.getColumn(name);
    }
    return column;
}