Java CyTable.createListColumn方法代码示例

import org.cytoscape.model.CyTable; //导入方法依赖的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; //导入方法依赖的package包/类
public static void addProperties(Long suid, CyTable table,Map<String,Object> props){
	
	for(Entry<String,Object> obj : props.entrySet()){
		if(table.getColumn(obj.getKey()) == null){
			if(obj.getValue().getClass() == ArrayList.class){
				table.createListColumn(obj.getKey(), CyUtils.getArrayListType((ArrayList)obj.getValue()), false);
			} else {
				table.createColumn(obj.getKey(), obj.getValue().getClass(), false);
			}
		}

		CyUtils.addValueToTable(suid,obj.getKey(),obj.getValue(),table);

	}
	
}
 

import org.cytoscape.model.CyTable; //导入方法依赖的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.CyTable; //导入方法依赖的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.CyTable; //导入方法依赖的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;
}
 

import org.cytoscape.model.CyTable; //导入方法依赖的package包/类
private static String detectImmutableProblem(String key, CyTable table, Class<?> valueClass, Class<?> colClass){
	
	CyColumn col = table.getColumn(key);
	
	String newKey = key; // trying to make this less confusing with the extra variables

	if(col.isImmutable() && !matchingValues(valueClass,colClass)){
		newKey = key + "_cannot_change_original";
		
		// we had this problem before and fixed it, now use the fixed column instead of the previous one!
		if(table.getColumn(newKey) == null){
			if(table.getColumn(key).getListElementType() != null){
				table.createListColumn(newKey,table.getColumn(key).getListElementType() , false);
				
			} else {
				table.createColumn(newKey, table.getColumn(key).getType(), false);
			}
			
			// populate the new column!
			List<CyRow> rows = table.getAllRows();
			for(CyRow row : rows){
				if(row.isSet(key)){
					table.getRow(row.get("SUID", Long.class)).set(newKey, row.getRaw(key));
				}
			}
			
		}
	}
	
	return newKey;
	
}
 

import org.cytoscape.model.CyTable; //导入方法依赖的package包/类
private void addEdgeAttributes(final CyEdge element, final String column, final String entry)
{
    final CyTable table = network.getRow(element).getTable();
    if (table.getColumn(column) == null)
        table.createListColumn(column, String.class, false);
    List<String> value = Arrays.asList(entry.split(";"));
    network.getRow(element).set(column, value);
}
 

import org.cytoscape.model.CyTable; //导入方法依赖的package包/类
private static void createListColumn(CyTable table, String name, Class<?> type) {
	if(table.getColumn(name) == null)
		table.createListColumn(name, type, true);
}
 

import org.cytoscape.model.CyTable; //导入方法依赖的package包/类
private void copyColumn(CyColumn col, CyTable subTable) {
	if (List.class.isAssignableFrom(col.getType()))
		subTable.createListColumn(col.getName(), col.getListElementType(), false);
	else
		subTable.createColumn(col.getName(), col.getType(), false);	
}
 

import org.cytoscape.model.CyTable; //导入方法依赖的package包/类
@Override
protected void setNodeAttribute(CyNode node, String colName, Object value)
{
	// Turn URIs into strings
	if (value instanceof RdfNode) { value = value.toString(); }
	
	// Turn Float into Double. Float not accepted by Cytoscape as column type.
	if (value instanceof Float) { value = ((Number)value).doubleValue(); }
	
	CyTable table = myNet.getDefaultNodeTable();
	if ("label".equals(colName))
	{
		// legacy hack - where label is used in sparql, map to attribute "name"
		table.getRow(node.getSUID()).set("name", "" + value);
	}
	else
	{
		// if the column doesn't yet exist, crate it first
		if (table.getColumn(colName) == null)
		{
			if (colName.endsWith("_list"))
			{
				table.createListColumn(colName, String.class, true);
			}
			else
			{
				Class<?> valueClass = value.getClass();
				//NB: Float not accepted by Cytoscape, must be Double.
				if (valueClass == Double.class ||
					valueClass == Integer.class ||
					valueClass == Boolean.class ||
					valueClass == Long.class ||
					valueClass == String.class)
				{
					table.createColumn(colName, valueClass, true);						
				}
				else
				{
					throw new IllegalStateException ("Unable to handle attribute values of class " + valueClass);
				}
			}
		}
		
		
		try
		{
			if (colName.endsWith("_list"))
			{
				List<String> data = table.getRow(node.getSUID()).getList(colName, String.class);
				if (data == null)
				{
					data = new ArrayList<String>();
					data.add(StringUtils.safeToString(value));
					table.getRow(node.getSUID()).set(colName, data);
				}
				else
				{
					data.add(StringUtils.safeToString(value));
				}
			}
			else
			{
				// TODO: check for type mismatches?
				table.getRow(node.getSUID()).set(colName, value);
			}
		}
		catch (IllegalStateException e)
		{
			// class cast problem...
			// TODO...
			e.printStackTrace();
		}
	}
}
 

import org.cytoscape.model.CyTable; //导入方法依赖的package包/类
public static void addValueToTable(Long suid, String key, Object value, CyTable table) {				
	
	Class<?> valueClass = value.getClass();
	
	String fixedKey = detectImmutableProblem(key, table, valueClass, table.getColumn(key).getType());
	
	Class<?> colClass = table.getColumn(fixedKey).getType();
	Class<?> colTypeClass = table.getColumn(fixedKey).getListElementType();
	
	if(valueClass.equals(colClass)){
		table.getRow(suid).set(fixedKey, value);
		return;
	}
	
	if(colClass.equals(Long.class) && valueClass.equals(Integer.class)){
		table.getRow(suid).set(fixedKey, Long.valueOf(((Integer)value).longValue()));
		return;
	}
	
	// both lists!
	if(valueClass.equals(ArrayList.class) && colClass.equals(List.class)){
		if(colTypeClass.equals(getArrayListType(value))){
			table.getRow(suid).set(fixedKey, value);
		} else {
			System.out.println("same property but different value types in the arrays!!");
			// why is here no else? because I don't want to start casting around! Neo4j allows properties to be different between nodes
			// Cytoscape does not. 
		}
		
	} else { // one is not a list!!
		if(valueClass.equals(ArrayList.class)){ // need to change the colClass
			
			// use the data from the original column!
			Map<Long,Object> currData = new HashMap<Long,Object>();
			
			List<CyRow> rows = table.getAllRows();
			
			for(CyRow row : rows){
				if(row.isSet(fixedKey)){
					currData.put(row.get("SUID", Long.class),row.getRaw(fixedKey));
				}
			}
			// 
			
			table.deleteColumn(fixedKey);
			
			table.createListColumn(fixedKey, getArrayListType(value), false);
			
			for(Entry<Long,Object> e : currData.entrySet()){
				ArrayList fixedOldValue = new ArrayList();
				fixedOldValue.add(e.getValue());
				
				table.getRow(e.getKey()).set(fixedKey, fixedOldValue);
			}
		}
		
		if(colClass.equals(List.class)){
			ArrayList newValue = new ArrayList();
			newValue.add(value);
			table.getRow(suid).set(fixedKey, newValue);
		}
		
	}
}