Java CyTable.getColumn方法代码示例

import org.cytoscape.model.CyTable; //导入方法依赖的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
@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 checkColumn(CyTable table,
                         String name,
                         Class<?> type) {
    CyColumn column = table.getColumn(name);
    if (column == null) {
        table.createColumn(name, type, false);
    }
}
 

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
@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.CyTable; //导入方法依赖的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.CyTable; //导入方法依赖的package包/类
private String getColumnName() {
	CyTable table = network.getDefaultNodeTable();
	final String originalName = algorithm.getColumnName();
	
	String name = originalName;
	int suffix = 2;
	while(table.getColumn(name) != null && table.getColumn(name).isImmutable()) {
		name = originalName + "_" + (suffix++);
	}
	return name;
}
 

import org.cytoscape.model.CyTable; //导入方法依赖的package包/类
private void createNodeAttributeIfNotExists(String colName)
{
	CyTable table = myNet.getDefaultNodeTable();
	if (table.getColumn(colName) == null)
	{
		table.createColumn(colName, String.class, true);
	}
}
 

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 Double minScoreThreshold() {
	String proteinGraphName = proteinGraph.getSelectedItem().toString();
	if (proteinGraphName.equals(" - Select Network - ")) {
		JOptionPane.showMessageDialog(this, "Please select a protein graph under 'Search'");
	} else {
		CyNetwork nw = null;
		for (CyNetwork network: CyActivator.networkManager.getNetworkSet()) {
			if (network.getRow(network).get(CyNetwork.NAME, String.class).equals(proteinGraphName)) {
				nw = network; 
				break;
			}
		}
		
		CyTable nodeTable = nw.getDefaultEdgeTable();
		if(nodeTable.getColumn("weight") != null) {
			// Network has weight column
			CyColumn column = nodeTable.getColumn("weight");
			List<Double> values = column.getValues(Double.class);
			Double avgWeight = 0.0;
			for (Double value : values) {
				avgWeight += value;
			}
			avgWeight = avgWeight / values.size();
			return avgWeight * Integer.valueOf(minSize.getText()) / 10;
		} else {
			// No weight column
			return 0.5;
		}
		
	}
	return -1.0;
}
 

import org.cytoscape.model.CyTable; //导入方法依赖的package包/类
/**
 * Return zero or more Ensembl gene ids from the specified Ensembl gene id column for the specified node.
 *
 * @param node node
 * @param network network
 * @param ensemblGeneIdColumn Ensembl gene id column
 * @return zero or more Ensembl gene ids from the specified Ensembl gene id column for the specified node
 */
static Iterable<String> ensemblGeneIds(final CyNode node, final CyNetwork network, final String ensemblGeneIdColumn)
{
    CyTable table = network.getDefaultNodeTable();
    CyRow row = table.getRow(node.getSUID());
    CyColumn column = table.getColumn(ensemblGeneIdColumn);

    if (column != null)
    {
        Class<?> columnClass = column.getType();
        if (String.class.equals(columnClass))
        {
            String ensemblGeneId = row.get(ensemblGeneIdColumn, String.class);
            if (ensemblGeneId != null)
            {
                return ImmutableList.of(ensemblGeneId);
            }
        }
        else if (columnClass.equals(List.class))
        {
            Class<?> listClass = column.getListElementType();
            if (String.class.equals(listClass))
            {
                return row.getList(ensemblGeneIdColumn, String.class);
            }
        }
    }
    return Collections.<String>emptyList();
}
 

import org.cytoscape.model.CyTable; //导入方法依赖的package包/类
/**
 * Add the specified count in the specified column name to the specified node.
 *
 * @param node node
 * @param network network
 * @param columnName column name
 * @param count count
 */
static void addCount(final CyNode node, final CyNetwork network, final String columnName, final int count)
{
    CyTable table = network.getDefaultNodeTable();
    CyRow row = table.getRow(node.getSUID());
    if (table.getColumn(columnName) == null)
    {
        table.createColumn(columnName, Integer.class, false);
    }
    // todo:  or add to current value
    row.set(columnName, count);
}