Java CyRow.get方法代码示例

import org.cytoscape.model.CyRow; //导入方法依赖的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.CyRow; //导入方法依赖的package包/类
public static Set<CyNode> getNodesWithValue(
		final CyNetwork net, final CyTable table,
		final String colname, final Object value)
{
	final Collection<CyRow> matchingRows = table.getMatchingRows(colname, value);
	final Set<CyNode> nodes = new HashSet<CyNode>();
	final String primaryKeyColname = table.getPrimaryKey().getName();
	for (final CyRow row : matchingRows)
	{
		final Long nodeId = row.get(primaryKeyColname, Long.class);
		if (nodeId == null)
			continue;
		final CyNode node = net.getNode(nodeId);
		if (node == null)
			continue;
		nodes.add(node);
	}
	return nodes;
}
 

import org.cytoscape.model.CyRow; //导入方法依赖的package包/类
public static Set<CyEdge> getEdgeWithValue(
		final CyNetwork net, final CyTable table,
		final String colname, final Object value)
{
	final Collection<CyRow> matchingRows = table.getMatchingRows(colname, value);
	final Set<CyEdge> edges = new HashSet<CyEdge>();
	final String primaryKeyColname = table.getPrimaryKey().getName();
	for (final CyRow row : matchingRows)
	{
		final Long edgeId = row.get(primaryKeyColname, Long.class);
		if (edgeId == null)
			continue;
		final CyEdge edge = net.getEdge(edgeId);
		if (edge == null)
			continue;
		edges.add(edge);
	}
	return edges;
}
 

import org.cytoscape.model.CyRow; //导入方法依赖的package包/类
/**
 * Gets the index of the data series row corresponding to a given CyRow under this mapping
 * @param row
 * @return -1 if there is no row for this CyRow, or the index of the associated row.
 * @throws DataSeriesException if the CyRow contains an invalid ID.
 */
public int getDataSeriesRow(CyRow row)
{
	Integer rowID = row.get(columnName, DataSeriesMappingManager.MAPPING_COLUMN_CLASS);
	if(rowID == null)
	{
		return -1;
	}
	int tsRow = dataSeries.idToRow(rowID);
	if(tsRow < 0)
	{
		throw new DataSeriesException("Requesting non existent row id (" + tsRow + ") from Data Series " + dataSeries.getName());			
	}
	return tsRow;
}
 

import org.cytoscape.model.CyRow; //导入方法依赖的package包/类
LabelFunction getLabelFunction(Long[] nodeMappings,
                               String nameColumn) {
    return i -> {
        Long suid = nodeMappings[i];
        CyRow row = nodeTable.getRow(suid);
        return row.get(nameColumn, String.class);
    };
}
 

import org.cytoscape.model.CyRow; //导入方法依赖的package包/类
private static <T> void safeGet(CyRow row, String column, Class<T> type, Consumer<T> consumer) {
	try {
		T value = row.get(column, type);
		if(value == null) {
			System.err.println("AutoAnnotate.importModel - Can't find display option for " + column);
		}
		else {
			consumer.accept(value);
		}
	} catch(ClassCastException e) { 
		System.err.println("AutoAnnotate.importModel - Error loading display options for " + column);
		e.printStackTrace();
	}
}
 

import org.cytoscape.model.CyRow; //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.CyRow; //导入方法依赖的package包/类
@Override
public String makeLabel(CyNetwork network, Collection<CyNode> nodes, String labelColumn) {
	CyNode node = nodes.stream().findFirst().get();
	CyRow row = network.getRow(node);
	String label = row.get(CyNetwork.NAME, String.class);
	return label;
}
 

import org.cytoscape.model.CyRow; //导入方法依赖的package包/类
public List<String> getSelectedElements() {
    List<CyNode> nodes = CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true);
    List<CyEdge> edges = CyTableUtil.getEdgesInState(network, CyNetwork.SELECTED, true);
    if(nodes.size() == 1 && edges.isEmpty()) {
        CyNode node = nodes.get(0);
        String nodeGOTerm = network.getRow(node).get(GOTermColumn, String.class);
        
        if (Unknown.equals(nodeGOTerm) || Unnanotated.equals(nodeGOTerm)) {
           return null;
        }
        
        return Arrays.asList(network.getRow(node).get(CyNetwork.NAME, String.class));
    } 
    else if (nodes.isEmpty() && edges.size() == 1) {
        CyEdge edge = edges.get(0);
        CyRow sourceRow = network.getRow(edge.getSource());
        CyRow targetRow = network.getRow(edge.getTarget());
        String sourceGOTerm = sourceRow.get(GOTermColumn, String.class);
        String targetGOTerm = targetRow.get(GOTermColumn, String.class);
        
        if (Unknown.equals(sourceGOTerm) || Unnanotated.equals(sourceGOTerm)
                || Unknown.equals(targetGOTerm) || Unnanotated.equals(targetGOTerm)) {
           return null;
        }
        
        return Arrays.asList(sourceRow.get(CyNetwork.NAME, String.class), targetRow.get(CyNetwork.NAME, String.class));
    }
    return null;
}
 

import org.cytoscape.model.CyRow; //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.CyRow; //导入方法依赖的package包/类
/**
 * Initialize group index.
 */
private void initGroupIndex(CyNetwork network, CyTable nodeTable) {
    groupIndex = new HashMap<String, CyGroup>();
    Set<CyGroup> groups = groupManager.getGroupSet(network);
    
    for (CyGroup group : groups) {
    	long SUID = group.getGroupNode().getSUID();
    	CyRow row = nodeTable.getRow(SUID);
    	
    	String groupName = row.get(CyNetwork.NAME, String.class);
    	groupIndex.put(groupName, group);
    }
}
 

import org.cytoscape.model.CyRow; //导入方法依赖的package包/类
private void addIHOPLinks(CyNetwork network, CyNode node, StringBuffer buf) {
	CyRow row = network.getRow(node,CyNetwork.HIDDEN_ATTRS);
	String ihopLinks = row.get(BIOPAX_IHOP_LINKS, String.class);
	if (ihopLinks != null) {
		buf.append("<ul>");
		buf.append(ihopLinks);
		buf.append("</ul>");
	}
}
 

import org.cytoscape.model.CyRow; //导入方法依赖的package包/类
@Override
public void run(TaskMonitor tm) throws Exception {
	CyNetwork network = targetNetwork.getSelectedValue();
	CyTable targetTable = mappingManager.getMappingTable(network, targetClass.getSelectedValue().getTargetClass());
	
	//Create the actual mapping
	CyColumn mappingColumn = null;
	if(createNewColumn)
	{
		targetTable.createColumn(newColumnName, DataSeriesMappingManager.MAPPING_COLUMN_CLASS, false);
		mappingColumn = targetTable.getColumn(newColumnName);
	}
	else
	{
		mappingColumn = targetTable.getColumn(existingColumnForMapping.getSelectedValue());
	}
	
	if(mappingColumn == null)
	{
		throw new DataSeriesException("Could not get/create the column for mapping");
	}
	
	if(!mappingColumn.getType().equals(DataSeriesMappingManager.MAPPING_COLUMN_CLASS))
	{
		throw new DataSeriesException("The mapping column is of wrong type (should be " + DataSeriesMappingManager.MAPPING_COLUMN_CLASS.getSimpleName() + ", is" + mappingColumn.getType().getSimpleName() + ")");
	}
	
	mappingManager.mapDataSeriesRowsToTableColumn(targetNetwork.getSelectedValue(), targetClass.getSelectedValue().targetClass, mappingColumn.getName(), dataSeries.getSelectedValue());
	
	//Fill the mapping column 
	if(mapByRowNames)
	{
		CyColumn rowNamesColumn = targetTable.getColumn(mapRowNamesWithColumn.getSelectedValue());
		if(rowNamesColumn == null || !rowNamesColumn.getType().equals(String.class))
		{
			throw new DataSeriesException("The column for row names matches (" + mapRowNamesWithColumn.getSelectedValue() + ") has to exist and be of type string.");
		}
		
		int mapped = 0;
		int notMapped = 0;
		int empty = 0;
		for(CyRow row : targetTable.getAllRows())
		{
			String rowNameInData = row.get(mapRowNamesWithColumn.getSelectedValue(), String.class);
			if(rowNameInData == null || rowNameInData.isEmpty())
			{
				row.set(mappingColumn.getName(), null);					
				empty++;
			}
			else
			{
				List<String> rowNames = dataSeries.getSelectedValue().getRowNames();
				int rowIndex = rowNames.indexOf(rowNameInData);
				if(rowIndex < 0)
				{
					row.set(mappingColumn.getName(), null);					
					notMapped++;
				}
				else
				{
					int rowID = dataSeries.getSelectedValue().getRowID(rowIndex);
					if (rowNames.lastIndexOf(rowNameInData) != rowIndex)
					{
						userLogger.warn("The data series '" + dataSeries.getSelectedValue().getName() + "' contains multiple rows with name '" +  rowNameInData + "'. Mapping the node '" + rowNameInData + "' to row ID " + rowID); 
					}
					row.set(mappingColumn.getName(), rowID);						
					mapped++;
				}
			}				
		}
		
		userLogger.info("Mapped " + mapped + " rows to data series " + dataSeries.getSelectedValue().getName() + ", " + notMapped + " rows could not be mapped, " + empty + " rows were empty.");			
	}
}
 

import org.cytoscape.model.CyRow; //导入方法依赖的package包/类
@Override
	public CyMenuItem createMenuItem(CyNetworkView netView,
			View<CyNode> nodeView) 
	{		
		JMenu submenu = new JMenu ("SPARQL");
		
		MarrsProject project = projectMgr.getProject();
		if (project != null) 
		{				
			CyTable tab = netView.getModel().getDefaultNodeTable();
			CyNode node = nodeView.getModel();
			CyRow row = tab.getRow(node.getSUID());
			
			for (int i = 0; i < project.getRowCount(); ++i)
			{
				MarrsQuery q = project.getRow(i);
				if (q.isContextQuery())
				{
					Map<String, String> queryContext = q.getContext();
					
					boolean nodeMatchesContext = true;
					
					for (String key : queryContext.keySet())
					{
						String expectedValue = queryContext.get(key);
						String actualValue = row.get(key, String.class);
						
						if (!expectedValue.equals(actualValue))
						{
							nodeMatchesContext = false;
						}
					}
					
					if (nodeMatchesContext)
					{
						submenu.add(new QueryAction(q, node, row.get("id", String.class)));
					}
				}
			}							
		}
		
//		JMenuItem menuItem = new JMenuItem("Node View Context Menu Item");
//		menuItem.addActionListener(this);
		CyMenuItem cyMenuItem = new CyMenuItem(submenu, 0);
		return cyMenuItem;
	}
 

import org.cytoscape.model.CyRow; //导入方法依赖的package包/类
/**
 * Shows details about BioPAX Entities 
 * that were mapped to the selected nodes.
 * 
 * @param network
 * @param nodes
 */
public void updateNodeDetails(CyNetwork network, Collection<CyNode> nodes) {
	textPane.setText(""); //clear
	StringBuffer buf = new StringBuffer("<html><body>");
	buf.append("<dl>");
	for (CyNode selected : nodes) {			
		CyRow row = network.getRow(selected);
		// name
		String s = row.get(CyNetwork.NAME, String.class);
		buf.append("<dt><strong>").append(s).append("</strong>");
		// type (to the text buffer)
		String type = row.get(BioPaxUtil.BIOPAX_ENTITY_TYPE, String.class);
		if (type != null) {
			buf.append(" (BioPAX: <em>").append(type).append("</em>)");
		}
		buf.append("</dt>").append("<dd>").append("<dl>");
		// organism
		s = row.get("entityReference/organism/displayName", String.class);
		if(s == null)
			s = row.get("organism/displayName", String.class);
		if (s != null) {
			buf.append("<dt>").append("Organism").append("</dt>")
			.append("<dd>").append(s).append("</dd>");
		}        
		// cellular location
		List<?> clTerms = row.getList("cellularLocation/term", String.class); //list
		if (clTerms != null && !clTerms.isEmpty()) {
			buf.append("<dt>").append("Cellular Location").append("</dt>")
			.append("<dd>").append(clTerms.toString().replaceAll("\\[|\\]", "")).append("</dd>");
		}
		
		// chemical modification
		addAttributeList(network, selected, null, BIOPAX_CHEMICAL_MODIFICATIONS_LIST, "Chemical Modifications:", buf);
		// data source
		addAttributeList(network, selected, null, "dataSource", "Data sources:", buf);        		
		// links
		addLinks(network, selected, buf);
		buf.append("</dl>");
		buf.append("</dd><hr/>");			
	}
	
	buf.append("</dl>");
	buf.append("</body></html>");
	
	textPane.setText(buf.toString());
	textPane.setCaretPosition(0);
   }