Examples with CyTable org.cytoscape.model.CyTable used on opensource projects

Example 31 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class InvertSelectedNodesTaskTest method testRun.

@Test
public void testRun() throws Exception {
    final CyTable nodeTable = mock(CyTable.class);
    when(net.getDefaultNodeTable()).thenReturn(nodeTable);
    UndoSupport undoSupport = mock(UndoSupport.class);
    // more setup
    when(r3.get("selected", Boolean.class)).thenReturn(false);
    when(r4.get("selected", Boolean.class)).thenReturn(true);
    final CyEventHelper eventHelper = mock(CyEventHelper.class);
    // run the task
    Task t = new InvertSelectedNodesTask(undoSupport, net, networkViewManager, eventHelper);
    t.run(tm);
    // check that the expected rows were set
    verify(r3, times(1)).set("selected", true);
    verify(r4, times(1)).set("selected", false);
}

Example 32 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class InvertSelectedEdgesTaskTest method testRun.

@Test
public void testRun() throws Exception {
    final CyTable edgeTable = mock(CyTable.class);
    when(net.getDefaultEdgeTable()).thenReturn(edgeTable);
    UndoSupport undoSupport = mock(UndoSupport.class);
    // more setup
    when(r1.get("selected", Boolean.class)).thenReturn(false);
    when(r2.get("selected", Boolean.class)).thenReturn(true);
    // run the task
    Task t = new InvertSelectedEdgesTask(undoSupport, net, networkViewManager, eventHelper);
    t.run(tm);
    // check that the expected rows were set
    verify(r1, times(1)).set("selected", true);
    verify(r2, times(1)).set("selected", false);
}

Example 33 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class FilterMainPanel method getCyAttributesList.

/**
 * Get the list of attribute names for either "node" or "edge". The attribute names will be
 * prefixed either with "node." or "edge.". Those attributes whose data type is neither
 * "String" nor "numeric" will be excluded
 */
private List<String> getCyAttributesList(final CyNetwork network, final String pType) {
    final Vector<String> attributeList = new Vector<String>();
    CyTable table = null;
    if (pType.equalsIgnoreCase("node") && network.getNodeCount() > 0) {
        table = network.getDefaultNodeTable();
    } else if (pType.equalsIgnoreCase("edge") && network.getEdgeCount() > 0) {
        table = network.getDefaultEdgeTable();
    }
    if (table != null) {
        final Collection<CyColumn> columns = new HashSet<CyColumn>(table.getColumns());
        for (final CyColumn column : columns) {
            if (column != null) {
                // Show all attributes, with type of String or Number
                final Class<?> type = column.getType();
                // only show user visible attributes,with type = Number/String/List
                if (type == Integer.class || type == Double.class || type == Boolean.class || type == String.class || type == List.class) {
                    attributeList.add(pType + "." + column.getName());
                }
            }
        }
        // Alphabetical sort
        final Collator collator = Collator.getInstance(Locale.getDefault());
        Collections.sort(attributeList, collator);
    }
    return attributeList;
}

Example 34 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class EnhancedSearchIndex method createDocument.

/**
 * Make a Document object with an un-indexed identifier field and indexed
 * attribute fields
 */
private static Document createDocument(CyNetwork network, CyIdentifiable graphObject, String graphObjectType, long index) {
    Document doc = new Document();
    String identifier = Long.toString(index);
    doc.add(new Field(EnhancedSearch.INDEX_FIELD, identifier, Field.Store.YES, Field.Index.ANALYZED));
    doc.add(new Field(EnhancedSearch.TYPE_FIELD, graphObjectType, Field.Store.YES, Field.Index.ANALYZED));
    CyRow cyRow = network.getRow(graphObject);
    CyTable cyDataTable = cyRow.getTable();
    Set<String> attributeNames = CyTableUtil.getColumnNames(cyDataTable);
    for (final String attrName : attributeNames) {
        // Handle whitespace characters and case in attribute names
        String attrIndexingName = EnhancedSearchUtils.replaceWhitespace(attrName);
        attrIndexingName = attrIndexingName.toLowerCase();
        // Determine type
        Class<?> valueType = cyDataTable.getColumn(attrName).getType();
        if (valueType == String.class) {
            String attrValue = network.getRow(graphObject).get(attrName, String.class);
            if (attrValue == null) {
                continue;
            }
            doc.add(new Field(attrIndexingName, attrValue, Field.Store.YES, Field.Index.ANALYZED));
        } else if (valueType == Integer.class) {
            if (network.getRow(graphObject).get(attrName, Integer.class) == null) {
                continue;
            }
            int attrValue = network.getRow(graphObject).get(attrName, Integer.class);
            NumericField field = new NumericField(attrIndexingName);
            field.setIntValue(attrValue);
            doc.add(field);
        } else if (valueType == Double.class) {
            if (network.getRow(graphObject).get(attrName, Double.class) == null) {
                continue;
            }
            double attrValue = network.getRow(graphObject).get(attrName, Double.class);
            NumericField field = new NumericField(attrIndexingName);
            field.setDoubleValue(attrValue);
            doc.add(field);
        } else if (valueType == Boolean.class) {
            if (network.getRow(graphObject).get(attrName, Boolean.class) != null) {
                String attrValue = network.getRow(graphObject).get(attrName, Boolean.class).toString();
                doc.add(new Field(attrIndexingName, attrValue, Field.Store.YES, Field.Index.ANALYZED));
            }
        } else if (valueType == List.class) {
            List attrValueList = network.getRow(graphObject).get(attrName, List.class);
            if (attrValueList != null) {
                for (int j = 0; j < attrValueList.size(); j++) {
                    String attrValue = attrValueList.get(j).toString();
                    doc.add(new Field(attrIndexingName, attrValue, Field.Store.YES, Field.Index.ANALYZED));
                }
            }
        }
    }
    return doc;
}

Example 35 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class AttributeFields method initFields.

/**
 * Initialize this object with attribute fields names and their type.
 * Eventually, fields[i] will hold attribute field name and types[i] will hold its type.
 * fields[] and types[] contain both node and edge attributes.
 * ID (INDEX_FIELD) is treated as another attribute of type string.
 * There are probably better ways to do this, but there you go :)
 */
private void initFields(final CyNetwork network) {
    CyTable nodeCyDataTable = network.getDefaultNodeTable();
    for (final CyColumn column : nodeCyDataTable.getColumns()) columnTypeMap.put(EnhancedSearchUtils.replaceWhitespace(column.getName()).toLowerCase(), column.getType());
    CyTable edgeCyDataTable = network.getDefaultEdgeTable();
    for (final CyColumn column : edgeCyDataTable.getColumns()) columnTypeMap.put(EnhancedSearchUtils.replaceWhitespace(column.getName()).toLowerCase(), column.getType());
}