Examples with Filter org.cytoscape.filter.model.Filter used on opensource projects

Example 1 with Filter

use of org.cytoscape.filter.model.Filter in project cytoscape-impl by cytoscape.

the class CyTransformerReaderImpl method readCompositeFilter.

@SuppressWarnings({ "unchecked", "rawtypes" })
private void readCompositeFilter(JsonParser parser, CompositeFilter composite) throws IOException {
    JsonToken firstToken = parser.nextToken();
    if (firstToken == JsonToken.END_OBJECT) {
        return;
    }
    if (firstToken != JsonToken.FIELD_NAME) {
        throw new IOException("Expected: " + JsonToken.FIELD_NAME + ". Got: " + firstToken);
    }
    assertEquals(FilterIO.TRANSFORMERS_FIELD, parser.getCurrentName());
    assertEquals(JsonToken.START_ARRAY, parser.nextToken());
    while (true) {
        Filter filter = (Filter) readTransformer(parser);
        if (filter == null) {
            break;
        }
        composite.append(filter);
    }
    assertEquals(JsonToken.END_ARRAY, parser.getCurrentToken());
    assertNextToken(parser, JsonToken.END_OBJECT);
}

Example 2 with Filter

use of org.cytoscape.filter.model.Filter in project cytoscape-impl by cytoscape.

the class FilterIOTest method testSubFilterTransformerRoundTrip.

@SuppressWarnings("rawtypes")
@Test
public void testSubFilterTransformerRoundTrip() throws Exception {
    ColumnFilter columnFilter = new ColumnFilter();
    columnFilter.setColumnName("MyColName");
    columnFilter.setPredicateAndCriterion(Predicate.CONTAINS, "blah");
    AdjacencyTransformer adjacency = new AdjacencyTransformer();
    adjacency.setAction(Action.REPLACE);
    adjacency.setEdgesAre(EdgesAre.INCOMING);
    adjacency.setFilterTarget(What.EDGES);
    adjacency.setOutput(What.EDGES);
    adjacency.getCompositeFilter().append(columnFilter);
    CyTransformerWriter writer = new CyTransformerWriterImpl();
    ByteArrayOutputStream stream = new ByteArrayOutputStream();
    writer.write(stream, FilterIO.createNamedTransformer("transformer1", adjacency));
    // String serialized = stream.toString("utf-8");
    TransformerManagerImpl transformerManager = new TransformerManagerImpl();
    Map<String, String> properties = Collections.emptyMap();
    transformerManager.registerFilterFactory(new ColumnFilterFactory(), properties);
    transformerManager.registerElementTransformerFactory(new AdjacencyTransformerFactory(), properties);
    CyTransformerReaderImpl reader = new CyTransformerReaderImpl();
    reader.registerTransformerManager(transformerManager, null);
    ByteArrayInputStream inputStream = new ByteArrayInputStream(stream.toByteArray());
    NamedTransformer<?, ?>[] transformers = reader.read(inputStream);
    Assert.assertNotNull(transformers);
    Assert.assertEquals(1, transformers.length);
    NamedTransformer<?, ?> namedTransformer = transformers[0];
    Assert.assertNotNull(namedTransformer);
    Assert.assertEquals("transformer1", namedTransformer.getName());
    List children = namedTransformer.getTransformers();
    Assert.assertEquals(1, children.size());
    Transformer child = (Transformer) children.get(0);
    Assert.assertNotNull(child);
    Assert.assertTrue(child instanceof AdjacencyTransformer);
    AdjacencyTransformer adjacency2 = (AdjacencyTransformer) child;
    Assert.assertEquals(adjacency.getAction(), adjacency2.getAction());
    Assert.assertEquals(adjacency.getEdgesAre(), adjacency2.getEdgesAre());
    Assert.assertEquals(adjacency.getFilterTarget(), adjacency2.getFilterTarget());
    Assert.assertEquals(adjacency.getOutput(), adjacency2.getOutput());
    CompositeFilter<?, ?> composite = adjacency2.getCompositeFilter();
    Assert.assertEquals(1, composite.getLength());
    Filter filter = composite.get(0);
    Assert.assertTrue(filter instanceof ColumnFilter);
    ColumnFilter columnFilter2 = (ColumnFilter) filter;
    Assert.assertEquals(columnFilter.getColumnName(), columnFilter2.getColumnName());
    Assert.assertEquals(columnFilter.getPredicate(), columnFilter2.getPredicate());
    Assert.assertEquals(columnFilter.getCriterion(), columnFilter2.getCriterion());
}

Example 3 with Filter

use of org.cytoscape.filter.model.Filter in project cytoscape-impl by cytoscape.

the class ColumnFilter method accepts.

@SuppressWarnings("unchecked")
@Override
public boolean accepts(CyNetwork context, CyIdentifiable element) {
    if (columnName == null || rawCriterion == null || predicate == null) {
        // This filter is incomplete.
        return false;
    }
    Class<?> tableType = getTableType();
    if (tableType != null && !tableType.isAssignableFrom(element.getClass())) {
        return false;
    }
    CyRow row = context.getRow(element);
    CyTable table = row.getTable();
    CyColumn column = table.getColumn(columnName);
    if (column == null) {
        return false;
    }
    Class<?> columnType = column.getType();
    if (columnType.equals(List.class)) {
        Class<?> listElementType = column.getListElementType();
        if (String.class.equals(listElementType)) {
            List<String> list = row.getList(columnName, String.class);
            return listMatch(anyMatch, list, item -> stringDelegate.accepts(stringCriterion, lowerCaseCriterion, item, caseSensitive));
        } else if (Number.class.isAssignableFrom(listElementType)) {
            List<Number> list = (List<Number>) row.getList(columnName, listElementType);
            return listMatch(anyMatch, list, number -> numericDelegate.accepts(lowerBound, upperBound, number));
        } else if (Boolean.class.equals(listElementType)) {
            List<Boolean> list = (List<Boolean>) row.getList(columnName, listElementType);
            if (list != null) {
                for (Boolean value : list) {
                    if (value != null && booleanCriterion.equals(value)) {
                        return true;
                    }
                }
            }
        }
    } else if (columnType.equals(String.class)) {
        String value = row.get(columnName, String.class);
        return stringDelegate.accepts(stringCriterion, lowerCaseCriterion, value, caseSensitive);
    } else if (Number.class.isAssignableFrom(columnType)) {
        Number value = row.get(columnName, (Class<Number>) columnType);
        return numericDelegate.accepts(lowerBound, upperBound, value);
    } else if (Boolean.class.equals(columnType)) {
        Boolean value = row.get(columnName, Boolean.class);
        return booleanCriterion.equals(value);
    }
    return false;
}

Example 4 with Filter

use of org.cytoscape.filter.model.Filter in project cytoscape-impl by cytoscape.

the class FilterIOTest method testNestedFilterRoundTrip.

@SuppressWarnings("rawtypes")
@Test
public void testNestedFilterRoundTrip() throws Exception {
    DegreeFilter degreeFilter = new DegreeFilter();
    degreeFilter.setCriterion(new Double[] { 0.2, 5.5 });
    degreeFilter.setEdgeType(CyEdge.Type.ANY);
    CompositeFilter<CyNetwork, CyIdentifiable> composite = new CompositeFilterImpl<CyNetwork, CyIdentifiable>(CyNetwork.class, CyIdentifiable.class);
    composite.setType(Type.ANY);
    composite.append(degreeFilter);
    CyTransformerWriter writer = new CyTransformerWriterImpl();
    ByteArrayOutputStream stream = new ByteArrayOutputStream();
    writer.write(stream, FilterIO.createNamedTransformer("filter1", composite));
    String serialized = stream.toString("utf-8");
    TransformerManagerImpl transformerManager = new TransformerManagerImpl();
    Map<String, String> properties = Collections.emptyMap();
    transformerManager.registerFilterFactory(new DegreeFilterFactory(), properties);
    transformerManager.registerFilterFactory(new CompositeFilterFactory<CyNetwork, CyIdentifiable>(CyNetwork.class, CyIdentifiable.class), properties);
    CyTransformerReaderImpl reader = new CyTransformerReaderImpl();
    reader.registerTransformerManager(transformerManager, null);
    ByteArrayInputStream inputStream = new ByteArrayInputStream(stream.toByteArray());
    NamedTransformer<?, ?>[] transformers = reader.read(inputStream);
    Assert.assertNotNull(transformers);
    Assert.assertEquals(1, transformers.length);
    NamedTransformer<?, ?> namedTransformer = transformers[0];
    Assert.assertNotNull(namedTransformer);
    Assert.assertEquals("filter1", namedTransformer.getName());
    List children = namedTransformer.getTransformers();
    Assert.assertEquals(1, children.size());
    Transformer child = (Transformer) children.get(0);
    Assert.assertNotNull(child);
    Assert.assertTrue(child instanceof CompositeFilter);
    CompositeFilter composite2 = (CompositeFilter) child;
    Assert.assertEquals(composite.getType(), composite2.getType());
    Assert.assertEquals(composite.getLength(), composite2.getLength());
    Filter filter = composite2.get(0);
    Assert.assertTrue(filter instanceof DegreeFilter);
    DegreeFilter degreeFilter2 = (DegreeFilter) filter;
    Assert.assertArrayEquals((Number[]) degreeFilter.getCriterion(), (Number[]) degreeFilter2.getCriterion());
    Assert.assertEquals(degreeFilter.getEdgeType(), degreeFilter2.getEdgeType());
}