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

Example 6 with CompositeFilter

use of org.cytoscape.filter.model.CompositeFilter 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 7 with CompositeFilter

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

the class CyTransformerWriterImpl method write.

private void write(JsonGenerator generator, Transformer<?, ?> transformer) throws IOException {
    generator.writeStartObject();
    try {
        generator.writeStringField(FilterIO.ID_FIELD, transformer.getId());
        generator.writeObjectFieldStart(FilterIO.PARAMETERS_FIELD);
        try {
            Map<String, Object> parameters = FilterIO.getParameters(transformer);
            for (Entry<String, Object> entry : parameters.entrySet()) {
                String name = entry.getKey();
                Object value = entry.getValue();
                writeField(generator, name, value);
            }
        } catch (IntrospectionException e) {
            throw new IOException(e);
        } finally {
            generator.writeEndObject();
        }
        if (transformer instanceof CompositeFilter || transformer instanceof SubFilterTransformer) {
            CompositeFilter<?, ?> composite;
            if (transformer instanceof SubFilterTransformer)
                composite = ((SubFilterTransformer<?, ?>) transformer).getCompositeFilter();
            else
                composite = (CompositeFilter<?, ?>) transformer;
            generator.writeArrayFieldStart(FilterIO.TRANSFORMERS_FIELD);
            try {
                for (int i = 0; i < composite.getLength(); i++) {
                    write(generator, composite.get(i));
                }
            } finally {
                generator.writeEndArray();
            }
        }
    } finally {
        generator.writeEndObject();
    }
}

Example 8 with CompositeFilter

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

the class FilterPanelController method createView.

@Override
public JComponent createView(FilterPanel parent, Transformer<CyNetwork, CyIdentifiable> filter, int depth) {
    // CompositeFilterImpl needs a CompositeFilterPanel but the top is blank so view will be null
    JComponent view = transformerViewManager.createView(filter);
    if (view instanceof InteractivityChangedListener) {
        ((InteractivityChangedListener) view).handleInteractivityChanged(isInteractive);
    }
    if (filter instanceof CompositeFilter) {
        String addButtonTT = transformerViewManager.getAddButtonTooltip(filter);
        CompositeFilterController controller = CompositeFilterController.createFor(view, addButtonTT);
        return new CompositeFilterPanel<FilterPanel>(parent, this, controller, (CompositeFilter<CyNetwork, CyIdentifiable>) filter, depth);
    }
    if (view == null)
        throw new IllegalArgumentException("view could not be created for: " + filter.getId());
    return view;
}

Example 9 with CompositeFilter

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

the class FilterIOTest method testLoadOldTopologyFilter.

/**
 * The topology filter was made a composite filter in 3.3. Older versions of cytoscape
 * will export a topology filter without the "transformers" field that is part of
 * composite filters. The filter json parser was enhanced to support this.
 */
@SuppressWarnings("rawtypes")
@Test
public void testLoadOldTopologyFilter() throws IOException {
    TransformerManagerImpl transformerManager = new TransformerManagerImpl();
    Map<String, String> properties = Collections.emptyMap();
    transformerManager.registerFilterFactory(new CompositeFilterFactory<CyNetwork, CyIdentifiable>(CyNetwork.class, CyIdentifiable.class), properties);
    transformerManager.registerFilterFactory(new TopologyFilterFactory(), properties);
    transformerManager.registerFilterFactory(new ColumnFilterFactory(), properties);
    String path = "./src/test/resources/testData/filter/topology-filter-3.2.json";
    byte[] encoded = Files.readAllBytes(Paths.get(path));
    // String contents = new String(encoded);
    // System.out.println(contents);
    CyTransformerReaderImpl reader = new CyTransformerReaderImpl();
    reader.registerTransformerManager(transformerManager, null);
    ByteArrayInputStream inputStream = new ByteArrayInputStream(encoded);
    NamedTransformer<?, ?>[] transformers = reader.read(inputStream);
    Assert.assertNotNull(transformers);
    Assert.assertEquals(1, transformers.length);
    NamedTransformer<?, ?> namedTransformer = transformers[0];
    Assert.assertNotNull(namedTransformer);
    Assert.assertEquals("Default filter", 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 composite = (CompositeFilter) child;
    Assert.assertEquals(2, composite.getLength());
    Assert.assertTrue(composite.get(0) instanceof TopologyFilter);
    Assert.assertTrue(composite.get(1) instanceof ColumnFilter);
    TopologyFilter topology = (TopologyFilter) composite.get(0);
    Assert.assertEquals(0, topology.getLength());
    Assert.assertEquals(Integer.valueOf(4), topology.getDistance());
    Assert.assertEquals(Integer.valueOf(5), topology.getThreshold());
    ColumnFilter column = (ColumnFilter) composite.get(1);
    Assert.assertEquals("name", column.getColumnName());
}

Example 10 with CompositeFilter

use of org.cytoscape.filter.model.CompositeFilter 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());
}