Examples with CyTransformerWriter org.cytoscape.io.write.CyTransformerWriter used on opensource projects

Example 1 with CyTransformerWriter

use of org.cytoscape.io.write.CyTransformerWriter in project cytoscape-impl by cytoscape.

the class FilterIO method writeFilters.

public void writeFilters(File file, NamedTransformer<CyNetwork, CyIdentifiable>[] namedTransformers) throws IOException {
    BufferedOutputStream stream = new BufferedOutputStream(new FileOutputStream(file));
    CyTransformerWriter writer = serviceRegistrar.getService(CyTransformerWriter.class);
    writer.write(stream, namedTransformers);
    stream.close();
}

Example 2 with CyTransformerWriter

use of org.cytoscape.io.write.CyTransformerWriter in project cytoscape-impl by cytoscape.

the class FilterIOTest method testSerializationRoundTrip.

@Test
public void testSerializationRoundTrip() throws Exception {
    DegreeFilter degreeFilter = new DegreeFilter();
    degreeFilter.setCriterion(new Double[] { 0.2, 5.5 });
    degreeFilter.setEdgeType(CyEdge.Type.ANY);
    DummyFilter dummyFilter = new DummyFilter();
    CyTransformerWriter writer = new CyTransformerWriterImpl();
    ByteArrayOutputStream stream = new ByteArrayOutputStream();
    writer.write(stream, FilterIO.createNamedTransformer("filter1", degreeFilter), FilterIO.createNamedTransformer("filter2", dummyFilter));
    String serialized = stream.toString("utf-8");
    TransformerManagerImpl transformerManager = new TransformerManagerImpl();
    Map<String, String> properties = Collections.emptyMap();
    transformerManager.registerFilterFactory(new DegreeFilterFactory(), properties);
    transformerManager.registerFilterFactory(new DummyFilterFactory(), properties);
    CyTransformerReaderImpl reader = new CyTransformerReaderImpl();
    reader.registerTransformerManager(transformerManager, null);
    ByteArrayInputStream inputStream = new ByteArrayInputStream(stream.toByteArray());
    NamedTransformer<?, ?>[] transformers = reader.read(inputStream);
    ByteArrayOutputStream stream2 = new ByteArrayOutputStream();
    writer.write(stream2, transformers);
    String serialized2 = stream2.toString("utf-8");
    Assert.assertEquals(serialized, serialized2);
}

Example 3 with CyTransformerWriter

use of org.cytoscape.io.write.CyTransformerWriter 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 4 with CyTransformerWriter

use of org.cytoscape.io.write.CyTransformerWriter 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());
}