Examples with VisualStyle org.cytoscape.view.vizmap.VisualStyle used on opensource projects

Example 51 with VisualStyle

use of org.cytoscape.view.vizmap.VisualStyle in project EnrichmentMapApp by BaderLab.

the class ApplyEMStyleTask method getVisualStyle.

private VisualStyle getVisualStyle(EnrichmentMap map) {
    String vsName = EMStyleBuilder.getStyleName(map);
    VisualStyle vs = getExistingVisualStyle(vsName);
    if (vs == null) {
        vs = visualStyleFactory.createVisualStyle(vsName);
        visualMappingManager.addVisualStyle(vs);
    }
    return vs;
}

Example 52 with VisualStyle

use of org.cytoscape.view.vizmap.VisualStyle in project cytoscape-impl by cytoscape.

the class VisualStyleSerializerTest method testCy270Vizmap.

@Test
@SuppressWarnings("unchecked")
public void testCy270Vizmap() throws Exception {
    Properties props = loadVizmapProps("v270_vizmap.props");
    Set<VisualStyle> styles = serializer.createVisualStyles(props);
    assertEquals(2, styles.size());
    assertVisualStylesNotNull(styles, new String[] { "default", "Binary_SIF_Version_1" });
    // Test visual styles (defaults, mappings and dependencies)
    // -----
    VisualStyle s = getVisualStyleByTitle(styles, "Binary_SIF_Version_1");
    assertEquals(new Color(255, 153, 153), s.getDefaultValue(NODE_FILL_COLOR));
    assertEquals(new Color(255, 255, 0), s.getDefaultValue(NODE_SELECTED_PAINT));
    assertEquals(NodeShapeVisualProperty.ELLIPSE, s.getDefaultValue(NODE_SHAPE));
    assertEquals(70, s.getDefaultValue(NODE_WIDTH).intValue());
    assertEquals(30, s.getDefaultValue(NODE_HEIGHT).intValue());
    assertEquals(35, s.getDefaultValue(NODE_SIZE).intValue());
    assertEquals(125, s.getDefaultValue(NODE_TRANSPARENCY).intValue());
    assertEquals(new Color(0, 0, 0), s.getDefaultValue(NODE_BORDER_PAINT));
    assertEquals(1, s.getDefaultValue(NODE_BORDER_WIDTH).intValue());
    assertEquals(255, s.getDefaultValue(NODE_BORDER_TRANSPARENCY).intValue());
    assertEquals("", s.getDefaultValue(NODE_LABEL));
    assertEquals(Font.decode("Default-PLAIN-12"), s.getDefaultValue(NODE_LABEL_FONT_FACE));
    assertEquals(12, s.getDefaultValue(NODE_LABEL_FONT_SIZE).intValue());
    assertEquals(new Color(0, 0, 0), s.getDefaultValue(NODE_LABEL_COLOR));
    assertEquals(100, s.getDefaultValue(NODE_LABEL_WIDTH).intValue());
    assertEquals(255, s.getDefaultValue(NODE_LABEL_TRANSPARENCY).intValue());
    assertEquals(LineTypeVisualProperty.SOLID, s.getDefaultValue(NODE_BORDER_LINE_TYPE));
    assertEquals("", s.getDefaultValue(NODE_TOOLTIP));
    assertEquals(Boolean.TRUE, s.getDefaultValue(NODE_NESTED_NETWORK_IMAGE_VISIBLE));
    assertEquals(4, s.getDefaultValue(EDGE_WIDTH).intValue());
    assertEquals(new Color(0, 0, 0), s.getDefaultValue(EDGE_UNSELECTED_PAINT));
    assertEquals(new Color(0, 0, 0), s.getDefaultValue(EDGE_STROKE_UNSELECTED_PAINT));
    assertEquals(new Color(255, 0, 0), s.getDefaultValue(EDGE_STROKE_SELECTED_PAINT));
    assertEquals(255, s.getDefaultValue(EDGE_TRANSPARENCY).intValue());
    assertEquals(LineTypeVisualProperty.SOLID, s.getDefaultValue(EDGE_LINE_TYPE));
    assertEquals("", s.getDefaultValue(EDGE_LABEL));
    assertEquals(Font.decode("SanSerif-PLAIN-10"), s.getDefaultValue(EDGE_LABEL_FONT_FACE));
    assertEquals(10, s.getDefaultValue(EDGE_LABEL_FONT_SIZE).intValue());
    assertEquals(new Color(0, 0, 0), s.getDefaultValue(EDGE_LABEL_COLOR));
    assertEquals(255, s.getDefaultValue(EDGE_LABEL_TRANSPARENCY).intValue());
    assertEquals(ArrowShapeVisualProperty.NONE, s.getDefaultValue(EDGE_SOURCE_ARROW_SHAPE));
    assertEquals(ArrowShapeVisualProperty.NONE, s.getDefaultValue(EDGE_TARGET_ARROW_SHAPE));
    assertEquals("", s.getDefaultValue(EDGE_TOOLTIP));
    PassthroughMapping<String, String> nLabelMp = (PassthroughMapping<String, String>) s.getVisualMappingFunction(NODE_LABEL);
    assertEquals("biopax.node_label", nLabelMp.getMappingColumnName());
    assertEquals(String.class, nLabelMp.getMappingColumnType());
    assertNull(s.getVisualMappingFunction(EDGE_LABEL));
    DiscreteMapping<String, Paint> nColorMp = (DiscreteMapping<String, Paint>) s.getVisualMappingFunction(NODE_FILL_COLOR);
    assertEquals("biopax.entity_type", nColorMp.getMappingColumnName());
    assertEquals(String.class, nColorMp.getMappingColumnType());
    assertEquals(new Color(153, 153, 255), nColorMp.getMapValue("Complex"));
    assertNull(nColorMp.getMapValue("Protein"));
    DiscreteMapping<String, Paint> eColorMp = (DiscreteMapping<String, Paint>) s.getVisualMappingFunction(EDGE_STROKE_UNSELECTED_PAINT);
    assertEquals(INTERACTION, eColorMp.getMappingColumnName());
    assertEquals(String.class, eColorMp.getMappingColumnType());
    // Test a few entries
    assertEquals(new Color(255, 192, 0), eColorMp.getMapValue("COMPONENT_OF"));
    assertEquals(new Color(255, 0, 0), eColorMp.getMapValue("CO_CONTROL_DEPENDENT_ANTI"));
    assertEquals(new Color(0, 176, 80), eColorMp.getMapValue("CO_CONTROL_DEPENDENT_SIMILAR"));
    assertEquals(new Color(253, 149, 166), eColorMp.getMapValue("CO_CONTROL_INDEPENDENT_ANTI"));
    assertEquals(new Color(0, 176, 80), eColorMp.getMapValue("CO_CONTROL_DEPENDENT_SIMILAR"));
    DiscreteMapping<String, ArrowShape> eTgtArrowMp = (DiscreteMapping<String, ArrowShape>) s.getVisualMappingFunction(EDGE_TARGET_ARROW_SHAPE);
    assertEquals(INTERACTION, eTgtArrowMp.getMappingColumnName());
    assertEquals(String.class, eTgtArrowMp.getMappingColumnType());
    assertEquals(ArrowShapeVisualProperty.ARROW, eTgtArrowMp.getMapValue("COMPONENT_OF"));
    assertEquals(ArrowShapeVisualProperty.ARROW, eTgtArrowMp.getMapValue("METABOLIC_CATALYSIS"));
    assertEquals(ArrowShapeVisualProperty.ARROW, eTgtArrowMp.getMapValue("SEQUENTIAL_CATALYSIS"));
    assertEquals(ArrowShapeVisualProperty.ARROW, eTgtArrowMp.getMapValue("SEQUENTIAL_CATALYSIS"));
    assertEquals(ArrowShapeVisualProperty.ARROW, eTgtArrowMp.getMapValue("STATE_CHANGE"));
    assertNull(eTgtArrowMp.getMapValue("INTERACTS_WITH"));
    VisualPropertyDependency<?> dep1 = getDependency(s, NODE_SIZE_LOCKED_DEPENDENCY);
    assertFalse(dep1.isDependencyEnabled());
}

Example 53 with VisualStyle

use of org.cytoscape.view.vizmap.VisualStyle in project cytoscape-impl by cytoscape.

the class VisualStyleSerializerTest method testCy252Vizmap.

@Test
@SuppressWarnings("unchecked")
public void testCy252Vizmap() throws Exception {
    Properties props = loadVizmapProps("v252_vizmap.props");
    Set<VisualStyle> styles = serializer.createVisualStyles(props);
    assertEquals(5, styles.size());
    assertVisualStylesNotNull(styles, new String[] { "default", "Sample1", "Sample2", "Sample3", "SimpleBioMoleculeEditor" });
    // Test one style
    // -----
    VisualStyle s3 = getVisualStyleByTitle(styles, "Sample3");
    assertEquals(new Color(0, 0, 0), s3.getDefaultValue(NETWORK_BACKGROUND_PAINT));
    assertEquals(new Color(255, 255, 255), s3.getDefaultValue(NODE_FILL_COLOR));
    assertEquals(new Color(255, 255, 0), s3.getDefaultValue(NODE_SELECTED_PAINT));
    assertEquals(NodeShapeVisualProperty.ROUND_RECTANGLE, s3.getDefaultValue(NODE_SHAPE));
    assertEquals(80, s3.getDefaultValue(NODE_WIDTH).intValue());
    assertEquals(30, s3.getDefaultValue(NODE_HEIGHT).intValue());
    assertEquals(180, s3.getDefaultValue(NODE_TRANSPARENCY).intValue());
    assertEquals(new Color(153, 153, 255), s3.getDefaultValue(NODE_BORDER_PAINT));
    assertEquals(2, s3.getDefaultValue(NODE_BORDER_WIDTH).intValue());
    assertEquals(255, s3.getDefaultValue(NODE_BORDER_TRANSPARENCY).intValue());
    assertEquals(new Font("Arial-BoldMT", Font.PLAIN, 12), s3.getDefaultValue(NODE_LABEL_FONT_FACE));
    assertEquals(16, s3.getDefaultValue(NODE_LABEL_FONT_SIZE).intValue());
    assertEquals(new Color(255, 255, 255), s3.getDefaultValue(NODE_LABEL_COLOR));
    assertEquals(255, s3.getDefaultValue(NODE_LABEL_TRANSPARENCY).intValue());
    assertEquals(LineTypeVisualProperty.SOLID, s3.getDefaultValue(NODE_BORDER_LINE_TYPE));
    assertEquals("", s3.getDefaultValue(NODE_TOOLTIP));
    assertEquals(1, s3.getDefaultValue(EDGE_WIDTH).intValue());
    assertEquals(new Color(153, 153, 255), s3.getDefaultValue(EDGE_UNSELECTED_PAINT));
    assertEquals(new Color(153, 153, 255), s3.getDefaultValue(EDGE_STROKE_UNSELECTED_PAINT));
    assertEquals(new Color(255, 0, 0), s3.getDefaultValue(EDGE_STROKE_SELECTED_PAINT));
    assertEquals(255, s3.getDefaultValue(EDGE_TRANSPARENCY).intValue());
    assertEquals(LineTypeVisualProperty.SOLID, s3.getDefaultValue(EDGE_LINE_TYPE));
    assertEquals(Font.decode("SanSerif-PLAIN-10"), s3.getDefaultValue(EDGE_LABEL_FONT_FACE));
    assertEquals(14, s3.getDefaultValue(EDGE_LABEL_FONT_SIZE).intValue());
    assertEquals(new Color(255, 255, 204), s3.getDefaultValue(EDGE_LABEL_COLOR));
    assertEquals(255, s3.getDefaultValue(EDGE_LABEL_TRANSPARENCY).intValue());
    assertEquals(ArrowShapeVisualProperty.NONE, s3.getDefaultValue(EDGE_SOURCE_ARROW_SHAPE));
    assertEquals(ArrowShapeVisualProperty.NONE, s3.getDefaultValue(EDGE_TARGET_ARROW_SHAPE));
    assertEquals("", s3.getDefaultValue(EDGE_TOOLTIP));
    PassthroughMapping<String, String> nLabelMp = (PassthroughMapping<String, String>) s3.getVisualMappingFunction(NODE_LABEL);
    assertEquals(NAME, nLabelMp.getMappingColumnName());
    assertEquals(String.class, nLabelMp.getMappingColumnType());
    PassthroughMapping<String, String> eLabelMp = (PassthroughMapping<String, String>) s3.getVisualMappingFunction(EDGE_LABEL);
    assertEquals(INTERACTION, eLabelMp.getMappingColumnName());
    assertEquals(String.class, eLabelMp.getMappingColumnType());
    PassthroughMapping<String, String> nTooltipMp = (PassthroughMapping<String, String>) s3.getVisualMappingFunction(NODE_TOOLTIP);
    assertEquals("gal4RGexp", nTooltipMp.getMappingColumnName());
    assertEquals(String.class, nTooltipMp.getMappingColumnType());
    ContinuousMapping<Double, Paint> nColorMp = (ContinuousMapping<Double, Paint>) s3.getVisualMappingFunction(NODE_FILL_COLOR);
    assertEquals("gal4RGexp", nColorMp.getMappingColumnName());
    assertEquals(Number.class, nColorMp.getMappingColumnType());
    assertEquals(3, nColorMp.getPointCount());
    assertEquals(-2.4059998989105242, nColorMp.getPoint(0).getValue(), 0.0001);
    assertEquals(new Color(0, 153, 0), nColorMp.getPoint(0).getRange().equalValue);
    assertEquals(new Color(0, 153, 0), nColorMp.getPoint(0).getRange().greaterValue);
    assertEquals(Color.BLACK, nColorMp.getPoint(0).getRange().lesserValue);
    assertEquals(-3.254413627473696E-8, nColorMp.getPoint(1).getValue(), 0.0001);
    assertEquals(Color.WHITE, nColorMp.getPoint(1).getRange().equalValue);
    assertEquals(Color.WHITE, nColorMp.getPoint(1).getRange().greaterValue);
    assertEquals(Color.WHITE, nColorMp.getPoint(1).getRange().lesserValue);
    assertEquals(1.2239999999999998, nColorMp.getPoint(2).getValue(), 0.0001);
    assertEquals(new Color(255, 0, 0), nColorMp.getPoint(2).getRange().equalValue);
    assertEquals(new Color(255, 255, 255), nColorMp.getPoint(2).getRange().greaterValue);
    assertEquals(new Color(255, 0, 0), nColorMp.getPoint(2).getRange().lesserValue);
    DiscreteMapping<String, Paint> eColorMp = (DiscreteMapping<String, Paint>) s3.getVisualMappingFunction(EDGE_STROKE_UNSELECTED_PAINT);
    assertEquals(INTERACTION, eColorMp.getMappingColumnName());
    assertEquals(String.class, eColorMp.getMappingColumnType());
    assertEquals(new Color(102, 255, 255), eColorMp.getMapValue("pd"));
    assertEquals(new Color(255, 255, 255), eColorMp.getMapValue("pp"));
    DiscreteMapping<String, LineType> eTypeMp = (DiscreteMapping<String, LineType>) s3.getVisualMappingFunction(EDGE_LINE_TYPE);
    assertEquals(INTERACTION, eTypeMp.getMappingColumnName());
    assertEquals(LineTypeVisualProperty.LONG_DASH, eTypeMp.getMapValue("pd"));
    assertEquals(LineTypeVisualProperty.SOLID, eTypeMp.getMapValue("pp"));
    VisualPropertyDependency<?> dep1 = getDependency(s3, NODE_SIZE_LOCKED_DEPENDENCY);
    assertFalse(dep1.isDependencyEnabled());
}

Example 54 with VisualStyle

use of org.cytoscape.view.vizmap.VisualStyle in project cytoscape-impl by cytoscape.

the class VisualStyleSerializerTest method setUp.

@Before
public void setUp() throws Exception {
    evtHelper = mock(CyEventHelper.class);
    twoDRoot = new NullVisualProperty("2D_ROOT", "2D Root Visual Property");
    lexicon = new BasicVisualLexicon(twoDRoot);
    VisualStyle defaultStyle = new DummyVisualStyle(DEFAULT_STYLE_NAME);
    final VisualStyleFactory visualStyleFactory = mockVisualStyleFactory(defaultStyle);
    final VisualMappingFunctionFactory discreteMappingFactory = mockMappingFunctionFactory(DiscreteMapping.class);
    final VisualMappingFunctionFactory continuousMappingFactory = mockMappingFunctionFactory(ContinuousMapping.class);
    final VisualMappingFunctionFactory passthroughMappingFactory = mockMappingFunctionFactory(PassthroughMapping.class);
    final RenderingEngineManager renderingEngineManager = mock(RenderingEngineManager.class);
    when(renderingEngineManager.getDefaultVisualLexicon()).thenReturn(lexicon);
    serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyEventHelper.class)).thenReturn(evtHelper);
    when(serviceRegistrar.getService(VisualStyleFactory.class)).thenReturn(visualStyleFactory);
    when(serviceRegistrar.getService(RenderingEngineManager.class)).thenReturn(renderingEngineManager);
    when(serviceRegistrar.getService(VisualMappingFunctionFactory.class, "(mapping.type=discrete)")).thenReturn(discreteMappingFactory);
    when(serviceRegistrar.getService(VisualMappingFunctionFactory.class, "(mapping.type=continuous)")).thenReturn(continuousMappingFactory);
    when(serviceRegistrar.getService(VisualMappingFunctionFactory.class, "(mapping.type=passthrough)")).thenReturn(passthroughMappingFactory);
    final CalculatorConverterFactory calcFactory = new CalculatorConverterFactory();
    serializer = new VisualStyleSerializer(calcFactory, serviceRegistrar);
}

Example 55 with VisualStyle

use of org.cytoscape.view.vizmap.VisualStyle in project cytoscape-impl by cytoscape.

the class CySessionManagerImpl method setCurrentSession.

@Override
public void setCurrentSession(CySession sess, final String fileName) {
    // Always remove the current session first
    if (!disposed)
        disposeCurrentSession();
    if (sess == null) {
        logger.debug("Creating empty session...");
        final VisualMappingManager vmMgr = serviceRegistrar.getService(VisualMappingManager.class);
        final Set<VisualStyle> styles = vmMgr.getAllVisualStyles();
        final Set<CyProperty<?>> props = getAllProperties();
        sess = new CySession.Builder().properties(props).visualStyles(styles).build();
    } else {
        logger.debug("Restoring the session...");
        // Save the selected networks first, so the selection state can be restored later.
        final List<CyNetwork> selectedNetworks = new ArrayList<>();
        final Set<CyNetwork> networks = sess.getNetworks();
        for (CyNetwork n : networks) {
            final Boolean selected = n.getDefaultNetworkTable().getRow(n.getSUID()).get(CyNetwork.SELECTED, Boolean.class);
            if (Boolean.TRUE.equals(selected))
                selectedNetworks.add(n);
        }
        restoreProperties(sess);
        restoreNetworks(sess);
        restoreTables(sess);
        restoreNetworkViews(sess, selectedNetworks);
        restoreNetworkSelection(sess, selectedNetworks);
        restoreVisualStyles(sess);
        restoreCurrentVisualStyle();
    }
    currentFileName = fileName;
    disposed = false;
    final CyEventHelper eventHelper = serviceRegistrar.getService(CyEventHelper.class);
    eventHelper.fireEvent(new SessionLoadedEvent(this, sess, getCurrentSessionFileName()));
}