Examples with PassthroughMapping org.cytoscape.view.vizmap.mappings.PassthroughMapping used on opensource projects

Example 6 with PassthroughMapping

use of org.cytoscape.view.vizmap.mappings.PassthroughMapping in project clusterMaker2 by RBVI.

the class NetworkColorDialog method actionPerformed.

/**
 *  DOCUMENT ME!
 *
 * @param e DOCUMENT ME!
 */
public void actionPerformed(ActionEvent e) {
    // Are we the source of the event?
    String command = e.getActionCommand();
    if (command.equals("done")) {
        animating = false;
        this.setVisible(false);
    } else if (command.equals("up")) {
        shiftList(-1);
    } else if (command.equals("down")) {
        shiftList(1);
    } else if (command.equals("vizmap")) {
        String attribute = (String) attributeSelector.getSelectedValue();
        MapTask task = new MapTask(attribute, "-heatMap", false);
        taskManager.execute(new TaskIterator(task));
    } else if (command.equals("animate")) {
        if (animating) {
            animating = false;
            animateButton.setText("Animate Vizmap");
            return;
        }
        // Get the selected attributes
        Object[] attributeArray = attributeSelector.getSelectedValues();
        if (attributeArray.length < 2) {
            // Really nothing to animate if we only have one map
            MapTask task = new MapTask((String) attributeArray[0], "-heatMap", false);
            taskManager.execute(new TaskIterator(task));
            return;
        }
        if (currentAttribute == null) {
            // Build the necessary vizmap entries
            styles = new VisualStyle[attributeArray.length];
            for (int i = 0; i < attributeArray.length; i++) {
                styles[i] = createNewStyle((String) attributeArray[i], "-" + (String) attributeArray[i], false, false);
            }
        }
        // Change the animate button
        animateButton.setText("Stop animation");
        animating = true;
        // Set up the animation task
        Animate a = new Animate(styles, attributeArray);
        a.start();
    } else if (command.equals("heatstrip")) {
        // Get the selected attributes
        Object[] attributeArray = attributeSelector.getSelectedValues();
        // We need to use enhancedgraphics for this.
        // 1) create a heatstrip command
        // 2) Write it into a column for every node
        // 3) Add a passthrough mapper for custom graphics
        String heatstrip = "heatstripchart: separation=\"1\" attributelist=\"";
        for (Object attr : attributeArray) heatstrip += attr.toString() + ",";
        // strip off the extra comma
        heatstrip = heatstrip.substring(0, heatstrip.length() - 1);
        String colorSpec = getColorSpec();
        heatstrip += "\" colorlist=\"" + colorSpec + "\" position=south showlabels=false size=30x60\"";
        CyNetwork net = clusterManager.getNetwork();
        String columnName = "clusterMaker-heatStrip";
        CyTable nodeTable = net.getDefaultNodeTable();
        if (nodeTable.getColumn(columnName) == null)
            nodeTable.createColumn(columnName, String.class, false);
        for (CyNode node : net.getNodeList()) {
            nodeTable.getRow(node.getSUID()).set(columnName, heatstrip);
        }
        VisualStyle style = ViewUtils.getCurrentVisualStyle(clusterManager);
        if (!style.getTitle().endsWith("-heatStrip"))
            style = ViewUtils.copyStyle(clusterManager, style, "-heatStrip");
        // Get the default lexicon (CUSTOMGRAPHICS aren't in the basic lexicon)
        VisualLexicon currentLexicon = ((RenderingEngineManager) clusterManager.getService(RenderingEngineManager.class)).getDefaultVisualLexicon();
        VisualProperty customGraphicsVP = currentLexicon.lookup(CyNode.class, "NODE_CUSTOMGRAPHICS_1");
        if (customGraphicsVP == null)
            System.err.println("couldn't get NODE CUSTOM GRAPHICS");
        // Get a function factory
        VisualMappingFunctionFactory vmff = clusterManager.getService(VisualMappingFunctionFactory.class, "(mapping.type=passthrough)");
        PassthroughMapping map = (PassthroughMapping) vmff.createVisualMappingFunction(columnName, String.class, customGraphicsVP);
        style.addVisualMappingFunction(map);
        // TODO: Do we want to mess with the CUSTOMGRAPHICS_POSITION?
        ViewUtils.setVisualStyle(clusterManager, clusterManager.getNetworkView(), style);
    }
}

Example 7 with PassthroughMapping

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

the class EMStyleBuilder method setEdgeWidth.

private void setEdgeWidth(VisualStyle vs, EMStyleOptions options) {
    String prefix = options.getAttributePrefix();
    EnrichmentMap map = options.getEnrichmentMap();
    if (options.isPostAnalysis()) {
        // Replace the edge width mapping that was created by EnrichmentMapVisualStyle
        String widthAttribute = Columns.EDGE_WIDTH_FORMULA_COLUMN.with(prefix, null);
        PassthroughMapping<Double, Double> edgewidth = (PassthroughMapping<Double, Double>) pmFactory.createVisualMappingFunction(widthAttribute, Double.class, BasicVisualLexicon.EDGE_WIDTH);
        vs.addVisualMappingFunction(edgewidth);
    } else {
        // Continous Mapping - set edge line thickness based on the number of genes in the overlap
        ContinuousMapping<Double, Double> cm = (ContinuousMapping<Double, Double>) cmFactory.createVisualMappingFunction(Columns.EDGE_SIMILARITY_COEFF.with(prefix, null), Double.class, EDGE_WIDTH);
        Double underWidth = 0.5;
        Double minWidth = 1.0;
        Double maxWidth = 5.0;
        Double overWidth = 6.0;
        // Create boundary conditions
        BoundaryRangeValues<Double> bv4 = new BoundaryRangeValues<>(underWidth, minWidth, minWidth);
        BoundaryRangeValues<Double> bv5 = new BoundaryRangeValues<>(maxWidth, maxWidth, overWidth);
        // Silence events fired by this mapping to prevent unnecessary style and view updates
        eventHelper.silenceEventSource(cm);
        try {
            cm.addPoint(map.getParams().getSimilarityCutoff(), bv4);
            cm.addPoint(1.0, bv5);
        } finally {
            eventHelper.unsilenceEventSource(cm);
        }
        vs.addVisualMappingFunction(cm);
    }
}

Example 8 with PassthroughMapping

use of org.cytoscape.view.vizmap.mappings.PassthroughMapping 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 9 with PassthroughMapping

use of org.cytoscape.view.vizmap.mappings.PassthroughMapping 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 10 with PassthroughMapping

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

the class VisualPropertySheetItem method updateMappingIcon.

private void updateMappingIcon() {
    if (!model.isVisualMappingAllowed())
        return;
    final JToggleButton btn = getMappingBtn();
    final VisualMappingFunction<?, T> mapping = model.getVisualMappingFunction();
    final String colName = mapping != null ? mapping.getMappingColumnName() : null;
    final IconManager iconManager = servicesUtil.get(IconManager.class);
    btn.setFont(iconManager.getIconFont(16.0f));
    if (btn.isSelected())
        btn.setForeground(UIManager.getColor("Table.focusCellForeground"));
    else
        btn.setForeground(getForegroundColor());
    if (mapping == null) {
        btn.setText("");
        btn.setToolTipText("No Mapping");
    } else if (mapping instanceof DiscreteMapping) {
        btn.setText(DISCRETE_ICON);
        btn.setToolTipText("Discrete Mapping for column \"" + colName + "\"");
    } else if (mapping instanceof ContinuousMapping) {
        btn.setText(CONTINUOUS_ICON);
        btn.setToolTipText("Continuous Mapping for column \"" + colName + "\"");
    } else if (mapping instanceof PassthroughMapping) {
        btn.setText(PASSTHROUGH_ICON);
        btn.setToolTipText("Passthrough Mapping for column \"" + colName + "\"");
    }
}