org.cytoscape.view.presentation.customgraphics

Interface CyCustomGraphics2Factory<T extends CustomGraphicLayer>

public interface CyCustomGraphics2Factory<T extends CustomGraphicLayer>

Factory to create CyCustomGraphics2 objects. CyCustomGraphics2Factory objects are registered as OSGi services and will be used by Renderers to create the actual custom graphics implementations. Note that the type parameter T of CyCustomGraphics2Factory is the type of the underlying CustomGraphicLayer not the type of the resulting CyCustomGraphics2 object this factory creates.

The pattern is to register CyCustomGraphics2Factory implementations as OSGi services in your CyActivator class.

 CyCustomGraphics2Factory myCustomGraphics2Factory = new MyCustomGraphics2Factory();
 registerService(bundleContext, myCustomGraphics2Factory, CyCustomGraphics2Factory.class, new Properties());
 

Charts

Cytoscape provides some predefined custom graphics factories for creating charts. These factories can be retreived as OSGi services by using their IDs.

Bar Chart	org.cytoscape.BarChart
Box Chart	org.cytoscape.BoxChart
Heat Map Chart	org.cytoscape.HeatMapChart
Line Chart	org.cytoscape.LineChart
Pie Chart	org.cytoscape.PieChart
Ring Chart	org.cytoscape.RingChart
Linear Gradient	org.cytoscape.LinearGradient
Radial Gradient	org.cytoscape.RadialGradient

To retrieve a reference to a predefined chart factory you must use an OSGi service listener. For example:

 public class CustomChartListener {
        private static final String FACTORY_ID = "org.cytoscape.PieChart";
        private CyCustomGraphics2Factory<?> factory;
        
        public void addCustomGraphicsFactory(CyCustomGraphics2Factory<?> factory, Map<Object,Object> serviceProps) {
                if(FACTORY_ID.equals(factory.getId())) {
                        this.factory = factory;
                }
        }
        
        public void removeCustomGraphicsFactory(CyCustomGraphics2Factory<?> factory, Map<Object,Object> serviceProps) {
                this.factory = null;
        }
        
        public CyCustomGraphics2Factory<?> getFactory() {
                return factory;
        }
 }
 

Register the listener in your CyActivator class.

   CustomChartListener customChartListener = new CustomChartListener();
   registerServiceListener(context, customChartListener, "addCustomGraphicsFactory", "removeCustomGraphicsFactory", CyCustomGraphics2Factory.class);
 

Use the factory to create an instance of CyCustomGraphics2 for your charts. The data and appearance of the charts are controlled by a Map of properties that are passed to the getInstance() method.

 CyCustomGraphics2Factory<?> customGraphicsFactory = customChartListener.getFactory();
 CyColumnIdentifierFactory columnIdFactory; // Get OSGi service
 
 CyColumnIdentifier columnId = columnIdFactory.createColumnIdentifier(chartColumn);
 Map<String,Object> chartProps = new HashMap<String,Object>();
 chartProps.put("cy_dataColumns", Arrays.asList(columnId)); 
 chartProps.put("cy_colorScheme", "CONTRASTING");
                
 CyCustomGraphics2<?> customGraphics = customGraphicsFactory.getInstance(chartProps);

 // Set the custom graphics on the visual style
 VisualStyle visualStyle = visualMappingManager.getCurrentVisualStyle();
 CyApplicationManager appManager; // Get OSGi service
 RenderingEngine engine = appManager.getCurrentRenderingEngine();
 VisualLexicon lexicon = engine.getVisualLexicon();
 VisualProperty<CyCustomGraphics> visualProperty = lexicon.lookup(CyNode.class, "NODE_CUSTOMGRAPHICS_1");
 
 if (visualProperty != null)
     visualStyle.setDefaultValue(visualProperty, customGraphics);
 

Chart Properties

All built-in properties start with the "cy_" prefix. If you are writing an App that provides additional properties please specify your own prefix in order to prevent name collisions.

All Charts

Property Name	Type	Description
cy_dataColumns	List<CyColumnIdentifier>	Names of data columns from the default node table. Columns of type List become separate groups (or data series) in the chart (for example a ring chart will have a separate ring for each group). The column type must be numerical.
cy_values	List<Double>	Specific values to use for each segment of the chart. If cy_dataColumns is specified, this property does not need to be set.
cy_colors	List<java.awt.Color>	List of specific colors to use with each data column (if the column contains single numbers) or value. The color list should have one entry for every corresponding entry in the cy_dataColumns property list, if the list contains only columns of simple numerical types (no List types). If cy_dataColumns contains List-typed columns, it must contain as many colors as elements in the list values.
cy_colorScheme	String	Name of a predefined color scheme. Use this property instead of cy_colors to have the colors chosen automatically. Values: CONTRASTING, MODULATED, RAINBOW, RANDOM
cy_itemLabels	List<String>	Labels to use for each segment of the chart (for example each slice of a pie chart.) The label list should have one entry for every corresponding entry in the cy_dataColumns property list.
cy_itemLabelsColumn	CyColumnIdentifier	Name of a data column to use for value labels. The column should be of type List, each element in the list will be used as a label.
cy_showItemLabels	Boolean	Set to true to show value labels
cy_borderWidth	Float	Border width
cy_borderColor	java.awt.Color	Border color

Bar/Box/Line/Heat Charts

Property Name	Type	Description
cy_orientation	String	Values: HORIZONTAL, VERTICAL
cy_domainLabelsColumn	CyColumnIdentifier	Name of a data column to use for domain labels. The column should be of type List.
cy_rangeLabelsColumn	CyColumnIdentifier	Name of a data column to use for range labels. The column should be of type List.
cy_domainLabelPosition	String	Values: STANDARD, DOWN_45, DOWN_90, UP_45, UP_90
cy_globalRange	Boolean	If true, all charts' range (min and max bounds) will be automatically set to the network-wide range.
cy_range	List<Double>	Allows the global range to be set manually. Must be a list with exactly two elements. Specifies the lower (first element) and upper bound for the range axis. The property cy_range must be set to true.
cy_showDomainAxis	Boolean	Set to true to show the domain axis.
cy_showRangeAxis	Boolean	Set to true to show the range axis.
cy_axisWidth	Float	Axis stroke width.
cy_axisColor	java.awt.Color	Axis line color.

Bar Charts

Property Name	Type	Description
cy_type	String	Values: GROUPED, STACKED, HEAT_STRIPS, UP_DOWN
cy_separation	Double	Separation between bars. Value must be between 0.0 and 0.5

Line Charts

Property Name	Type	Description
cy_lineWidth	Float	Line width

Pie Charts

Property Name	Type	Description
cy_startAngle	Double	Start angle for the first pie section.

Ring Charts

Property Name	Type	Description
cy_startAngle	Double	Start angle for the first section.
cy_holeSize	Double	Width of the hole in the center of the ring.

Gradients

Property Name	Type	Description
cy_gradientFractions	List<Float>	Numbers ranging from 0.0 to 1.0 specifying the distribution of colors along the gradient. See javadocs for java.awt.MultipleGradientPaint for more detail.
cy_gradientColors	List<java.awt.Color>	List of colors corresponding to each fraction value.

Linear Gradient

Property Name	Type	Description
cy_angle	Double	Slope (rotation) of the gradient, in degrees.

Radial Gradient

Property Name	Type	Description
cy_center	java.awt.geom.Point2D	Center of the gradient. Each coordinate must be between 0.0 and 1.0.

Module: presentation-api

To use this in your app, include the following dependency in your POM:

<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>presentation-api</artifactId>
</dependency>

Cytoscape Backwards Compatibility (SPI Interface): We expect that this interface will be implemented. Therefore to maintain backwards compatibility this interface will only be modified for major version updates.

Field Summary

Fields

Modifier and Type	Field and Description
static String	GROUP Optional property key that tells Cytoscape under which group it should add the editor created by this factory (see createEditor(CyCustomGraphics2)).

Method Summary

Modifier and Type	Method and Description
JComponent	createEditor(CyCustomGraphics2<T> customGraphics) Creates a UI component that configures the given CyCustomGraphics2.
String	getDisplayName() Return the CyCustomGraphics2 name which is will be displayed to the user.
Icon	getIcon(int width, int height)
String	getId() Return the prefix to identify this Custom Graphics factory.
CyCustomGraphics2<T>	getInstance(CyCustomGraphics2<T> customGraphics) Get a new instance of a CyCustomGraphics2 that is a clone of the passed argument.
CyCustomGraphics2<T>	getInstance(Map<String,Object> properties) Get a new instance of a CyCustomGraphics2 with the passed properties.
CyCustomGraphics2<T>	getInstance(String input) Get a new instance of a CyCustomGraphics2.
Class<? extends CyCustomGraphics2<T>>	getSupportedClass()

Field Detail

GROUP

static final String GROUP

Optional property key that tells Cytoscape under which group it should add the editor created by this factory (see createEditor(CyCustomGraphics2)).

See Also:

Constant Field Values

Method Detail

getId

String getId()

Return the prefix to identify this Custom Graphics factory. This is used by the passthrough mapping logic to figure out if a given String value should be mapped to this factory.

Returns:

the prefix for this CyCustomGraphics2Factory

getDisplayName

String getDisplayName()

Return the CyCustomGraphics2 name which is will be displayed to the user.

Returns:

display name as String.

getIcon

Icon getIcon(int width,
             int height)

Parameters:

width -

height -

Returns:

an optional icon that represents a custom graphics type.

getInstance

CyCustomGraphics2<T> getInstance(String input)

Get a new instance of a CyCustomGraphics2. The string argument may be used by some implementations to create the initial CyCustomGraphics2 objects. This is the method that will be used to take a String passthrough mapping and create the correct CyCustomGraphics2 instance. Note that the prefix defined above will get removed from the string before this method is called.

Parameters:

input - a possible input string that may be used to create the instance. Not all implementations will use this.

Returns:

the new instance

getInstance

CyCustomGraphics2<T> getInstance(CyCustomGraphics2<T> customGraphics)

Get a new instance of a CyCustomGraphics2 that is a clone of the passed argument.

Parameters:

customGraphics - another Custom Graphics

Returns:

the new instance

getInstance

CyCustomGraphics2<T> getInstance(Map<String,Object> properties)

Get a new instance of a CyCustomGraphics2 with the passed properties. The properties object should contain the same keys that are returned by the corresponding CyCustomGraphics2.getProperties() implementation.

Parameters:

properties - optional properties to initialize the new custom graphics.

Returns:

the new instance

getSupportedClass

Class<? extends CyCustomGraphics2<T>> getSupportedClass()

Returns:

the class that this factory creates. This is used by the deserialization mechanism to find the factory method that can deserialize a given string.

createEditor

JComponent createEditor(CyCustomGraphics2<T> customGraphics)

Creates a UI component that configures the given CyCustomGraphics2.

Parameters:

customGraphics - the CyCustomGraphics2 to be configured.

Returns:

a UI panel that configures the given CyCustomGraphics2 or null if the factory does not want to provide a visual editor.