Developing Cytoscape plugins
cytoscape.org
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1
Developing Cytoscape plugins
1.
2.
3.
4.
5.
6.
Cytoscape and plugins
Documentation
Basic Cytoscape architecture
Plugins in Cytoscape
Using an IDE
Creating a plugin
1.
2.
3.
4.
Extending CytoscapePluging
Controlling the UI
Creating and manipulating your network
Additional topics
7. The future: Cytoscape 3.0
cytoscape.org
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2
1. Cytoscape and plugins
1. Setup of this part of the course
2. Overview of Cytoscape from a programmer’s
point of view
3. Questions and feedback
cytoscape.org
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3
1. Cytoscape and Plugins
1. Setup of this part of the course
• Goal: build a functioning sample plugin
– Controlling UI
– Manipulating networks programmatically
• First: ppt showing Cytoscape structure etc
• Next: slides with codesamples working towards a plugin
–
–
–
–
IDE of choice: Eclipse
SamplePlugin project
Including the functioning codesamples
Micro assignments – code yourself – toy around!
cytoscape.org
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4
1. Cytoscape and Plugins
2. Overview of Cytoscape from a
programmer’s point of view
• Java; >=1.5
• Object Oriented
• Fully Open Source: LGP license
– But please cite literature ref for funding purposes!
• Cline ea Nature Protocols 2007
• Plugins: jars, loaded upon startup when in /plugins dir
cytoscape.org
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5
1. Cytoscape and Plugins
3. Questions and feedback
• Short intro on developer level:
– What have you developed lately?
– Familiarity with
• Java?
• Eclipse?
• Cytoscape (plugin) development?
– Special wishes?
cytoscape.org
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2. Documentation
1. API
2. Wiki: the nugget pages
3. Community
cytoscape.org
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2. Documentation
1. API
• Through cytoscape.org:
– http://chianti.ucsd.edu/Cyto-2_7_0/javadoc/
cytoscape.org
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8
2. Documentation
2. Wiki: the nugget pages
• Developer home page:
– http://cytoscape.wodaklab.org/wiki/Developer_Homepage
• Plugin developer tutorial:
– http://cytoscape.wodaklab.org/wiki/Cytoscape_Plugin_Tutorial
• Developers cookbook:
– http://cytoscape.wodaklab.org/wiki/plugin_developer_tutorial
• Note: suffers from generic wikiproblem; container for all docs,
some outdated some irrelevant...
cytoscape.org
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2. Documentation
3. Community
• General communication
–
–
–
–
Cytoscape.org website
Cytoscape wiki
Cytoscape announce google mailing list
Cytoscape discuss google mailing list
• Internal communication (open to core Cytoscape
developers)
– Weekly conference call
– Internal development mailing list
• See here:
http://cytoscape.wodaklab.org/wiki/Community_development_process
cytoscape.org
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10
3. Basic Cytoscape architecture
1. Layers / Concepts
2. Graphs / Attributes
3. API
cytoscape.org
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11
3. Basic Cytoscape architecture
1. Layers: Concepts
• Graphs and Data
Graphs (CyNetworks)
Data (CyAttributes)
VizMapper
cytoscape.org
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12
3. Basic Cytoscape architecture
1. Layers: Concepts
• Graphs and Data
– Graphs and Networks
• Root Graph: ONE graph to rule them all....
– All nodes and edges are part of the root graph
• A network is a subset (projection) of the root graph
• A network view is a visualization of a network
• The Vizmapper maps attributes values to visual
presentation
– Attributes
• Typed values that can be associated with CyNetworks,
CyNodes, and CyEdges
cytoscape.org
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3. Basic Cytoscape architecture
2. Graphs / Attributes
RootGraph
CyNetwork
cytoscape.org
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14
3. Basic Cytoscape architecture
2. Graphs / Attributes
– Attributes are not really "attributes"
• Attributes are data values that might be associated
with networks, nodes, and edges
– You can read in attributes for nodes/edges you haven't
created yet
– Attributes are associated to nodes/edges by identifier
(name)
• Attributes are typed
– Support for Integer, Double, Boolean, String, List, and Map
(dictionaries)
– Attributes are accessed by type, attribute name, object
identifier (name)
cytoscape.org
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15
3. Basic Cytoscape architecture
2. Graphs / Attributes
 Root Graph Implications
• Two nodes with the same identifier in different networks
are the same node
– Once initialized with an id this will stay
– They will have the same attributes
– VizMap overrides (which are implemented as attributes)
will effect all presentations of the node
cytoscape.org
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3. Basic Cytoscape architecture
3. API: toplevel
cytoscape.org
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3. Basic Cytoscape architecture
3. API: under the hood
Cytoscape
giny
Cytoscape
giny
Implementatio
n
cytoscape.org
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Model
View
CyNetwork
CyNode
CyEdge
CyNetworkView
CyNodeView
CyEdgeView
GraphPerspective
Node
Cytoscape API
Edge
fing
FGraphPerspective
FNode
Edge
GraphView
NodeView
EdgeView
ding
DGraphView
DNodeView
DEdgeView
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3. Basic Cytoscape architecture
3. API
• Graphs, Views, and Data (Attributes)
– Views depend on Graphs
– Data doesn't depend on anything
• Graph
–
–
–
CyNetwork -> GraphPerspective (giny) -> FGraphPerspective (fing)
CyNode -> Node (giny) -> FNode (fing)
CyEdge -> Edge (giny) -> FEdge (fing)
• View
–
–
–
CyNetworkView -> GraphView (giny) -> DGraphView (ding)
CyNodeView -> NodeView (giny) -> DNodeView (ding)
CyEdgeView -> EdgeView (giny) -> DEdgeView (ding)
• Data
–
CyAttributes
• Note: library dependencies introduce some peculiarities
– Casts to specific types sometimes necessary
– Use of lowlevel rootgraphindex
– etc
cytoscape.org
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19
3. Basic Cytoscape architecture
3. API
• Navigating the Cytoscape API
– Cytoscape class
• Abstract static class
• Starting point for most Cytoscape functionality
• Contains factory methods for creating graph objects,
views
• Fires all events
– Other useful classes
• CyGroupManager: group-related information
• CyLayouts: information about currently loaded layout
algorithms
cytoscape.org
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20
3. Basic Cytoscape architecture
3. API
• Navigating the Cytoscape API
– CyNetwork class
• Collection of CyNodes (and CyEdges)
• Unifies graph with data
– CyNetworkView
• Visualization of CyNetwork
• Collection of CyNodeViews (and CyEdgeViews)
– CytoscapeDesktop
• Manages CyNetworkViews
• Updates focus
• Manages CytoPanels
cytoscape.org
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21
3. Basic Cytoscape architecture
3. API
• Navigating the Cytoscape API
– CyAttributes
• Three global sets associated with
– Networks
– Nodes
– Edges
• MultiHashMap datastructure
cytoscape.org
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22
4. Plugins in Cytoscape
1.
2.
3.
4.
cytoscape.org
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Core and others
Registering your plugin
Pluginmanager
Plugin communication
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4. Plugins in Cytoscape
1. Core and others
– It’s not all in cytoscape…
• Cytoscape has four different groups of functionality:
– cytoscape/: the core application
– corelibs/: corelibs are parts of Cytoscape that are called by core
routines, but never call any core routines. Much of the graph
implementation is here.
– coreplugins/: a significant piece of the Cytoscape functionality is
“hidden” in the plugins that are delivered with cytoscape. As with any
plugin, these are not directly available through the API. Including:
»
»
»
»
»
Layouts
Data browser
Editor
Table import, SBML reader, and PSI-MI readers
Filters
– csplugins/: User-developed plugins add significant functionality. Many
of those are available as source
cytoscape.org
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24
4. Plugins in Cytoscape
1. Core and others
cytoscape.org
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25
4. Plugins in Cytoscape
2. Registering your plugin
• Define a plugin.props file for your plugin (based on
sample)
• Create a jar from your plugin including a manifest file
 ANT build tools exist...
cytoscape.org
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26
4. Plugins in Cytoscape
3. Pluginmanager
•
Automated process to give users access to your plugin
through Cytoscape itself
1. Check that your plugin conforms to the requirements on former
slide (manifest and plugin.props files are required).
2. Go to
http://chianti.ucsd.edu/cyto_web/plugins/pluginsubmittype.php
and follow the instructions to submit your plugin.
3. Send an announcement to the announcement mailing list.
cytoscape.org
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27
4. Plugins in Cytoscape
4. Plugin communication
• Some rudimentary, but currently basically not possible
– Call layout
– Check if loaded
• In 2.8 there will be a Command interface facilitating that
• In 3.0 essentially everything will be plugin, communicating
by default
cytoscape.org
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28
5. Using an IDE
Eclipse as an example….
• ANT: <= 2.7
• Maven: > 2.8 (and ANT)
cytoscape.org
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29
5. Using an IDE
•
•
•
•
Store the SamplePlugin dir in the workspace dir
In Eclipse : Import>Existing project
Set the libraries necessary
Set the Run configuration
• At home: use svn directly, use the Ant build config
cytoscape.org
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30
5. Using an IDE: Eclipse (ANT)
cytoscape.org
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31
5. Using an IDE: Eclipse (ANT)
cytoscape.org
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32
5. Using an IDE: Eclipse (ANT)
cytoscape.org
[email protected]
33
5. Using an IDE: Eclipse (ANT)
cytoscape.org
[email protected]
34
5. Using an IDE: Eclipse (ANT)
cytoscape.org
[email protected]
35
5. Using an IDE: Eclipse (ANT)
cytoscape.org
[email protected]
36
5. Using an IDE: Eclipse (ANT)
cytoscape.org
[email protected]
37
5. Using an IDE: Eclipse (ANT)
cytoscape.org
[email protected]
38
5. Using an IDE: Eclipse (ANT)
cytoscape.org
[email protected]
39
5. Using an IDE: Eclipse (ANT)
cytoscape.org
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40
5. Using an IDE: Eclipse (ANT)
• …and run and debug!
cytoscape.org
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41
5. Using an IDE: Eclipse (Maven)
• Will become simpler with the plugin archetype
• Default from 2.8 on
• First upload takes a while…
cytoscape.org
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42
5. Using an IDE: Eclipse (Maven)
cytoscape.org
[email protected]
43
5. Using an IDE: Eclipse (Maven)
cytoscape.org
[email protected]
44
5. Using an IDE: Eclipse (Maven)
cytoscape.org
[email protected]
45
5. Using an IDE: Eclipse (Maven)
cytoscape.org
[email protected]
46
5. Using an IDE: Eclipse (Maven)
cytoscape.org
[email protected]
47
5. Using an IDE: Eclipse (Maven)
cytoscape.org
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48
5. Using an IDE: Eclipse (Maven)
• Yet in beta;
• Debugging etc in IDE (Eclipse) underway
cytoscape.org
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49
5. Using an IDE: Eclipse
• Check double check:
– Everybody has a compiling and running project?
cytoscape.org
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50
6. Creating a plugin
1.
2.
3.
4.
cytoscape.org
[email protected]
Extending CytoscapePlugin
Controlling the UI
Generating and manipulating your network
Additional topics
51
6. Creating a plugin:
1. Extending CytoscapePlugin
cytoscape.org
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52
6. Creating a plugin:
1. Extending CytoscapePlugin
• A class in your plugin should extend CytoscapePlugin
– The constructor for this class will be called when your plugin is
loaded
• Store your jar in {cytoscape}/plugins
• Plugin information is provided by a property file
– Usually in resources/plugins.props
cytoscape.org
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53
6. Creating a plugin:
2. Controlling the UI
1. Menu items
2. Cytopanels
cytoscape.org
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54
6. Creating a plugin:
2. Controlling the UI
1. Menu items
1. Extend from CytoscapeAction
2. Attach to menu
2. Cytopanels
1. Get a panel from desktop
2. Add yourPanel extending JPanel
cytoscape.org
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55
Plugin Lab Time
Controlling the UI
• Toy around with the existing tutorials (>tutorials>)
– See what they do
– Locate relevant code
• Read
– http://cytoscape.wodaklab.org/wiki/CytoPanel_Tutorial
• MicroAssignment
– Create your own button in the Menu
– When clicked it writes to your panel
cytoscape.org
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56
6. Creating a plugin:
3. Generating and manipulating your network
1. Creating nodes, edges, and networks
2. Mapping data: attributes
3. Link visually: Vizmapper
cytoscape.org
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57
6.3 Generating and manipulating your
network
1. Creating nodes, edges, and networks
• Working with:
–
–
–
–
Networks, Edges, Nodes
Views of the above
Creating, Selecting
Library dependencies
• Walk through of code of simple tutorials
cytoscape.org
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58
Some peculiarities
•
cyNetwork.nodesList()
Note, this returns a list of Nodes, not CyNodes. They can be safely cast
•
cyNetwork.edgesList()
Note, this returns a list of Edges, not CyEdges. They can be safely cast
•
•
•
cyNode.getRootGraphIndex()
cyEdge.getRootGraphIndex()
cyNetwork.getAdjacentEdgeIndicesArray(int,true,true,true)
Note, this takes root graph indices and returns and array of root graph
indices, these methods tend to be faster, for large sets…
• cyNetwork.getConnectingEdges(list)
cytoscape.org
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59
6.3 Generating and manipulating your
network
2. Mapping data: attributes
Think of attributes as tables
– 3 tables of attributes for the 3 graph objects
– Cytoscape.getNetworkAttributes()
– Cytoscape.getNodeAttributes()
– Cytoscape.getEdgeAttributes()
cytoscape.org
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And 6 Attribute Types
•
•
•
•
•
•
TYPE_BOOLEAN (Boolean)
TYPE_FLOATING (Double)
TYPE_INTEGER (Integer)
TYPE_STRING (String)
TYPE_SIMPLE_LIST (List)
TYPE_SIMPLE_MAP (Map)
cytoscape.org
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61
Resulting API methods:
Setting attributes
cyAttributes.setAttribute(objectName,attrName,value)
cyAttributes.setListAttribute(objectName,attrName,list)
cyAttributes.setMapAttribute(objectName,attrName,map)
Getting attributes
cyAttributes.hasAttribute(objectName,attrName)
cyAttributes.getBooleanAttribute(objectName,attrName)
cyAttributes.getDoubleAttribute(objectName,attrName)
cyAttributes.getIntegerAttribute(objectName,attrName)
cyAttributes.getListAttribute(objectName,attrName)
cyAttributes.getMapAttribute(objectName,attrName)
…and some additional characteristics
cyAttributes.setUserEditable(name,boolean)
cyAttributes.setUserVisible(name,boolean)
cytoscape.org
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62
Plugin Lab Time
Creating networks - Adding data
• Demo tutorials
• Read
– http://cytoscape.wodaklab.org/wiki/Concepts_Document
– http://cytoscape.wodaklab.org/wiki/CytoscapeData
• MicroAssignment
– Create your own network
– Add some data attributes
– Set the positions of nodes based on values of the
attributes
cytoscape.org
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63
6.3 Generating and manipulating your
network
3. Linking Visuals
• Remember central idea:
Graphs (CyNetworks)
Data (CyAttributes)
VizMapper
cytoscape.org
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64
Linking Visuals: the Vizmapper
• Summary:
– Get the VisualMappingManager
– Get the Catalog that keeps track of all mappingcalculators
– Create your style
• Create Node, Edge, and Global AppearanceCalculators
• Construct a calculator for each VisualProperty
• Create a PassThrough, Discrete, or Continuous mapper
that maps an attribute to a VisualProperty
• Set the calculator in the AppearanceCalculator
• Create the style with all three AppearanceCalculators
– Set your style in the NetworkView
– Add your style to the catalog
– Apply the style: applyStyle or redrawGraph
cytoscape.org
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65
Plugin Lab Time
Mapping visuals
• Demo relevant tutorials
• Read:
http://cytoscape.wodaklab.org/wiki/Visual_Mapping_Syste
m_Guide
• Micro Assignment
– Map visuals based on the network and data you created
– Use a calculator to set values
cytoscape.org
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66
6. Creating a plugin
4. Additional topics
• Additional Topics
• Walkthrough code: an example plugin
–
–
–
–
Events
TaskMonitor
Tunables
Layouts
• Any additional ???
– Webstart?
– Groups?
cytoscape.org
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67
Events
• Cytoscape and CytoscapeDesktop are event firing
classes
• Any event listener needs to implement
java.beans.PropertyChangeListener
• Add your listener to Cytoscape or CytoscapeDesktop
Cytoscape.getSwingPropertyChangeSupport().addProperty
ChangeListener(this);
cytoscape.org
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68
Events
Event
Firing Class
CYTOSCAPE_EXIT
Cytoscape
NETWORK_CREATED
Cytoscape
NETWORK_DESTROYED
Cytoscape
ATTRIBUTES_CHANGED
Cytoscape
NETWORK_VIEW_CREATED
CytoscapeDesktop
NETWORK_VIEW_DESTROYED
CytoscapeDesktop
NETWORK_VIEW_FOCUS
CytoscapeDesktop
NETWORK_VIEW_FOCUSED
CytoscapeDesktop
cytoscape.org
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69
Tunables
• Tunables
– Serves three purposes:
• Persistence of values
• Automatic UI generation
• External access to plugin parameters
– Tunables are typed
cytoscape.org
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70
Tunables
• Tunable objects take 7 arguments
–
–
–
–
–
–
–
name: the name of the tunable
description: the description of the tunable
type: the tunable type
value: the initial value of the tunable
lowerBound: the lower bound of the tunable
upperBound: the upper bound of the tunable
flag: flags to provide hints to the UI generators
cytoscape.org
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71
Tunable Types
• Types
–
–
–
–
–
–
–
–
–
INTEGER
DOUBLE
BOOLEAN
STRING
NODEATTRIBUTE
EDGEATTRIBUTE
LIST
GROUP
BUTTON
cytoscape.org
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72
Tunable Bounds and Flags
•
Bounds and flags
– Bounds provide:
• upper/lower bounds of numeric quantities
• The list for a List
• An initial list for attributes (to allow alternative choices)
– Flags provide hints for the UI
• MULTISELECT to allow multiple selection in a list
• USESLIDER to use a slider for numeric values (must also have
bounds)
• IMMUTABLE to display the value but not allow editing
• COLLAPSABLE to implement collapsible groups
• NOINPUT for internal parameters that aren't presented to the user
• NUMERICATTRIBUTE to restrict attribute presentation to numeric
values
cytoscape.org
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73
Tunable Interaction
• Interaction
– BUTTON tunable
• Lower bound is an ActionListener
• Called when the button is pressed
– A TunableValueListener
• Can be added to any Tunable
• Caller will be notified when a tunable value changes
cytoscape.org
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LayoutProperties
• Two functions
– Collect all Tunables into a list
– Generate a single JPanel with all of the Tunable
interfaces
• LayoutProperties handles GROUPing
• Example: tunableSampler
cytoscape.org
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Layouts
• Layouts should all inherit from AbstractLayout
• Registering layouts
– CyLayout.addLayout(algorithm, menu)
– Information about capabilities are determined through
callbacks
– Registered layouts can be "found" by plugins by calling
CyLayout.getLayout(name)
• Cytoscape's layout menu takes care of tasks
– Use LayoutTask if you want to call a layout yourself on a
separate thread:
• LayoutTask(layout,view)
• TaskManager.executeTask(layoutTask,
LayoutTask.getDefaultTaskConfig())
cytoscape.org
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76
Layouts
• Layout callbacks:
– LayoutProperties getSettings():
• Return your list of Tunables
– updateSettings():
• Update all of the Tunables values
– revertSettings():
• Revert all Tunables values to the default
– JPanel getSettingsPanel():
• Return the settings panel for this layout
• Return from LayoutProperties.getTunablePanel()
cytoscape.org
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Layouts
• Using an existing layout
– Get the CyLayoutAlgorithm:
• CyLayoutAlgorithm alg = CyLayouts.getLayout(String);
– Get the Tunables:
• LayoutProperties props = alg.getSettings();
– Set the Tunables you want:
• Tunable t1 = props.get(String);
• t1.setValue(Object);
• alg.updateSettings();
– Set appropriate flags (will also be Tunables):
• alg.setSelectedOnly(boolean);
• alg.setLayoutAttribute(String);
– Do the layout:
• alg.doLayout(CyNetworkView, TaskMonitor);
cytoscape.org
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Group concepts
• A group is a collection of nodes and their edges
• A node may be defined in multiple groups
• A group is represented by a node, which might itself be part of a
group
– Groups are hierarchical
cytoscape.org
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79
Creating groups
•
CyGroupManager.createGroup(name,list, viewer)
cytoscape.org
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80
Using groups
•
•
•
•
•
•
•
•
•
•
•
•
•
cyGroup.addNode(node)
cyGroup.addInnerEdge(edge)
cyGroup.addOuterEdge(edge)
cyGroup.getNodes()
cyGroup.getInnerEdges()
cyGroup.getOuterEdges()
cyGroup.getGroupNode()
cyGroup.getState()
cyGroup.removeNode()
cyGroup.setState(int)
cyNode.inGroup(group)
cyNode.getGroups()
cyNode.isaGroup()
cytoscape.org
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81
GroupViewers
• Group is visualized by a CyGroupViewer
• The CyGroupViewer for a group can be changed
• Common usage for creating lots of groups:
– Create group with no viewer
– Set viewer:
• CyGroupManager.setGroupViewer(group,
viewer, view, false)
– On last group:
• CyGroupManager.setGroupViewer(group,
viewer, view, true)
cytoscape.org
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82
Plugin Lab Time
• Demo relevant tutorials: which topics???
• Micro Assignment
– Create or elaborate your own plugin using one of the
advanced topics
cytoscape.org
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83
7. The future: Cytoscape 3.0
cytoscape.org
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84
2.x: Disadvantages
Cytoscape 2.x works OK but…..
•
•
•
•
•
•
•
One big graph
Layers interconnected
No clean ModelViewController separation
Library dependencies
Library versioning
Plugins cannot communicate
Plugin versioning
cytoscape.org
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85
Layers
Model
View
Cytoscape
CyNetwork
CyNode
CyEdge
CyNetworkView
CyNodeView
CyEdgeView
giny
GraphPerspective
Node
Edge
GraphView
NodeView
EdgeView
Cytoscape’s
Giny
Implementation
cytoscape.org
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fing
FGraphPerspective
FNode
Edge
Cytoscape API
ding
DGraphView
DNodeView
DEdgeView
86
NextGen Cytoscape 3.0
Goals
• Easier interface for plugin writers to understand and use.
• Better modularity or layering making it easier for
components of Cytoscape can be used in different
contexts.
• Clean up/refactor the structure of the existing Cytoscape
core so that it can be more easily maintained, modified,
and extended in the future.
• Make backwards compatibility easier to maintain.
• Clean up the user interface so that it's easier for users.
cytoscape.org
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87
NextGen Cytoscape 3.0
Desired features
• All features of 2.7
• Layer Cytoscape; allow alternative uses of Cytoscape.
• Separate the view from the model; various headless (or
alternatively headed) modes
• Command layer; GUI it currently too tightly coupled with
actions. Should be extensible for plugin writers
• Improved Event handling; currently mish-mash of events,
clean interface is needed.
• Custom graphics.
• Improve build process and package structure; simplify
the build process
• Local Attributes; allow attributes specific to networks.
• Dynamic language support; for dynamic (scripting)
languages
cytoscape.org
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Cytoscape 3, OSGi, and Spring Framework
• Based on slides from Keiichiro Ono, UCSD
• Cytoscape Core Developer
cytoscape.org
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89
Outline
•
•
•
•
Dependency Injection
What is Spring Framework?
OSGi and Spring
Integration to Cytoscape 3
cytoscape.org
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Dependency Injection (DI)
• A Design Pattern to achieve:
✓Separate configuration from use
✓Low Coupling
✓Easy unit testing
cytoscape.org
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Why DI? (1)
•
Cytoscape 3 will be an expandable, and UI-independent
platform
• Desktop application, Web application, or Web Service
• Plugins interact to each other to build complex
services/functions
cytoscape.org
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92
Why DI? (2)
•
OSGi solves:
– Library versioning/dependency/conflict problem
➡ Important for applications with plugin architecture
– Dynamic loading problem
– Modularity
– Interface-Based Design (Service Framework)
cytoscape.org
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93
Why DI? (3)
•
Remaining Issues
– How can we make Cytoscape re-configurable?
–From Desktop to Sever Backend
– How can we manage instances of components
➡ DI Pattern helps to solve these problems
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Summary
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Dependency Injection pattern is useful for applications
with plugin architecture
DI pattern makes application scalable
Spring DM provides simpler way to manage OSGi
services
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Current status of Cy3
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Core plugins are being ported to Cy3
Plugin development not yet possible
Keep an eye on the development modules page
Docs not yet complete
Learning curve quite steep
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Feedback!
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Quirks
Annoyances
Dev suggestions
Features?
…
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