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Plugin Developer's Guide
This is an overview of how JBrowse 2 plugins work, and how to write them.
A plugin is primarily a bundle of "pluggable element types", which are the fundamental building blocks of JBrowse applications (such as JBrowse Desktop, JBrowse Embedded, etc).
Plugins all share a common architecture and plugin loading system, but a given plugin does not have to be designed to work in all JBrowse applications. JBrowse plugins are reusable packages that can be integrated in different ways to build applications.
A View is a self-contained visualization of data. Many views have tracks (LinearGenomeView, CircularView), but some do not (SpreadsheetView). Some views contain other views within themselves. For example, BreakpointSplitView contains two or more LinearGenomeViews and displays connections between them.
- LinearGenomeView
- CircularView
- BreakpointSplitView
- SpreadsheetView
- SvInspectorView
A data adapter produces data (usually genome features, but not necessarily) that is consumed by other things. Examples of data adapters include the VcfTabixAdapter that reads features from Tabix-indexed VCF files, the BamAdapter that reads features from BAM files, and the SPARQLAdapter that reads features from SPARQL endpoints.
- VcfTabixAdapter
- BamAdapter
- BigBedAdapter
- SPARQLAdapter
A connection is a package of track configurations, usually loaded from a remote source of configuration information such as a UCSC Track Hub or a JBrowse v1 installation.
- JBrowse1Connection
- UCSCTrackHubConnection
- TheTrackHubRegistryConnection
A renderer produces a visualization of a set of data. It fetches data from a data adapter and produces a React element that visualizes that data.
Many of the renderers in JBrowse 2 are ServerSideRenderers, which do their data fetching and visualization work outside the main JavaScript process in a worker process (most often a Web Worker, but other worker types are supported).
- PileupRenderer
- SvgFeatureRenderer
- LollipopRenderer
- DivSequenceRenderer
- Wiggle track renderers: DensityRenderer, LinePlotRenderer, XYPlotRenderer
A track is a visualization of the data in a data adapter, drawn with a certain renderer. It is basically the "glue" that allows the results of a renderer to be displayed inside a view. Most tracks have a fixed kind of renderer and are configurable to use many different data adapters.
- BasicTrack for LinearGenomeView
- StructuralVariantChordTrack for CircularView
A drawer widget is a UI element that lives in the "side drawer" of some JBrowse apps, such as JBrowse Desktop.
- BaseFeatureDrawerWidget - displays basic feature details
- VariantFeatureDrawerWidget - variant-specific version of feature details
- AlignmentsFeatureDrawerWidget - alignment-specific version of feature details
- HierarchicalTrackSelectorDrawerWidget - turns tracks on and off in the view it's bound to
- AddTrackDrawerWidget - wizard-like stepper UI for adding tracks to a dataset
- AddConnectionDrawerWidget - wizard-like stepper UI for adding connections to a dataset
TODO