Description

An object representing a genome browser session. As a derivative of TrackDb, each session contains a set of loaded tracks. In addition, it has a set of views, in the form of BrowserView instances, on those tracks. Note that this is a virtual class; a concrete implementation is provided by each backend driver.

Objects from the Class

A virtual Class: No objects may be created from it. See browserSession for obtaining an instance of an implementation for a particular genome browser.

Methods

This specifies the API implemented by each browser backend. Note that a backend is not required to support all operations, and that each backend often has additional parameters for each of the methods. See the backend-specific documentation for more details. The only built-in backend is UCSCSession.

If a method is denoted as virtual, it must be implemented by the backend to support the corresponding feature. Otherwise, the fallback behavior is described.

virtual browserView(object, range = range(object), track = trackNames(object), ...)

Constructs a BrowserView of range for this session.

virtual browserViews(object, ...)

Gets the BrowserView instances belonging to this session.

activeView(object, ...)

Returns the BrowserView that is currently active in the session. Fallback calls browserViews and queries each view with activeView.

range(x, ...)

Gets the GRanges representing the range of the genome currently displayed by the browser (i.e. the range shown by the active view) or a default value (possibly NULL) if no views exist.

virtual getSeq(object, range = range(object), ...)

gets a genomic sequence of range from this session.

virtual sequence(object, ...) <- value

Loads a sequence into the session.

virtual track(object, name = deparse(substitute(track)), view = TRUE, ...) <- value

Loads one or more tracks into the session and optionally open a view of the track.

x[[i]] <- value

Loads the track value into session x, under the name i. Shortcut to above.

x$name <- value

Loads the track value into session x, under the name name. Shortcut to above.

virtual track(object, ...)

Gets a track from a session.

x[[i]]

Gets the track named i from session x. A shortcut to track.

x$name

Gets the track named name from session x. A shortcut to track.

virtual trackNames(object, ...)

Gets the names of the tracks stored in this session.

virtual genome(x), genome(x) <- value

Gets or sets the genome identifier (e.g. “hg18”) for the session.

virtual close(con, ...)

Close this session.

show(object, ...)

Output a textual description of this session.

Author(s)

Michael Lawrence

See Also

browserSession for obtaining implementations of this class for a particular genome browser.