BrowserSession-class: Class "BrowserSession"
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.
See Also
browserSession for obtaining implementations of this
class for a particular genome browser.