Description
Reference classes extending this virtual class must have a draw method, so their objects can be managed by tk.browse and browsePlot.Extends
All reference classes extend and inherit methods from Fields
name:- Custom name for the object, as a
character vector of length 1.
parameters:- A
list, storing object-specific parameters to use as draw arguments.
Methods
callParams(chrom, start, end, ...):-
Called with draw() arguments, it returns the final argument list handling default and overloaded parameters.
- chrom, start, end, ... : arguments passed to draw().
check(warn = ):-
Raises an error if the object is not valid, else returns TRUE
chromosomes():-
[Virtual method]
Returns the chromosome list as a vector. NULL is valid if non relevant, but should be avoided when possible.
defaultParams(...):-
Returns class-specific defaults for graphical parameters. Inheriting class should overload it to define their own defaults.
- ... : may be used by inheriting methods, especially for inter-dependant parameters.
draw(chrom, start = , end = , ...):-
[Virtual method]
Draws the object content corresponding to the defined genomic window, usually in a single plot area with coordinates in x and custom data in y.
Overloading methods should use .self$callParams(chrom, start, end ...) to handle drawing parameters and NA coordinates in a consistent way.
- chrom : single integer, numeric or character value, the chromosomal location.
- start : single integer or numeric value, inferior boundary of the window. NA should refer to 0.
- end : single integer or numeric value, superior boundary of the window. NA should refer to .self$getChromEnd().
- ... : additionnal drawing parameters (precede but do not overwrite parameters stored in the object).
fix.param(parent = ):-
Edit drawing parameters using a Tcl-tk GUI
- parent : tcltk parent frame for inclusion, or NULL.
getChromEnd(chrom):-
[Virtual method]
Returns as a single integer value the ending position of the object description of the given chromosome. NA (integer) is valid if non relevant, but should be avoided when possible.
- chrom : single integer, numeric or character value, the chromosomal location. NA is not required to be handled.
getName():-
'name' field accessor.
getParam(name, ...):-
Returns the parameter stored, or the default value if no custom value is stored for it.
- name : single character value, the name of the parameter to return.
- ... : to be passed to defaultParams(), especially for inter-dependant parameters.
initialize(name = , parameters = , ...):setName(value):-
'name' field mutator.
setParam(name, value):-
Updates a parameter stored in the object.
- name : single character value, the name of the parameter to set.
- value : the new value to assign to the parameter (any type). If missing the parameter is discarded, thus returning to dynamic default value.
The following methods are inherited (from the corresponding class):
- callSuper ()
- copy ()
- export ()
- field ()
- getClass ()
- getRefClass ()
- import ()
- initFields ()
- show (, overloaded)
- trace ()
- untrace ()
- usingMethods ()