drawable.list-class: Class '"drawable.list"'

In Rgb: The R Genome Browser

Class "drawable.list"

Description

The purpose of this class is to store and manage a collection of drawable objects. These collections are to be used by tk.browse and browsePlot as input.

Objects can be created by the drawable.list constructor, and edited / created using the tk.tracks Tcl-tk interface.

By default, the drawable.list$add() method is only able to handle objects from drawable-inheriting classes saved in RDT or RDS individual files. This can however be extended defining functions named drawableFromFile.EXTENSION and drawableFromClass.CLASS, in the global environment or a package. Such a function will take the same arguments as the drawable.list$add() method, and will only have to return a drawable-inheriting object.

Extends

All reference classes extend and inherit methods from envRefClass.

Fields

classes:

Read-only, returns a vector of objects classes.

count:

Read-only, returns the length of objects, as a single integer.

files:

Character vector, the paths where each drawable object is to be stored.

hidden:

Logical vector, whether each object is to drawn or hidden in plots.

names:

Read-only, returns a vector of objects 'name' fields.

objects:

List of drawable-inheriting objects.

Methods

add(file, track = , hidden = , ...):

Add a track to the list.
- file : single character value, the path to the file containing the 'drawable' object to add.
- track : a 'drawable' object to add. If NULL, will be extracted from 'file'.
- hidden : single logical value, whether the track is to be shown on plots or hidden. This value can be changed later. - ... : further arguments to be passed to drawableFromFile.EXTENSION or drawableFromClass.CLASS, if relevant.

check(warn = ):

Raises an error if the object is not valid, else returns TRUE

fix.files(parent = ):

Edit drawable list using a Tcl-tk GUI
- parent : tcltk parent frame for inclusion, or NULL.

fix.param(selection = , parent = ):

Edit drawing parameters using a Tcl-tk GUI
- selection : single integer value, the position of the track selected in the list.
- parent : tcltk parent frame for inclusion, or NULL.

get(index, what = ):

Returns a single 'what' from the series
- index : single numeric value, the position of the track to get.
- what : single character value, the field to be exracted.

getByClasses(classes, what = ):

Returns a subset of 'what' from the series, querying by class inheritance
- classes : character vector, the class names of the objects to get (inheriting classes are picked too).
- what : single character value, the field to be exracted.

getByNames(names, what = ):

Returns a subset of 'what' from the series, querying by track name
- names : character vector, the names of the objects to get.
- what : single character value, the field to be exracted.

getByPositions(positions, what = ):

Returns a subset of 'what' from the series, querying by position
- positions : integer vector, the positions of the objects to get.
- what : single character value, the field to be exracted.

getChromEnd(chrom):

Returns as a single integer value the maximal ending position of the object descriptions of the given chromosome.
- chrom : single integer, numeric or character value, the chromosomal location.

,

initialize(files = , objects = , hidden = , ...):

moveDown(toMove):

Increases the position of a track, switching position with the next one
- toMove : single numeric value, the position of the track to move.

moveUp(toMove):

Decreases the position of a track, switching position with the previous one
- toMove : single numeric value, the position of the track to move.

remove(toRemove):

Remove one or many tracks from the list
- toRemove : numeric vector, the positions of the tracks to remove.

The following methods are inherited (from the corresponding class):

• callSuper (envRefClass)

• copy (envRefClass)

• export (envRefClass)

• field (envRefClass)

• getClass (envRefClass)

• getRefClass (envRefClass)

• import (envRefClass)

• initFields (envRefClass)

• show (envRefClass, overloaded)

• trace (envRefClass)

• untrace (envRefClass)

• usingMethods (envRefClass)

Author(s)

Sylvain Mareschal

See Also

drawable.list, drawable-class, tk.browse, browsePlot

Rgb documentation built on Aug. 18, 2023, 5:05 p.m.