drawable.list-class {Rgb} | R Documentation

## 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`

[Package Rgb version 1.6.1 Index]