track.fasta-class {Rgb}

Class "track.fasta"

Description

"track.fasta" is a drawing wraper for FASTA files.

Notice the data are not stored directly in the object, but stay in the original FASTA file(s), thus exported track.fasta objects may be broken (the check method can confirm this).

Objects are produced by the track.fasta.multi and track.fasta.collection constructors.

Extends

Class sliceable, directly.
Class drawable, by class sliceable, distance 2.

All reference classes extend and inherit methods from envRefClass.

Fields

assembly:

Single character value, the assembly version for the coordinates stored in the object. Must have length 1, should not be NA.

files:

A data.frame, with 6 columns : file (character), header (character), startOffset (numeric), lineLength (integer), breakSize (integer) and contentSize (integer). Each row refers to a distinct chromosome, whose name is stored as row name.

organism:

Single character value, the name of the organism whose data is stored in the object. Must have length 1, should not be NA.

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

• name (drawable)

• parameters (drawable)

Methods

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

• callParams (drawable)

• callSuper (envRefClass)

• check (drawable, overloaded)

• chromosomes (drawable, overloaded)

• copy (envRefClass)

• defaultParams (sliceable, overloaded)

• draw (sliceable)

• export (envRefClass)

• field (envRefClass)

• fix.param (drawable)

• getChromEnd (sliceable, overloaded)

• getClass (envRefClass)

• getName (drawable)

• getParam (drawable)

• getRefClass (envRefClass)

• import (envRefClass)

• initFields (envRefClass)

• initialize (drawable, overloaded)

• setName (drawable)

• setParam (drawable)

• show (sliceable, overloaded)

• slice (sliceable, overloaded)

• trace (envRefClass)

• untrace (envRefClass)

• usingMethods (envRefClass)

Author(s)

Sylvain Mareschal

See Also

track.table, sliceable-class, drawable-class