# Introduction to object-oriented programming in R
# Classes and objects in R

###################################################################
# Basic definition of classes, inheritance and object generation
###################################################################

# 1. Definition of a class
# Definition of a class
setClass("sequence", representation(x="character"), prototype(x=character(3)));

# obtaining information about the class
getClass("sequence");

# 2. Construction of objects of a given class
# Object construction
s0<-new("sequence");
seq <- new("sequence", x = c("A","T",rep("C",4),rep("G",8),"T","A","T"));

# 3. Definition of classes with inheritance
setClass("Pairedseq",representation(y="character"), 
         prototype(x=character(3), y=character(3)), contains="sequence");

# obtaining information about the class
getClass("Pairedseq");

paired <- new("Pairedseq", x=c("UUC", "CCA", "GCA"), y=c("Phe", "Pro", "Ala"));

# A new class that inherits from Pairedseq
setClass("Threeseq",representation("Pairedseq",z="character"), 
         prototype(x=character(3), y=character(3), z=character(3)));
# obtaining information about the class
getClass("Threeseq");


# 4. Definition of a constructor for a given class
# Constructor
Pairedseq <- function(x,y) {
   if (length(x)!=length(y))
      stop("the two sequences must match in length.");
   new("Pairedseq",x=x,y=y)
}

# getting an object of class Pairedseq using the constructor
pseq <- Pairedseq(LETTERS[1:5],LETTERS[6:10]);
pseq <- Pairedseq(LETTERS[1:5],LETTERS[6:12]);  # error !



#######################################################################
# Slot accession, validity checking and relationships testing
#######################################################################
# Definition of the class track
setClass("track", representation(x = "numeric", y = "numeric"));

# Getting an object of class track
pos1 <- c(156, 182, 211, 212, 218, 220, 246, 247, 251, 252, 254, 258, 261, 263);
resp1 <- c(348, 325, 333, 345, 325, 334, 334, 332, 347, 335, 340, 337, 323, 327);
tr1 <- new("track", x = pos1, y = resp1);

# Slot accession
tr1@x;
slot(tr1,"x");
# getting slot names 
slotNames(tr1)
# getting names and classes of slots of a class
getSlots("track")


# Validity checking methods
# Validity checking for objects of class track
valid.track <- function(object) {
  if (any(is.na(object@x)) || any(is.na(object@y)))
    return ("x, y slots should not have NA values");
  if (!identical(length(object@x),length(object@y)))
     return ("x, y slots should have equal length");
  return(TRUE);
}

# Redefinition of class track with validity checking
setClass("track", representation(x = "numeric", y = "numeric"), validity=valid.track);
tr2<-new("track");
tr2<-new("track", x=rep(1,5), y=c(1,1,1,1,NA));  # error
tr2<-new("track", x=rep(1,5), y=rep(2,6));  # error
tr2<-new("track", x=rep(1,5), y=rep(2,5)); # OK

# Relations between classes
# Testing the is relation
is(tr2,"track");
# testing the extends relation
extends("sequence","numeric")
extends("Pairedseq","sequence")

# Definition of a new class
setClass("track.novel", "track");
getClass("track.novel");


# Removing a class
removeClass("track.novel");