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##~~~~~~~~~~~~~~~~~~~~~~~~~define class~~~~~~~~~~~~~~~~~~~~~~~~~
## new class
setClass(Class = 'trick',
         slots = c(id = 'character', time = 'matrix'),
         validity = function(object) {
           if (length(object@id) != nrow(object@time)) {
             warns <- paste('length of id is', length(object@id), 'is not equal to row number of time', nrow(object@time))
             return(warns)
           } else {
             return(TRUE)

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SSIndex <- function(i, len, wise = 5) {

  min <- i - wise
  min <- ifelse(min < 1, 1, min)

  max <- i + wise
  max <- ifelse(max > len, len, max)

  return(seq(min, max))
}

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#include <iostream>

int main() {
    double sum = 0.0;
    double step = 0.01;
    double each = 0.01;

    for (int i = 0; i < 100; ++i) {
        sum += step;
        step += each;

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###Download gff/fna/ptt/rnt annotation files of a prokaryotic genome ####

## Escherichia coli str. K-12 substr. MG1655 (E. coli)
## KEGG ID is 'eco' (http://www.genome.jp/kegg-bin/show_organism?org=eco)
## NCBI assembly ID is 'GCF_000005845.2' (https://www.ncbi.nlm.nih.gov/assembly/GCF_000005845.2)


library('ProGenome') ## version >= 0.06
library('magrittr')

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samtools view -b Example_Condition1.sam -o Example_Condition1.bam
samtools view -b Example_Condition2.sam -o Example_Condition2.bam

## reverse
samtools view -h -f 16 Example_Condition1.bam -o Example_Condition1_rev.bam
## forward
samtools view -h -F 16 Example_Condition1.bam -o Example_Condition1_forw.bam

## reverse
samtools view -h -f 16 Example_Condition2.bam -o Example_Condition2_rev.bam

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#include <iostream>
#include <limits>

using namespace std;

int main() {

    int a = numeric_limits<int>::min();
    int b = numeric_limits<int>::max();

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#include <stdio.h>
#include <limits.h>
#include <float.h>

int main() {

    int a = INT_MIN;
    int b = INT_MAX;
    double c = DBL_MIN;

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## set working path
setwd('/home/Yulong/RESEARCH/QAPTest/')

## to symmetric matrix
SymMat <- function(mat) {
  ## example
  ## tmp1 <- matrix(c(1, '-', '-', 2, 4, '-', 3, 5, 6), ncol = 3, byrow = TRUE)
  mat <- apply(mat, 1:2, as.character)
  mat <- ifelse(mat == '-', 0, mat)
  mat <- apply(mat, 1:2, as.numeric)

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#include <RcppArmadillo.h>
#include <RcppParallel.h>
#include <algorithm>
#include <cmath>

using namespace Rcpp;
using namespace RcppParallel;
using namespace arma;

// [[Rcpp::depends(RcppArmadillo, RcppParallel)]]

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library('microbenchmark')
library('Rcpp')
library('RcppParallel')
library('foreach')
library('parallel')
library('doParallel')
library('iterators')

sourceCpp('testrcpp.cpp')