3.swift

/* The Computer Language Benchmarks Game
 https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
 contributed by Ralph Ganszky

 for Swift 3.0+
 using multiple threads by splitting workload in
 random number generation and building output string.
 random number get generated as Int32 like in gcc-7
 by Jeremy Zerfas and normalized in a later step.
*/

import Foundation
import Dispatch

let linewidth = 60
let bufferLines = 10240
let rndBufSize = (bufferLines * linewidth)
let writeBufSize = (bufferLines * (linewidth + 1))

let IM: Int32 = 139968
let IA: Int32 = 3877
let IC: Int32 = 29573
var seed: Int32 = 42

typealias AminoAcid = (prob: Double, sym: String)
typealias CumAcid = (cprob: Int32, sym: Int8)

// String to repeat
let alu = "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTC" +
          "GAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTG" +
          "TAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCG" +
          "CCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA"

// Amino acids and their probabilities
var iub = [
    AminoAcid(0.27, "a"),
    AminoAcid(0.12, "c"),
    AminoAcid(0.12, "g"),
    AminoAcid(0.27, "t"),
    AminoAcid(0.02, "B"),
    AminoAcid(0.02, "D"),
    AminoAcid(0.02, "H"),
    AminoAcid(0.02, "K"),
    AminoAcid(0.02, "M"),
    AminoAcid(0.02, "N"),
    AminoAcid(0.02, "R"),
    AminoAcid(0.02, "S"),
    AminoAcid(0.02, "V"),
    AminoAcid(0.02, "W"),
    AminoAcid(0.02, "Y"),
]

var homosapiens = [
    AminoAcid(0.3029549426680, "a"),
    AminoAcid(0.1979883004921, "c"),
    AminoAcid(0.1975473066391, "g"),
    AminoAcid(0.3015094502008, "t"),
]

// Allocate some resources to buffer data and
// handle ownership by semaphores
let nBufs = 4   // need to be a power of two
var bufs = [UnsafeMutablePointer<Int32>]()
var cBufs = [UnsafeMutablePointer<Int8>]()
var pSemaphore = [DispatchSemaphore]()
var wSemaphore = [DispatchSemaphore]()
for _ in 0..<nBufs {
    bufs.append(UnsafeMutablePointer<Int32>.allocate(capacity: rndBufSize))
    cBufs.append(UnsafeMutablePointer<Int8>.allocate(capacity: writeBufSize))
    pSemaphore.append(DispatchSemaphore(value: 1))
    wSemaphore.append(DispatchSemaphore(value: 1))
}
defer {
    for i in 0..<nBufs {
	bufs[i].deallocate()
	cBufs[i].deallocate()
    }
}

// Let's have some queues to produce data, consume it
// and to syncronize data ownership
let cQueue = DispatchQueue(label: "Consumer", attributes: .concurrent)
let pQueue = DispatchQueue(label: "Producer", attributes: [])
let wQueue = DispatchQueue(label: "Writer", attributes: [])
let group = DispatchGroup()

// Binary search on acids
func bsearch(e: Int32, acids: [CumAcid]) -> Int8 {
    var low = 0
    var high = acids.count - 1
    while low <= high {
        let mid = low + (high - low) / 2
        if acids[mid].cprob >= e {
            high = mid - 1
        } else {
            low = mid + 1
        }
    }
    return acids[high + 1].sym
}

// Build a block in fasta format
func buildFastaBlockFromString(s: String) -> String {
    // Build block of linewidth characters wide string
    let block = String(repeating: s, count: linewidth)
    let blockUP = block.withCString{ s in s }
    var blockNl = UnsafeMutablePointer<Int8>.allocate(capacity: (block.utf16.count)+s.utf16.count*linewidth-1)
    defer {
        blockNl.deallocate()
    }
    var blockIn = blockNl
    for i in 0..<s.utf16.count {
        let beg = blockUP.advanced(by: i*linewidth)
        blockIn.assign(from: beg, count: linewidth)
        blockIn = blockIn.advanced(by: linewidth)
        if i < s.utf16.count - 1 {
            blockIn[0] = "\n".utf8.map{Int8($0)}[0]
            blockIn = blockIn.advanced(by: 1)
        }
    }
    
    // Recreate String
    return String(cString: blockNl)
}

// random
func random() -> Int32 {
    seed = (seed * IA + IC) % IM
    return seed
}

// Producer task
func genRandom(n: Int, block: Int) {
    for i in 0..<min(n, rndBufSize) {
        bufs[block][i] = random()
    }
}

// Consumer task
func consumeRandom(n: Int, block: Int, acids: [CumAcid]) {
    var bufPos = 0
    var lineCounter = 0
    for i in 0..<min(n, rndBufSize) {
        let c = bsearch(e: bufs[block][i], acids: acids)
        cBufs[block][bufPos] = c
        lineCounter += 1
        bufPos += 1
        if lineCounter == linewidth {
            cBufs[block][bufPos] = 10
            bufPos += 1
            lineCounter = 0
        }
    }
}

// Print random amino acid sequences
func randomFasta(n: Int, acids: [AminoAcid]) {
    
    // Adjust probability to cumulative
    var cumulative = 0.0
    var cumAcid = [CumAcid](repeating: (0, 0), count: acids.count)
    for (i, acid) in acids.enumerated() {
        cumulative += acid.prob
        cumAcid[i].cprob = Int32(cumulative*Double(IM))
        cumAcid[i].sym = acid.sym.utf16.map{Int8($0)}[0]
    }
    
    let junks = (n + rndBufSize - 1) / rndBufSize
    let remainder = n % rndBufSize
    var deferedWrite = [Int]()
    var writeBlock = 0
    group.enter()
    pQueue.async {

        for i in 0..<junks-1 {
            let block = i % bufs.count
            pSemaphore[block].wait()
            genRandom(n: rndBufSize, block: block)
            cQueue.async(group: group) {

                wSemaphore[block].wait()
                consumeRandom(n: rndBufSize, block: block, acids: cumAcid)
                pSemaphore[block].signal()
                wQueue.async(group: group) {

                    if block != writeBlock {
                        deferedWrite.append(block)
                    } else {
                        print(String(cString: cBufs[block]), terminator: "")
                        writeBlock = (writeBlock + 1) & (nBufs-1)
                        wSemaphore[block].signal()
                        if deferedWrite.count > 0 {
                            while deferedWrite.contains(writeBlock) {
                                let blk = writeBlock
                                print(String(cString: cBufs[blk]), terminator: "")
                                writeBlock = (writeBlock + 1) & (nBufs-1)
                                deferedWrite.remove(at: deferedWrite.index(of: blk)!)
                                wSemaphore[blk].signal()
                            }
                        }
                    }
                }
            }
        }
        group.leave()
    }
    group.wait()
    genRandom(n: remainder, block: 0)
    consumeRandom(n: remainder, block: 0, acids: cumAcid)

    let last = String(cString: cBufs[0])
    var stringRemainder = remainder+(remainder/linewidth)
    if stringRemainder % (linewidth+1) == 0 {
        stringRemainder -= 1
    }
    print(last[last.startIndex..<last.index(last.startIndex, offsetBy: stringRemainder)])
}

// Print alu string in fasta format
func repeatFasta(n: Int, alu: String) {
    var aluLen = n + n / linewidth
    let aluSize = alu.utf16.count + 1
    if aluLen > aluSize {
        for _ in 0..<aluLen/aluSize {
            print(alu)
        }
        aluLen -= (aluLen / aluSize) * aluSize
    }
    // Remove newline at the end because print adds it anyhow
    if n % linewidth == 0 {
        aluLen -= 1
    }
    if aluLen > 0 {
        print(alu[alu.startIndex..<alu.index(alu.startIndex, offsetBy: aluLen)])
    }
}

// Read command line parameters
let n: Int
if CommandLine.arguments.count > 1 {
    n = Int(CommandLine.arguments[1]) ?? 1000
} else {
    n = 1000
}

// Build block of linewidth characters wide string
let aluBlock = buildFastaBlockFromString(s: alu)

print(">ONE Homo sapiens alu")
repeatFasta(n: 2*n, alu: aluBlock)

print(">TWO IUB ambiguity codes")
randomFasta(n: 3*n, acids: iub)

print(">THREE Homo sapiens frequency")
randomFasta(n: 5*n, acids: homosapiens)