func Consumer(limit int, inChan <-chan Task) {
for i := 0; i < limit; i++ {
for s := range inChan {
fmt.Println(nm.PrettyPrint(nm.Nmw(s.a, s.b, s.sm)))
}
}
}
func main() {
var stdinContent string
stdinContent = repeat()
var allA, allB []nm.Sequence
allA, allB = splitOnMarker(stdinContent, "")
//fmt.Println(stdinContent)
//allA = FastaReader{file:fastaFileA}.getSequences()
//allB = FastaReader{file:fastaFileB}.getSequences()
//allA = FastaReaderStd{inputString: stdinContent}.getSequences()
//allB = FastaReaderStd{inputString: stdinContent}.getSequences()
eblosum62 := nm.MakeSubstitutionMatrix("EBLOSUM62")
eblosum62.SetMap("EBLOSUM62")
var maxCPU int = runtime.NumCPU()
var wg sync.WaitGroup
tasks := make(chan Task, 10000)
var resultStr []string
if len(allA)*len(allB) < maxCPU {
maxCPU = len(allA) * len(allB)
}
for i := 0; i < maxCPU; i++ {
wg.Add(1)
go func() {
for t := range tasks {
resultStr = append(resultStr, nm.PrettyPrint(nm.Nmw(t.a, t.b, t.sm)))
}
wg.Done()
}()
}
var seen map[string]bool
seen = make(map[string]bool)
var ok bool
var tmpkey string
for _, a := range allA {
if a.GetSequence() == "" {
continue
}
for _, b := range allB {
if b.GetSequence() == "" {
continue
}
tmpkey = b.GetHeader() + a.GetHeader()
ok = seen[tmpkey]
if ok {
continue
}
tmpkey = a.GetHeader() + b.GetHeader()
ok = seen[tmpkey]
if ok {
continue
}
seen[a.GetHeader()+b.GetHeader()] = true
seen[b.GetHeader()+a.GetHeader()] = true
tasks <- Task{a: a, b: b, sm: eblosum62}
}
}
close(tasks)
wg.Wait()
for _, v := range resultStr {
fmt.Print(v)
}
}