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Code refactoring

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This commit is contained in:
Eric Coissac
2022-01-14 17:32:12 +01:00
parent 5753723618
commit ef66ca4972
16 changed files with 260 additions and 260 deletions
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80
pkg/obiseq/batchiterator.go
View File

@@ -103,8 +103,8 @@ func (iterator IBioSequenceBatch) Split() IBioSequenceBatch {
buffer_size: iterator.pointer.buffer_size,
finished: false,
p_finished: iterator.pointer.p_finished}
new_iter := IBioSequenceBatch{&i}
return new_iter
newIter := IBioSequenceBatch{&i}
return newIter
}
func (iterator IBioSequenceBatch) Next() bool {
@@ -144,13 +144,13 @@ func (iterator IBioSequenceBatch) IBioSequence(sizes ...int) IBioSequence {
buffsize = sizes[0]
}
new_iter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
go func() {
@@ -158,13 +158,13 @@ func (iterator IBioSequenceBatch) IBioSequence(sizes ...int) IBioSequence {
batch := iterator.Get()
for _, s := range batch.slice {
new_iter.pointer.channel <- s
newIter.pointer.channel <- s
}
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
func (iterator IBioSequenceBatch) SortBatches(sizes ...int) IBioSequenceBatch {
@@ -174,13 +174,13 @@ func (iterator IBioSequenceBatch) SortBatches(sizes ...int) IBioSequenceBatch {
buffsize = sizes[0]
}
new_iter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequenceBatch(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
next_to_send := 0
@@ -189,11 +189,11 @@ func (iterator IBioSequenceBatch) SortBatches(sizes ...int) IBioSequenceBatch {
for iterator.Next() {
batch := iterator.Get()
if batch.order == next_to_send {
new_iter.pointer.channel <- batch
newIter.pointer.channel <- batch
next_to_send++
batch, ok := received[next_to_send]
for ok {
new_iter.pointer.channel <- batch
newIter.pointer.channel <- batch
delete(received, next_to_send)
next_to_send++
batch, ok = received[next_to_send]
@@ -202,10 +202,10 @@ func (iterator IBioSequenceBatch) SortBatches(sizes ...int) IBioSequenceBatch {
received[batch.order] = batch
}
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
@@ -216,13 +216,13 @@ func (iterator IBioSequenceBatch) Concat(iterators ...IBioSequenceBatch) IBioSeq
}
buffsize := iterator.BufferSize()
new_iter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequenceBatch(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.Channel())
newIter.Wait()
close(newIter.Channel())
}()
go func() {
@@ -234,7 +234,7 @@ func (iterator IBioSequenceBatch) Concat(iterators ...IBioSequenceBatch) IBioSeq
if s.order > max_order {
max_order = s.order
}
new_iter.Channel() <- MakeBioSequenceBatch(s.order+previous_max, s.slice...)
newIter.Channel() <- MakeBioSequenceBatch(s.order+previous_max, s.slice...)
}
previous_max = max_order + 1
@@ -245,14 +245,14 @@ func (iterator IBioSequenceBatch) Concat(iterators ...IBioSequenceBatch) IBioSeq
max_order = s.order + previous_max
}
new_iter.Channel() <- MakeBioSequenceBatch(s.order+previous_max, s.slice...)
newIter.Channel() <- MakeBioSequenceBatch(s.order+previous_max, s.slice...)
}
previous_max = max_order + 1
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
// Redistributes sequences from a IBioSequenceBatch into a new
@@ -266,13 +266,13 @@ func (iterator IBioSequenceBatch) Rebatch(size int, sizes ...int) IBioSequenceBa
buffsize = sizes[0]
}
new_iter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequenceBatch(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
go func() {
@@ -285,7 +285,7 @@ func (iterator IBioSequenceBatch) Rebatch(size int, sizes ...int) IBioSequenceBa
for _, s := range seqs.slice {
buffer = append(buffer, s)
if len(buffer) == size {
new_iter.Channel() <- MakeBioSequenceBatch(order, buffer...)
newIter.Channel() <- MakeBioSequenceBatch(order, buffer...)
order++
buffer = make(BioSequenceSlice, 0, size)
}
@@ -293,14 +293,14 @@ func (iterator IBioSequenceBatch) Rebatch(size int, sizes ...int) IBioSequenceBa
}
if len(buffer) > 0 {
new_iter.Channel() <- MakeBioSequenceBatch(order, buffer...)
newIter.Channel() <- MakeBioSequenceBatch(order, buffer...)
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
func (iterator IBioSequenceBatch) Destroy() {
@@ -331,13 +331,13 @@ func (iterator IBioSequenceBatch) PairWith(reverse IBioSequenceBatch, sizes ...i
iterator = iterator.Rebatch(batchsize)
reverse = reverse.Rebatch(batchsize)
new_iter := MakeIPairedBioSequenceBatch(buffsize)
newIter := MakeIPairedBioSequenceBatch(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
log.Println("End of association of paired reads")
}()
@@ -347,12 +347,12 @@ func (iterator IBioSequenceBatch) PairWith(reverse IBioSequenceBatch, sizes ...i
if !reverse.Next() {
log.Panicln("Etrange reverse pas prêt")
}
new_iter.Channel() <- MakePairedBioSequenceBatch(iterator.Get(),
newIter.Channel() <- MakePairedBioSequenceBatch(iterator.Get(),
reverse.Get())
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}

94
pkg/obiseq/iterator.go
View File

@@ -73,8 +73,8 @@ func (iterator IBioSequence) Split() IBioSequence {
all_done: iterator.pointer.all_done,
buffer_size: iterator.pointer.buffer_size,
p_finished: iterator.pointer.p_finished}
new_iter := IBioSequence{&i}
return new_iter
newIter := IBioSequence{&i}
return newIter
}
func (iterator IBioSequence) Next() bool {
@@ -132,16 +132,16 @@ func (iterator IBioSequence) IBioSequenceBatch(sizes ...int) IBioSequenceBatch {
buffsize = sizes[1]
}
new_iter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequenceBatch(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
for len(new_iter.Channel()) > 0 {
newIter.Wait()
for len(newIter.Channel()) > 0 {
time.Sleep(time.Millisecond)
}
close(new_iter.pointer.channel)
close(newIter.pointer.channel)
}()
go func() {
@@ -153,12 +153,12 @@ func (iterator IBioSequence) IBioSequenceBatch(sizes ...int) IBioSequenceBatch {
seq := iterator.Get()
batch.slice = append(batch.slice, seq)
}
new_iter.pointer.channel <- batch
newIter.pointer.channel <- batch
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
func (iterator IBioSequence) IBioSequence(sizes ...int) IBioSequence {
@@ -168,24 +168,24 @@ func (iterator IBioSequence) IBioSequence(sizes ...int) IBioSequence {
buffsize = sizes[0]
}
new_iter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
go func() {
for iterator.Next() {
s := iterator.Get()
new_iter.pointer.channel <- s
newIter.pointer.channel <- s
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
func (iterator IBioSequence) Skip(n int, sizes ...int) IBioSequence {
@@ -195,26 +195,26 @@ func (iterator IBioSequence) Skip(n int, sizes ...int) IBioSequence {
buffsize = sizes[0]
}
new_iter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
go func() {
for i := 0; iterator.Next(); i++ {
if i >= n {
s := iterator.Get()
new_iter.pointer.channel <- s
newIter.pointer.channel <- s
}
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
func (iterator IBioSequence) Head(n int, sizes ...int) IBioSequence {
@@ -224,13 +224,13 @@ func (iterator IBioSequence) Head(n int, sizes ...int) IBioSequence {
buffsize = sizes[0]
}
new_iter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
go func() {
@@ -238,17 +238,17 @@ func (iterator IBioSequence) Head(n int, sizes ...int) IBioSequence {
for i := 0; iterator.Next(); i++ {
if i < n {
s := iterator.Get()
new_iter.pointer.channel <- s
newIter.pointer.channel <- s
} else {
if not_done {
new_iter.Done()
newIter.Done()
not_done = false
}
}
}
}()
return new_iter
return newIter
}
// The 'Tail' method discard every data from the source iterator
@@ -260,14 +260,14 @@ func (iterator IBioSequence) Tail(n int, sizes ...int) IBioSequence {
buffsize = sizes[0]
}
new_iter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence(buffsize)
buffseq := make(BioSequenceSlice, n)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
go func() {
@@ -277,18 +277,18 @@ func (iterator IBioSequence) Tail(n int, sizes ...int) IBioSequence {
}
if i > n {
for j := 0; j < n; j++ {
new_iter.Channel() <- buffseq[(i+j)%n]
newIter.Channel() <- buffseq[(i+j)%n]
}
} else {
for j := 0; j < i; j++ {
new_iter.Channel() <- buffseq[j]
newIter.Channel() <- buffseq[j]
}
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
func (iterator IBioSequence) Concat(iterators ...IBioSequence) IBioSequence {
@@ -298,29 +298,29 @@ func (iterator IBioSequence) Concat(iterators ...IBioSequence) IBioSequence {
}
buffsize := iterator.BufferSize()
new_iter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
go func() {
for iterator.Next() {
s := iterator.Get()
new_iter.pointer.channel <- s
newIter.pointer.channel <- s
}
for _, iter := range iterators {
for iter.Next() {
s := iter.Get()
new_iter.pointer.channel <- s
newIter.pointer.channel <- s
}
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}

20
pkg/obiseq/pairedbatchiterator.go
View File

@@ -119,8 +119,8 @@ func (iterator IPairedBioSequenceBatch) Split() IPairedBioSequenceBatch {
buffer_size: iterator.pointer.buffer_size,
finished: false,
p_finished: iterator.pointer.p_finished}
new_iter := IPairedBioSequenceBatch{&i}
return new_iter
newIter := IPairedBioSequenceBatch{&i}
return newIter
}
func (iterator IPairedBioSequenceBatch) Next() bool {
@@ -160,13 +160,13 @@ func (iterator IPairedBioSequenceBatch) SortBatches(sizes ...int) IPairedBioSequ
buffsize = sizes[0]
}
new_iter := MakeIPairedBioSequenceBatch(buffsize)
newIter := MakeIPairedBioSequenceBatch(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
next_to_send := 0
@@ -175,11 +175,11 @@ func (iterator IPairedBioSequenceBatch) SortBatches(sizes ...int) IPairedBioSequ
for iterator.Next() {
batch := iterator.Get()
if batch.order == next_to_send {
new_iter.pointer.channel <- batch
newIter.pointer.channel <- batch
next_to_send++
batch, ok := received[next_to_send]
for ok {
new_iter.pointer.channel <- batch
newIter.pointer.channel <- batch
delete(received, next_to_send)
next_to_send++
batch, ok = received[next_to_send]
@@ -188,9 +188,9 @@ func (iterator IPairedBioSequenceBatch) SortBatches(sizes ...int) IPairedBioSequ
received[batch.order] = batch
}
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}

46
pkg/obiseq/workers.go
View File

@@ -25,25 +25,25 @@ func (iterator IBioSequence) MakeIWorker(worker SeqWorker, sizes ...int) IBioSeq
buffsize = sizes[0]
}
new_iter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
go func() {
for iterator.Next() {
seq := iterator.Get()
seq = worker(seq)
new_iter.pointer.channel <- seq
newIter.pointer.channel <- seq
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
func (iterator IBioSequenceBatch) MakeIWorker(worker SeqWorker, sizes ...int) IBioSequenceBatch {
@@ -58,16 +58,16 @@ func (iterator IBioSequenceBatch) MakeIWorker(worker SeqWorker, sizes ...int) IB
buffsize = sizes[1]
}
new_iter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequenceBatch(buffsize)
new_iter.Add(nworkers)
newIter.Add(nworkers)
go func() {
new_iter.Wait()
for len(new_iter.Channel()) > 0 {
newIter.Wait()
for len(newIter.Channel()) > 0 {
time.Sleep(time.Millisecond)
}
close(new_iter.pointer.channel)
close(newIter.pointer.channel)
log.Println("End of the batch workers")
}()
@@ -78,9 +78,9 @@ func (iterator IBioSequenceBatch) MakeIWorker(worker SeqWorker, sizes ...int) IB
for i, seq := range batch.slice {
batch.slice[i] = worker(seq)
}
new_iter.pointer.channel <- batch
newIter.pointer.channel <- batch
}
new_iter.Done()
newIter.Done()
}
log.Println("Start of the batch workers")
@@ -88,7 +88,7 @@ func (iterator IBioSequenceBatch) MakeIWorker(worker SeqWorker, sizes ...int) IB
go f(iterator.Split())
}
return new_iter
return newIter
}
func (iterator IBioSequenceBatch) MakeISliceWorker(worker SeqSliceWorker, sizes ...int) IBioSequenceBatch {
@@ -103,16 +103,16 @@ func (iterator IBioSequenceBatch) MakeISliceWorker(worker SeqSliceWorker, sizes
buffsize = sizes[1]
}
new_iter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequenceBatch(buffsize)
new_iter.Add(nworkers)
newIter.Add(nworkers)
go func() {
new_iter.Wait()
for len(new_iter.Channel()) > 0 {
newIter.Wait()
for len(newIter.Channel()) > 0 {
time.Sleep(time.Millisecond)
}
close(new_iter.pointer.channel)
close(newIter.pointer.channel)
log.Println("End of the batch slice workers")
}()
@@ -120,9 +120,9 @@ func (iterator IBioSequenceBatch) MakeISliceWorker(worker SeqSliceWorker, sizes
for iterator.Next() {
batch := iterator.Get()
batch.slice = worker(batch.slice)
new_iter.pointer.channel <- batch
newIter.pointer.channel <- batch
}
new_iter.Done()
newIter.Done()
}
log.Println("Start of the batch slice workers")
@@ -130,5 +130,5 @@ func (iterator IBioSequenceBatch) MakeISliceWorker(worker SeqSliceWorker, sizes
go f(iterator.Split())
}
return new_iter
return newIter
}