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Refactoring codes for removing buffer size options. An some other changes...

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Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
This commit is contained in:
Eric Coissac
2023-03-07 11:12:13 +07:00
parent 9811e440b8
commit d88de15cdc
52 changed files with 1172 additions and 421 deletions
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67
pkg/obiiter/batchiterator.go
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@ -60,17 +60,11 @@ type IBioSequence struct {
var NilIBioSequence = IBioSequence{pointer: nil}
func MakeIBioSequence(sizes ...int) IBioSequence {
buffsize := int32(0)
if len(sizes) > 0 {
buffsize = int32(sizes[0])
}
i := _IBioSequence{
channel: make(chan BioSequenceBatch, buffsize),
channel: make(chan BioSequenceBatch),
current: NilBioSequenceBatch,
pushBack: abool.New(),
buffer_size: buffsize,
batch_size: -1,
sequence_format: "",
finished: abool.New(),
@ -160,14 +154,6 @@ func (iterator IBioSequence) IsNil() bool {
return iterator.pointer == nil
}
func (iterator IBioSequence) BufferSize() int {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.BufferSize method on NilIBioSequenceBatch")
}
return int(atomic.LoadInt32(&iterator.pointer.buffer_size))
}
func (iterator IBioSequence) BatchSize() int {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.BatchSize method on NilIBioSequenceBatch")
@ -279,13 +265,8 @@ func (iterator IBioSequence) Finished() bool {
// Sorting the batches of sequences.
func (iterator IBioSequence) SortBatches(sizes ...int) IBioSequence {
buffsize := iterator.BufferSize()
if len(sizes) > 0 {
buffsize = sizes[0]
}
newIter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence()
newIter.Add(1)
@ -338,8 +319,7 @@ func (iterator IBioSequence) Concat(iterators ...IBioSequence) IBioSequence {
allPaired = allPaired && i.IsPaired()
}
buffsize := iterator.BufferSize()
newIter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence()
newIter.Add(1)
@ -396,8 +376,7 @@ func (iterator IBioSequence) Pool(iterators ...IBioSequence) IBioSequence {
}
nextCounter := goutils.AtomicCounter()
buffsize := iterator.BufferSize()
newIter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence()
newIter.Add(niterator)
@ -431,13 +410,8 @@ func (iterator IBioSequence) Pool(iterators ...IBioSequence) IBioSequence {
// indicated in parameter. Rebatching implies to sort the
// source IBioSequenceBatch.
func (iterator IBioSequence) Rebatch(size int, sizes ...int) IBioSequence {
buffsize := iterator.BufferSize()
if len(sizes) > 0 {
buffsize = sizes[0]
}
newIter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence()
newIter.Add(1)
@ -532,14 +506,9 @@ func (iterator IBioSequence) Count(recycle bool) (int, int, int) {
// iterator following the predicate value.
func (iterator IBioSequence) DivideOn(predicate obiseq.SequencePredicate,
size int, sizes ...int) (IBioSequence, IBioSequence) {
buffsize := iterator.BufferSize()
if len(sizes) > 0 {
buffsize = sizes[0]
}
trueIter := MakeIBioSequence(buffsize)
falseIter := MakeIBioSequence(buffsize)
trueIter := MakeIBioSequence()
falseIter := MakeIBioSequence()
trueIter.Add(1)
falseIter.Add(1)
@ -604,18 +573,13 @@ func (iterator IBioSequence) DivideOn(predicate obiseq.SequencePredicate,
// A function that takes a predicate and a batch of sequences and returns a filtered batch of sequences.
func (iterator IBioSequence) FilterOn(predicate obiseq.SequencePredicate,
size int, sizes ...int) IBioSequence {
buffsize := iterator.BufferSize()
nworkers := 4
if len(sizes) > 0 {
nworkers = sizes[0]
}
if len(sizes) > 1 {
buffsize = sizes[1]
}
trueIter := MakeIBioSequence(buffsize)
trueIter := MakeIBioSequence()
trueIter.Add(nworkers)
@ -661,18 +625,13 @@ func (iterator IBioSequence) FilterOn(predicate obiseq.SequencePredicate,
func (iterator IBioSequence) FilterAnd(predicate obiseq.SequencePredicate,
size int, sizes ...int) IBioSequence {
buffsize := iterator.BufferSize()
nworkers := 4
if len(sizes) > 0 {
nworkers = sizes[0]
}
if len(sizes) > 1 {
buffsize = sizes[1]
}
trueIter := MakeIBioSequence(buffsize)
trueIter := MakeIBioSequence()
trueIter.Add(nworkers)
@ -740,13 +699,7 @@ func (iterator IBioSequence) Load() obiseq.BioSequenceSlice {
func IBatchOver(data obiseq.BioSequenceSlice,
size int, sizes ...int) IBioSequence {
buffsize := 0
if len(sizes) > 0 {
buffsize = sizes[0]
}
newIter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence()
newIter.Add(1)