obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

rename the iterator class

Browse Source
This commit is contained in:
Eric Coissac
2023-01-22 22:04:17 +01:00
parent 4592855095
commit f97f92df72
37 changed files with 399 additions and 354 deletions
Download Patch File Download Diff File Expand all files Collapse all files

110
pkg/obiiter/batchiterator.go
View File

@ -15,7 +15,7 @@ import (
// Structure implementing an iterator over bioseq.BioSequenceBatch
// based on a channel.
type _IBioSequenceBatch struct {
type _IBioSequence struct {
channel chan BioSequenceBatch
current BioSequenceBatch
pushBack *abool.AtomicBool
@ -27,24 +27,24 @@ type _IBioSequenceBatch struct {
finished *abool.AtomicBool
}
type IBioSequenceBatch struct {
pointer *_IBioSequenceBatch
type IBioSequence struct {
pointer *_IBioSequence
}
// NilIBioSequenceBatch nil instance for IBioSequenceBatch
// NilIBioSequence nil instance for IBioSequenceBatch
//
// NilIBioSequenceBatch is the nil instance for the
// NilIBioSequence is the nil instance for the
// IBioSequenceBatch type.
var NilIBioSequenceBatch = IBioSequenceBatch{pointer: nil}
var NilIBioSequence = IBioSequence{pointer: nil}
func MakeIBioSequenceBatch(sizes ...int) IBioSequenceBatch {
func MakeIBioSequence(sizes ...int) IBioSequence {
buffsize := int32(0)
if len(sizes) > 0 {
buffsize = int32(sizes[0])
}
i := _IBioSequenceBatch{
i := _IBioSequence{
channel: make(chan BioSequenceBatch, buffsize),
current: NilBioSequenceBatch,
pushBack: abool.New(),
@ -58,11 +58,11 @@ func MakeIBioSequenceBatch(sizes ...int) IBioSequenceBatch {
i.all_done = &waiting
lock := sync.RWMutex{}
i.lock = &lock
ii := IBioSequenceBatch{&i}
ii := IBioSequence{&i}
return ii
}
func (iterator IBioSequenceBatch) Add(n int) {
func (iterator IBioSequence) Add(n int) {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.Add method on NilIBioSequenceBatch")
}
@ -70,7 +70,7 @@ func (iterator IBioSequenceBatch) Add(n int) {
iterator.pointer.all_done.Add(n)
}
func (iterator IBioSequenceBatch) Done() {
func (iterator IBioSequence) Done() {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.Done method on NilIBioSequenceBatch")
}
@ -78,7 +78,7 @@ func (iterator IBioSequenceBatch) Done() {
iterator.pointer.all_done.Done()
}
func (iterator IBioSequenceBatch) Unlock() {
func (iterator IBioSequence) Unlock() {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.Unlock method on NilIBioSequenceBatch")
}
@ -86,7 +86,7 @@ func (iterator IBioSequenceBatch) Unlock() {
iterator.pointer.lock.Unlock()
}
func (iterator IBioSequenceBatch) Lock() {
func (iterator IBioSequence) Lock() {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.Lock method on NilIBioSequenceBatch")
}
@ -94,7 +94,7 @@ func (iterator IBioSequenceBatch) Lock() {
iterator.pointer.lock.Lock()
}
func (iterator IBioSequenceBatch) RLock() {
func (iterator IBioSequence) RLock() {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.RLock method on NilIBioSequenceBatch")
}
@ -102,7 +102,7 @@ func (iterator IBioSequenceBatch) RLock() {
iterator.pointer.lock.RLock()
}
func (iterator IBioSequenceBatch) RUnlock() {
func (iterator IBioSequence) RUnlock() {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.RUnlock method on NilIBioSequenceBatch")
}
@ -110,7 +110,7 @@ func (iterator IBioSequenceBatch) RUnlock() {
iterator.pointer.lock.RUnlock()
}
func (iterator IBioSequenceBatch) Wait() {
func (iterator IBioSequence) Wait() {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.Wait method on NilIBioSequenceBatch")
}
@ -118,7 +118,7 @@ func (iterator IBioSequenceBatch) Wait() {
iterator.pointer.all_done.Wait()
}
func (iterator IBioSequenceBatch) Channel() chan BioSequenceBatch {
func (iterator IBioSequence) Channel() chan BioSequenceBatch {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.Channel method on NilIBioSequenceBatch")
}
@ -126,7 +126,7 @@ func (iterator IBioSequenceBatch) Channel() chan BioSequenceBatch {
return iterator.pointer.channel
}
func (iterator IBioSequenceBatch) IsNil() bool {
func (iterator IBioSequence) IsNil() bool {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.IsNil method on NilIBioSequenceBatch")
}
@ -134,7 +134,7 @@ func (iterator IBioSequenceBatch) IsNil() bool {
return iterator.pointer == nil
}
func (iterator IBioSequenceBatch) BufferSize() int {
func (iterator IBioSequence) BufferSize() int {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.BufferSize method on NilIBioSequenceBatch")
}
@ -142,7 +142,7 @@ func (iterator IBioSequenceBatch) BufferSize() int {
return int(atomic.LoadInt32(&iterator.pointer.buffer_size))
}
func (iterator IBioSequenceBatch) BatchSize() int {
func (iterator IBioSequence) BatchSize() int {
if iterator.pointer == nil {
log.Panic("call of IBioSequenceBatch.BatchSize method on NilIBioSequenceBatch")
}
@ -150,7 +150,7 @@ func (iterator IBioSequenceBatch) BatchSize() int {
return int(atomic.LoadInt32(&iterator.pointer.batch_size))
}
func (iterator IBioSequenceBatch) SetBatchSize(size int) error {
func (iterator IBioSequence) SetBatchSize(size int) error {
if size >= 0 {
atomic.StoreInt32(&iterator.pointer.batch_size, int32(size))
return nil
@ -159,10 +159,10 @@ func (iterator IBioSequenceBatch) SetBatchSize(size int) error {
return fmt.Errorf("size (%d) cannot be negative", size)
}
func (iterator IBioSequenceBatch) Split() IBioSequenceBatch {
func (iterator IBioSequence) Split() IBioSequence {
iterator.pointer.lock.RLock()
defer iterator.pointer.lock.RUnlock()
i := _IBioSequenceBatch{
i := _IBioSequence{
channel: iterator.pointer.channel,
current: NilBioSequenceBatch,
pushBack: abool.New(),
@ -174,11 +174,11 @@ func (iterator IBioSequenceBatch) Split() IBioSequenceBatch {
lock := sync.RWMutex{}
i.lock = &lock
newIter := IBioSequenceBatch{&i}
newIter := IBioSequence{&i}
return newIter
}
func (iterator IBioSequenceBatch) Next() bool {
func (iterator IBioSequence) Next() bool {
if iterator.pointer.pushBack.IsSet() {
iterator.pointer.pushBack.UnSet()
return true
@ -200,7 +200,7 @@ func (iterator IBioSequenceBatch) Next() bool {
return false
}
func (iterator IBioSequenceBatch) PushBack() {
func (iterator IBioSequence) PushBack() {
if !iterator.pointer.current.IsNil() {
iterator.pointer.pushBack.Set()
}
@ -210,11 +210,11 @@ func (iterator IBioSequenceBatch) PushBack() {
// currently pointed by the iterator. You have to use the
// 'Next' method to move to the next entry before calling
// 'Get' to retreive the following instance.
func (iterator IBioSequenceBatch) Get() BioSequenceBatch {
func (iterator IBioSequence) Get() BioSequenceBatch {
return iterator.pointer.current
}
func (iterator IBioSequenceBatch) Push(batch BioSequenceBatch) {
func (iterator IBioSequence) Push(batch BioSequenceBatch) {
if batch.IsNil() {
log.Panicln("A Nil batch is pushed on the channel")
}
@ -225,11 +225,11 @@ func (iterator IBioSequenceBatch) Push(batch BioSequenceBatch) {
iterator.pointer.channel <- batch
}
func (iterator IBioSequenceBatch) Close() {
func (iterator IBioSequence) Close() {
close(iterator.pointer.channel)
}
func (iterator IBioSequenceBatch) WaitAndClose() {
func (iterator IBioSequence) WaitAndClose() {
iterator.Wait()
for len(iterator.Channel()) > 0 {
@ -240,18 +240,18 @@ func (iterator IBioSequenceBatch) WaitAndClose() {
// Finished returns 'true' value if no more data is available
// from the iterator.
func (iterator IBioSequenceBatch) Finished() bool {
func (iterator IBioSequence) Finished() bool {
return iterator.pointer.finished.IsSet()
}
func (iterator IBioSequenceBatch) SortBatches(sizes ...int) IBioSequenceBatch {
func (iterator IBioSequence) SortBatches(sizes ...int) IBioSequence {
buffsize := iterator.BufferSize()
if len(sizes) > 0 {
buffsize = sizes[0]
}
newIter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequence(buffsize)
newIter.Add(1)
@ -288,14 +288,14 @@ func (iterator IBioSequenceBatch) SortBatches(sizes ...int) IBioSequenceBatch {
}
func (iterator IBioSequenceBatch) Concat(iterators ...IBioSequenceBatch) IBioSequenceBatch {
func (iterator IBioSequence) Concat(iterators ...IBioSequence) IBioSequence {
if len(iterators) == 0 {
return iterator
}
buffsize := iterator.BufferSize()
newIter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequence(buffsize)
newIter.Add(1)
@ -333,7 +333,7 @@ func (iterator IBioSequenceBatch) Concat(iterators ...IBioSequenceBatch) IBioSeq
return newIter
}
func (iterator IBioSequenceBatch) Pool(iterators ...IBioSequenceBatch) IBioSequenceBatch {
func (iterator IBioSequence) Pool(iterators ...IBioSequence) IBioSequence {
niterator := len(iterators) + 1
@ -343,7 +343,7 @@ func (iterator IBioSequenceBatch) Pool(iterators ...IBioSequenceBatch) IBioSeque
nextCounter := goutils.AtomicCounter()
buffsize := iterator.BufferSize()
newIter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequence(buffsize)
newIter.Add(niterator)
@ -351,7 +351,7 @@ func (iterator IBioSequenceBatch) Pool(iterators ...IBioSequenceBatch) IBioSeque
newIter.WaitAndClose()
}()
ff := func(iterator IBioSequenceBatch) {
ff := func(iterator IBioSequence) {
for iterator.Next() {
s := iterator.Get()
@ -372,14 +372,14 @@ func (iterator IBioSequenceBatch) Pool(iterators ...IBioSequenceBatch) IBioSeque
// IBioSequenceBatch with every batches having the same size
// indicated in parameter. Rebatching implies to sort the
// source IBioSequenceBatch.
func (iterator IBioSequenceBatch) Rebatch(size int, sizes ...int) IBioSequenceBatch {
func (iterator IBioSequence) Rebatch(size int, sizes ...int) IBioSequence {
buffsize := iterator.BufferSize()
if len(sizes) > 0 {
buffsize = sizes[0]
}
newIter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequence(buffsize)
newIter.Add(1)
@ -418,7 +418,7 @@ func (iterator IBioSequenceBatch) Rebatch(size int, sizes ...int) IBioSequenceBa
return newIter
}
func (iterator IBioSequenceBatch) Recycle() {
func (iterator IBioSequence) Recycle() {
log.Debugln("Start recycling of Bioseq objects")
recycled := 0
@ -434,14 +434,14 @@ func (iterator IBioSequenceBatch) Recycle() {
log.Debugf("End of the recycling of %d Bioseq objects", recycled)
}
func (iterator IBioSequenceBatch) Consume() {
func (iterator IBioSequence) Consume() {
for iterator.Next() {
batch := iterator.Get()
batch.Recycle()
}
}
func (iterator IBioSequenceBatch) Count(recycle bool) (int, int, int) {
func (iterator IBioSequence) Count(recycle bool) (int, int, int) {
variants := 0
reads := 0
nucleotides := 0
@ -465,7 +465,7 @@ func (iterator IBioSequenceBatch) Count(recycle bool) (int, int, int) {
return variants, reads, nucleotides
}
func (iterator IBioSequenceBatch) PairWith(reverse IBioSequenceBatch,
func (iterator IBioSequence) PairWith(reverse IBioSequence,
sizes ...int) IPairedBioSequenceBatch {
buffsize := iterator.BufferSize()
batchsize := 5000
@ -510,16 +510,16 @@ func (iterator IBioSequenceBatch) PairWith(reverse IBioSequenceBatch,
// A function that takes a predicate and returns two IBioSequenceBatch iterators.
// Sequences extracted from the input iterator are distributed among both the
// iterator following the predicate value.
func (iterator IBioSequenceBatch) DivideOn(predicate obiseq.SequencePredicate,
size int, sizes ...int) (IBioSequenceBatch, IBioSequenceBatch) {
func (iterator IBioSequence) DivideOn(predicate obiseq.SequencePredicate,
size int, sizes ...int) (IBioSequence, IBioSequence) {
buffsize := iterator.BufferSize()
if len(sizes) > 0 {
buffsize = sizes[0]
}
trueIter := MakeIBioSequenceBatch(buffsize)
falseIter := MakeIBioSequenceBatch(buffsize)
trueIter := MakeIBioSequence(buffsize)
falseIter := MakeIBioSequence(buffsize)
trueIter.Add(1)
falseIter.Add(1)
@ -578,8 +578,8 @@ func (iterator IBioSequenceBatch) DivideOn(predicate obiseq.SequencePredicate,
// Filtering a batch of sequences.
// A function that takes a predicate and a batch of sequences and returns a filtered batch of sequences.
func (iterator IBioSequenceBatch) FilterOn(predicate obiseq.SequencePredicate,
size int, sizes ...int) IBioSequenceBatch {
func (iterator IBioSequence) FilterOn(predicate obiseq.SequencePredicate,
size int, sizes ...int) IBioSequence {
buffsize := iterator.BufferSize()
nworkers := 4
@ -591,7 +591,7 @@ func (iterator IBioSequenceBatch) FilterOn(predicate obiseq.SequencePredicate,
buffsize = sizes[1]
}
trueIter := MakeIBioSequenceBatch(buffsize)
trueIter := MakeIBioSequence(buffsize)
trueIter.Add(nworkers)
@ -599,7 +599,7 @@ func (iterator IBioSequenceBatch) FilterOn(predicate obiseq.SequencePredicate,
trueIter.WaitAndClose()
}()
ff := func(iterator IBioSequenceBatch) {
ff := func(iterator IBioSequence) {
// iterator = iterator.SortBatches()
for iterator.Next() {
@ -633,7 +633,7 @@ func (iterator IBioSequenceBatch) FilterOn(predicate obiseq.SequencePredicate,
// Load all sequences availables from an IBioSequenceBatch iterator into
// a large obiseq.BioSequenceSlice.
func (iterator IBioSequenceBatch) Load() obiseq.BioSequenceSlice {
func (iterator IBioSequence) Load() obiseq.BioSequenceSlice {
chunck := obiseq.MakeBioSequenceSlice()
for iterator.Next() {
@ -648,7 +648,7 @@ func (iterator IBioSequenceBatch) Load() obiseq.BioSequenceSlice {
// It takes a slice of BioSequence objects, and returns an iterator that will return batches of
// BioSequence objects
func IBatchOver(data obiseq.BioSequenceSlice,
size int, sizes ...int) IBioSequenceBatch {
size int, sizes ...int) IBioSequence {
buffsize := 0
@ -656,7 +656,7 @@ func IBatchOver(data obiseq.BioSequenceSlice,
buffsize = sizes[1]
}
newIter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequence(buffsize)
newIter.Add(1)