Some code refactoring, a new version of obiuniq more efficient in memory and a first make file allowing to build obitools

pkg/obiiter/pairedbatchiterator.go

@@ -0,0 +1,221 @@
+package obiiter
+
+import (
+	"log"
+	"sync"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+)
+
+type PairedBioSequenceBatch struct {
+	forward obiseq.BioSequenceSlice
+	reverse obiseq.BioSequenceSlice
+	order   int
+}
+
+var NilPairedBioSequenceBatch = PairedBioSequenceBatch{nil, nil, -1}
+
+func MakePairedBioSequenceBatch(forward, reverse BioSequenceBatch) PairedBioSequenceBatch {
+	if forward.order != reverse.order {
+		log.Fatalf("Forward order : %d and reverse order : %d are not matching",
+			forward.order, reverse.order)
+	}
+
+	for i := range reverse.slice {
+		reverse.slice[i].ReverseComplement(true)
+	}
+
+	return PairedBioSequenceBatch{
+		forward: forward.slice,
+		reverse: reverse.slice,
+		order:   forward.order,
+	}
+}
+
+func (batch PairedBioSequenceBatch) Order() int {
+	return batch.order
+}
+
+func (batch PairedBioSequenceBatch) Reorder(newOrder int) PairedBioSequenceBatch {
+	batch.order = newOrder
+	return batch
+}
+
+
+func (batch PairedBioSequenceBatch) Length() int {
+	return len(batch.forward)
+}
+
+func (batch PairedBioSequenceBatch) Forward() obiseq.BioSequenceSlice {
+	return batch.forward
+}
+
+func (batch PairedBioSequenceBatch) Reverse() obiseq.BioSequenceSlice {
+	return batch.reverse
+}
+
+func (batch PairedBioSequenceBatch) IsNil() bool {
+	return batch.forward == nil
+}
+
+// Structure implementing an iterator over bioseq.BioSequenceBatch
+// based on a channel.
+type __ipairedbiosequencebatch__ struct {
+	channel     chan PairedBioSequenceBatch
+	current     PairedBioSequenceBatch
+	pushBack    bool
+	all_done    *sync.WaitGroup
+	buffer_size int
+	finished    bool
+	p_finished  *bool
+}
+
+type IPairedBioSequenceBatch struct {
+	pointer *__ipairedbiosequencebatch__
+}
+
+var NilIPairedBioSequenceBatch = IPairedBioSequenceBatch{pointer: nil}
+
+func MakeIPairedBioSequenceBatch(sizes ...int) IPairedBioSequenceBatch {
+	buffsize := 1
+
+	if len(sizes) > 0 {
+		buffsize = sizes[0]
+	}
+
+	i := __ipairedbiosequencebatch__{
+		channel:     make(chan PairedBioSequenceBatch, buffsize),
+		current:     NilPairedBioSequenceBatch,
+		pushBack:    false,
+		buffer_size: buffsize,
+		finished:    false,
+		p_finished:  nil,
+	}
+
+	i.p_finished = &i.finished
+	waiting := sync.WaitGroup{}
+	i.all_done = &waiting
+	ii := IPairedBioSequenceBatch{&i}
+	return ii
+}
+
+func (iterator IPairedBioSequenceBatch) Add(n int) {
+	iterator.pointer.all_done.Add(n)
+}
+
+func (iterator IPairedBioSequenceBatch) Done() {
+	iterator.pointer.all_done.Done()
+}
+
+func (iterator IPairedBioSequenceBatch) Wait() {
+	iterator.pointer.all_done.Wait()
+}
+
+func (iterator IPairedBioSequenceBatch) Channel() chan PairedBioSequenceBatch {
+	return iterator.pointer.channel
+}
+
+func (iterator IPairedBioSequenceBatch) IsNil() bool {
+	return iterator.pointer == nil
+}
+
+func (iterator IPairedBioSequenceBatch) BufferSize() int {
+	return iterator.pointer.buffer_size
+}
+
+func (iterator IPairedBioSequenceBatch) Split() IPairedBioSequenceBatch {
+	i := __ipairedbiosequencebatch__{
+		channel:     iterator.pointer.channel,
+		current:     NilPairedBioSequenceBatch,
+		pushBack:    false,
+		all_done:    iterator.pointer.all_done,
+		buffer_size: iterator.pointer.buffer_size,
+		finished:    false,
+		p_finished:  iterator.pointer.p_finished}
+	newIter := IPairedBioSequenceBatch{&i}
+	return newIter
+}
+
+func (iterator IPairedBioSequenceBatch) Next() bool {
+	if *(iterator.pointer.p_finished) {
+		return false
+	}
+
+	if iterator.pointer.pushBack {
+		iterator.pointer.pushBack = false
+		return true
+	}
+
+	next, ok := (<-iterator.pointer.channel)
+
+	if ok {
+		iterator.pointer.current = next
+		return true
+	}
+
+	iterator.pointer.current = NilPairedBioSequenceBatch
+	*iterator.pointer.p_finished = true
+	return false
+}
+
+func (iterator IPairedBioSequenceBatch) PushBack() {
+	if !iterator.pointer.current.IsNil() {
+		iterator.pointer.pushBack = true
+	}
+}
+
+// The 'Get' method returns the instance of BioSequenceBatch
+// 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 IPairedBioSequenceBatch) Get() PairedBioSequenceBatch {
+	return iterator.pointer.current
+}
+
+// Finished returns 'true' value if no more data is available
+// from the iterator.
+func (iterator IPairedBioSequenceBatch) Finished() bool {
+	return *iterator.pointer.p_finished
+}
+
+func (iterator IPairedBioSequenceBatch) SortBatches(sizes ...int) IPairedBioSequenceBatch {
+	buffsize := iterator.BufferSize()
+
+	if len(sizes) > 0 {
+		buffsize = sizes[0]
+	}
+
+	newIter := MakeIPairedBioSequenceBatch(buffsize)
+
+	newIter.Add(1)
+
+	go func() {
+		newIter.Wait()
+		close(newIter.pointer.channel)
+	}()
+
+	next_to_send := 0
+	received := make(map[int]PairedBioSequenceBatch)
+	go func() {
+		for iterator.Next() {
+			batch := iterator.Get()
+			if batch.order == next_to_send {
+				newIter.pointer.channel <- batch
+				next_to_send++
+				batch, ok := received[next_to_send]
+				for ok {
+					newIter.pointer.channel <- batch
+					delete(received, next_to_send)
+					next_to_send++
+					batch, ok = received[next_to_send]
+				}
+			} else {
+				received[batch.order] = batch
+			}
+		}
+		newIter.Done()
+	}()
+
+	return newIter
+
+}