rename the iterator class

pkg/obichunk/chunk_on_disk.go

@@ -35,12 +35,12 @@ func find(root, ext string) []string {
 	return a
 }
 
-func ISequenceChunkOnDisk(iterator obiiter.IBioSequenceBatch,
+func ISequenceChunkOnDisk(iterator obiiter.IBioSequence,
 	classifier *obiseq.BioSequenceClassifier,
-	sizes ...int) (obiiter.IBioSequenceBatch, error) {
+	sizes ...int) (obiiter.IBioSequence, error) {
 	dir, err := tempDir()
 	if err != nil {
-		return obiiter.NilIBioSequenceBatch, err
+		return obiiter.NilIBioSequence, err
 	}
 
 	bufferSize := iterator.BufferSize()
@@ -49,7 +49,7 @@ func ISequenceChunkOnDisk(iterator obiiter.IBioSequenceBatch,
 		bufferSize = sizes[0]
 	}
 
-	newIter := obiiter.MakeIBioSequenceBatch(bufferSize)
+	newIter := obiiter.MakeIBioSequence(bufferSize)
 
 	newIter.Add(1)
 

pkg/obichunk/chunks.go

@@ -1,16 +1,17 @@
 package obichunk
 
 import (
-	log "github.com/sirupsen/logrus"
 	"sync"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
 
-func ISequenceChunk(iterator obiiter.IBioSequenceBatch,
+func ISequenceChunk(iterator obiiter.IBioSequence,
 	classifier *obiseq.BioSequenceClassifier,
-	sizes ...int) (obiiter.IBioSequenceBatch, error) {
+	sizes ...int) (obiiter.IBioSequence, error) {
 
 	bufferSize := iterator.BufferSize()
 
@@ -18,7 +19,7 @@ func ISequenceChunk(iterator obiiter.IBioSequenceBatch,
 		bufferSize = sizes[0]
 	}
 
-	newIter := obiiter.MakeIBioSequenceBatch(bufferSize)
+	newIter := obiiter.MakeIBioSequence(bufferSize)
 
 	newIter.Add(1)
 

pkg/obichunk/subchunks.go

@@ -56,9 +56,9 @@ func (by _By) Sort(seqs []sSS) {
 // End of the sort interface
 //
 
-func ISequenceSubChunk(iterator obiiter.IBioSequenceBatch,
+func ISequenceSubChunk(iterator obiiter.IBioSequence,
 	classifier *obiseq.BioSequenceClassifier,
-	sizes ...int) (obiiter.IBioSequenceBatch, error) {
+	sizes ...int) (obiiter.IBioSequence, error) {
 
 	bufferSize := iterator.BufferSize()
 	nworkers := 4
@@ -71,7 +71,7 @@ func ISequenceSubChunk(iterator obiiter.IBioSequenceBatch,
 		bufferSize = sizes[1]
 	}
 
-	newIter := obiiter.MakeIBioSequenceBatch(bufferSize)
+	newIter := obiiter.MakeIBioSequence(bufferSize)
 
 	newIter.Add(nworkers)
 
@@ -88,7 +88,7 @@ func ISequenceSubChunk(iterator obiiter.IBioSequenceBatch,
 		return neworder
 	}
 
-	ff := func(iterator obiiter.IBioSequenceBatch,
+	ff := func(iterator obiiter.IBioSequence,
 		classifier *obiseq.BioSequenceClassifier) {
 
 		ordered := make([]sSS, 100)

pkg/obichunk/unique.go

@@ -12,14 +12,14 @@ import (
 // Runs dereplication algorithm on a  obiiter.IBioSequenceBatch
 // iterator.
 
-func IUniqueSequence(iterator obiiter.IBioSequenceBatch,
+func IUniqueSequence(iterator obiiter.IBioSequence,
-	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+	options ...WithOption) (obiiter.IBioSequence, error) {
 
 	var err error
 	opts := MakeOptions(options)
 	nworkers := opts.ParallelWorkers()
 
-	iUnique := obiiter.MakeIBioSequenceBatch(opts.BufferSize())
+	iUnique := obiiter.MakeIBioSequence(opts.BufferSize())
 
 	iterator = iterator.Speed("Splitting data set")
 
@@ -32,7 +32,7 @@ func IUniqueSequence(iterator obiiter.IBioSequenceBatch,
 			0)
 
 		if err != nil {
-			return obiiter.NilIBioSequenceBatch, err
+			return obiiter.NilIBioSequence, err
 		}
 
 	} else {
@@ -41,7 +41,7 @@ func IUniqueSequence(iterator obiiter.IBioSequenceBatch,
 			opts.BufferSize())
 
 		if err != nil {
-			return obiiter.NilIBioSequenceBatch, err
+			return obiiter.NilIBioSequence, err
 		}
 	}
 
@@ -65,14 +65,14 @@ func IUniqueSequence(iterator obiiter.IBioSequenceBatch,
 		return neworder
 	}
 
-	var ff func(obiiter.IBioSequenceBatch,
+	var ff func(obiiter.IBioSequence,
 		*obiseq.BioSequenceClassifier,
 		int)
 
 	cat := opts.Categories()
 	na := opts.NAValue()
 
-	ff = func(input obiiter.IBioSequenceBatch,
+	ff = func(input obiiter.IBioSequence,
 		classifier *obiseq.BioSequenceClassifier,
 		icat int) {
 		icat--
@@ -81,9 +81,9 @@ func IUniqueSequence(iterator obiiter.IBioSequenceBatch,
 			1,
 			opts.BufferSize())
 
-		var next obiiter.IBioSequenceBatch
+		var next obiiter.IBioSequence
 		if icat >= 0 {
-			next = obiiter.MakeIBioSequenceBatch(opts.BufferSize())
+			next = obiiter.MakeIBioSequence(opts.BufferSize())
 
 			iUnique.Add(1)
 

pkg/obiformats/batch_of_files_reader.go

@@ -10,13 +10,13 @@ import (
 func ReadSequencesBatchFromFiles(filenames []string,
 	reader IBatchReader,
 	concurrent_readers int,
-	options ...WithOption) obiiter.IBioSequenceBatch {
+	options ...WithOption) obiiter.IBioSequence {
 
 	if reader == nil {
 		reader = ReadSequencesFromFile
 	}
 
-	batchiter := obiiter.MakeIBioSequenceBatch(0)
+	batchiter := obiiter.MakeIBioSequence(0)
 	nextCounter := goutils.AtomicCounter()
 
 	batchiter.Add(concurrent_readers)

pkg/obiformats/batch_reader_type.go

@@ -2,4 +2,4 @@ package obiformats
 
 import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 
-type IBatchReader func(string, ...WithOption) (obiiter.IBioSequenceBatch, error)
+type IBatchReader func(string, ...WithOption) (obiiter.IBioSequence, error)

pkg/obiformats/dispatcher.go

@@ -2,15 +2,16 @@ package obiformats
 
 import (
 	"fmt"
-	log "github.com/sirupsen/logrus"
 	"sync"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 )
 
-type SequenceBatchWriterToFile func(iterator obiiter.IBioSequenceBatch,
+type SequenceBatchWriterToFile func(iterator obiiter.IBioSequence,
 	filename string,
-	options ...WithOption) (obiiter.IBioSequenceBatch, error)
+	options ...WithOption) (obiiter.IBioSequence, error)
 
 func WriterDispatcher(prototypename string,
 	dispatcher obiiter.IDistribute,

pkg/obiformats/ecopcr_read.go

@@ -120,7 +120,7 @@ func __read_ecopcr_bioseq__(file *__ecopcr_file__) (*obiseq.BioSequence, error)
 	return bseq, nil
 }
 
-func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
+func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
 	tag := make([]byte, 11)
 	n, _ := reader.Read(tag)
 
@@ -166,7 +166,7 @@ func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBat
 
 	opt := MakeOptions(options)
 
-	newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
+	newIter := obiiter.MakeIBioSequence(opt.BufferSize())
 	newIter.Add(1)
 
 	go func() {
@@ -208,7 +208,7 @@ func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBat
 	return newIter
 }
 
-func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
 	var reader io.Reader
 	var greader io.Reader
 	var err error
@@ -216,7 +216,7 @@ func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiiter.IB
 	reader, err = os.Open(filename)
 	if err != nil {
 		log.Printf("open file error: %+v", err)
-		return obiiter.NilIBioSequenceBatch, err
+		return obiiter.NilIBioSequence, err
 	}
 
 	// Test if the flux is compressed by gzip

pkg/obiformats/embl_read.go

@@ -84,7 +84,7 @@ func _EndOfLastEntry(buff []byte) int {
 	return -1
 }
 
-func _ParseEmblFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) {
+func _ParseEmblFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
 
 	for chunks := range input {
 		scanner := bufio.NewScanner(chunks.raw)
@@ -201,11 +201,11 @@ func _ReadFlatFileChunk(reader io.Reader, readers chan _FileChunk) {
 //	6    5  43 2    1
 //
 // <CR>?<LF>//<CR>?<LF>
-func ReadEMBL(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
+func ReadEMBL(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
 	opt := MakeOptions(options)
 	entry_channel := make(chan _FileChunk, opt.BufferSize())
 
-	newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
+	newIter := obiiter.MakeIBioSequence(opt.BufferSize())
 
 	nworkers := opt.ParallelWorkers()
 	newIter.Add(nworkers)
@@ -224,7 +224,7 @@ func ReadEMBL(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch
 	return newIter
 }
 
-func ReadEMBLFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+func ReadEMBLFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
 	var reader io.Reader
 	var greader io.Reader
 	var err error
@@ -232,7 +232,7 @@ func ReadEMBLFromFile(filename string, options ...WithOption) (obiiter.IBioSeque
 	reader, err = os.Open(filename)
 	if err != nil {
 		log.Printf("open file error: %+v", err)
-		return obiiter.NilIBioSequenceBatch, err
+		return obiiter.NilIBioSequence, err
 	}
 
 	// Test if the flux is compressed by gzip

pkg/obiformats/fastseq_header.go

@@ -15,8 +15,8 @@ func ParseGuessedFastSeqHeader(sequence *obiseq.BioSequence) {
 	}
 }
 
-func IParseFastSeqHeaderBatch(iterator obiiter.IBioSequenceBatch,
+func IParseFastSeqHeaderBatch(iterator obiiter.IBioSequence,
-	options ...WithOption) obiiter.IBioSequenceBatch {
+	options ...WithOption) obiiter.IBioSequence {
 	opt := MakeOptions(options)
 	return iterator.MakeIWorker(obiiter.AnnotatorToSeqWorker(opt.ParseFastSeqHeader()),
 		opt.ParallelWorkers(),

pkg/obiformats/fastseq_read.go

@@ -19,7 +19,7 @@ import (
 )
 
 func _FastseqReader(seqfile C.fast_kseq_p,
-	iterator obiiter.IBioSequenceBatch,
+	iterator obiiter.IBioSequence,
 	batch_size int) {
 	var comment string
 	i := 0
@@ -72,7 +72,6 @@ func _FastseqReader(seqfile C.fast_kseq_p,
 			ii = 0
 		}
 
-
 	}
 	if len(slice) > 0 {
 		iterator.Push(obiiter.MakeBioSequenceBatch(i, slice))
@@ -81,7 +80,7 @@ func _FastseqReader(seqfile C.fast_kseq_p,
 
 }
 
-func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
 	opt := MakeOptions(options)
 
 	name := C.CString(filename)
@@ -94,7 +93,7 @@ func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSe
 
 	if pointer == nil {
 		err = fmt.Errorf("cannot open file %s", filename)
-		return obiiter.NilIBioSequenceBatch, err
+		return obiiter.NilIBioSequence, err
 	}
 
 	size := int64(-1)
@@ -106,7 +105,7 @@ func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSe
 		size = -1
 	}
 
-	newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
+	newIter := obiiter.MakeIBioSequence(opt.BufferSize())
 	newIter.Add(1)
 
 	go func() {
@@ -126,9 +125,9 @@ func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSe
 	return newIter, err
 }
 
-func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequenceBatch {
+func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequence {
 	opt := MakeOptions(options)
-	newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
+	newIter := obiiter.MakeIBioSequence(opt.BufferSize())
 
 	newIter.Add(1)
 

pkg/obiformats/fastseq_write_fasta.go

@@ -61,13 +61,13 @@ func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader) []b
 	return bs.Bytes()
 }
 
-func WriteFasta(iterator obiiter.IBioSequenceBatch,
+func WriteFasta(iterator obiiter.IBioSequence,
 	file io.Writer,
-	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+	options ...WithOption) (obiiter.IBioSequence, error) {
 	opt := MakeOptions(options)
 
 	buffsize := iterator.BufferSize()
-	newIter := obiiter.MakeIBioSequenceBatch(buffsize)
+	newIter := obiiter.MakeIBioSequence(buffsize)
 
 	nwriters := opt.ParallelWorkers()
 
@@ -83,7 +83,7 @@ func WriteFasta(iterator obiiter.IBioSequenceBatch,
 		log.Debugln("End of the fasta file writing")
 	}()
 
-	ff := func(iterator obiiter.IBioSequenceBatch) {
+	ff := func(iterator obiiter.IBioSequence) {
 		for iterator.Next() {
 
 			batch := iterator.Get()
@@ -136,21 +136,21 @@ func WriteFasta(iterator obiiter.IBioSequenceBatch,
 	return newIter, nil
 }
 
-func WriteFastaToStdout(iterator obiiter.IBioSequenceBatch,
+func WriteFastaToStdout(iterator obiiter.IBioSequence,
-	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+	options ...WithOption) (obiiter.IBioSequence, error) {
 	options = append(options, OptionDontCloseFile())
 	return WriteFasta(iterator, os.Stdout, options...)
 }
 
-func WriteFastaToFile(iterator obiiter.IBioSequenceBatch,
+func WriteFastaToFile(iterator obiiter.IBioSequence,
 	filename string,
-	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+	options ...WithOption) (obiiter.IBioSequence, error) {
 
 	file, err := os.Create(filename)
 
 	if err != nil {
 		log.Fatalf("open file error: %v", err)
-		return obiiter.NilIBioSequenceBatch, err
+		return obiiter.NilIBioSequence, err
 	}
 
 	options = append(options, OptionCloseFile())

pkg/obiformats/fastseq_write_fastq.go

@@ -51,13 +51,13 @@ type FileChunck struct {
 	order int
 }
 
-func WriteFastq(iterator obiiter.IBioSequenceBatch,
+func WriteFastq(iterator obiiter.IBioSequence,
 	file io.Writer,
-	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+	options ...WithOption) (obiiter.IBioSequence, error) {
 	opt := MakeOptions(options)
 
 	buffsize := iterator.BufferSize()
-	newIter := obiiter.MakeIBioSequenceBatch(buffsize)
+	newIter := obiiter.MakeIBioSequence(buffsize)
 
 	nwriters := opt.ParallelWorkers()
 
@@ -77,7 +77,7 @@ func WriteFastq(iterator obiiter.IBioSequenceBatch,
 		log.Debugln("End of the fastq file writing")
 	}()
 
-	ff := func(iterator obiiter.IBioSequenceBatch) {
+	ff := func(iterator obiiter.IBioSequence) {
 		for iterator.Next() {
 			batch := iterator.Get()
 			chunk := FileChunck{
@@ -129,21 +129,21 @@ func WriteFastq(iterator obiiter.IBioSequenceBatch,
 	return newIter, nil
 }
 
-func WriteFastqToStdout(iterator obiiter.IBioSequenceBatch,
+func WriteFastqToStdout(iterator obiiter.IBioSequence,
-	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+	options ...WithOption) (obiiter.IBioSequence, error) {
 	options = append(options, OptionDontCloseFile())
 	return WriteFastq(iterator, os.Stdout, options...)
 }
 
-func WriteFastqToFile(iterator obiiter.IBioSequenceBatch,
+func WriteFastqToFile(iterator obiiter.IBioSequence,
 	filename string,
-	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+	options ...WithOption) (obiiter.IBioSequence, error) {
 
 	file, err := os.Create(filename)
 
 	if err != nil {
 		log.Fatalf("open file error: %v", err)
-		return obiiter.NilIBioSequenceBatch, err
+		return obiiter.NilIBioSequence, err
 	}
 
 	options = append(options, OptionCloseFile())

pkg/obiformats/genbank_read.go

@@ -26,7 +26,7 @@ const (
 	inSequence   gbstate = 4
 )
 
-func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) {
+func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
 
 	state := inHeader
 
@@ -107,11 +107,11 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) {
 
 }
 
-func ReadGenbank(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
+func ReadGenbank(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
 	opt := MakeOptions(options)
 	entry_channel := make(chan _FileChunk, opt.BufferSize())
 
-	newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
+	newIter := obiiter.MakeIBioSequence(opt.BufferSize())
 
 	nworkers := opt.ParallelWorkers()
 	newIter.Add(nworkers)
@@ -130,7 +130,7 @@ func ReadGenbank(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBa
 	return newIter
 }
 
-func ReadGenbankFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+func ReadGenbankFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
 	var reader io.Reader
 	var greader io.Reader
 	var err error
@@ -138,7 +138,7 @@ func ReadGenbankFromFile(filename string, options ...WithOption) (obiiter.IBioSe
 	reader, err = os.Open(filename)
 	if err != nil {
 		log.Printf("open file error: %+v", err)
-		return obiiter.NilIBioSequenceBatch, err
+		return obiiter.NilIBioSequence, err
 	}
 
 	// Test if the flux is compressed by gzip

pkg/obiformats/universal_read.go

@@ -43,7 +43,7 @@ func GuessSeqFileType(firstline string) string {
 }
 
 func ReadSequencesFromFile(filename string,
-	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+	options ...WithOption) (obiiter.IBioSequence, error) {
 	var file *os.File
 	var reader io.Reader
 	var greader io.Reader
@@ -53,7 +53,7 @@ func ReadSequencesFromFile(filename string,
 
 	if err != nil {
 		log.Fatalf("open file error: %v", err)
-		return obiiter.NilIBioSequenceBatch, err
+		return obiiter.NilIBioSequence, err
 	}
 
 	reader = file
@@ -72,7 +72,7 @@ func ReadSequencesFromFile(filename string,
 	tag, _ := breader.Peek(30)
 
 	if len(tag) < 30 {
-		newIter := obiiter.MakeIBioSequenceBatch()
+		newIter := obiiter.MakeIBioSequence()
 		newIter.Close()
 		return newIter, nil
 	}
@@ -98,5 +98,5 @@ func ReadSequencesFromFile(filename string,
 			filename, filetype)
 	}
 
-	return obiiter.NilIBioSequenceBatch, nil
+	return obiiter.NilIBioSequence, nil
 }

pkg/obiformats/universal_write.go

@@ -10,9 +10,9 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 )
 
-func WriteSequence(iterator obiiter.IBioSequenceBatch,
+func WriteSequence(iterator obiiter.IBioSequence,
 	file io.Writer,
-	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+	options ...WithOption) (obiiter.IBioSequence, error) {
 
 	iterator = iterator.Rebatch(1000)
 
@@ -22,7 +22,7 @@ func WriteSequence(iterator obiiter.IBioSequenceBatch,
 		batch := iterator.Get()
 		iterator.PushBack()
 
-		var newIter obiiter.IBioSequenceBatch
+		var newIter obiiter.IBioSequence
 		var err error
 
 		if len(batch.Slice()) > 0 {
@@ -42,24 +42,24 @@ func WriteSequence(iterator obiiter.IBioSequenceBatch,
 		return iterator, nil
 	}
 
-	return obiiter.NilIBioSequenceBatch, fmt.Errorf("input iterator not ready")
+	return obiiter.NilIBioSequence, fmt.Errorf("input iterator not ready")
 }
 
-func WriteSequencesToStdout(iterator obiiter.IBioSequenceBatch,
+func WriteSequencesToStdout(iterator obiiter.IBioSequence,
-	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+	options ...WithOption) (obiiter.IBioSequence, error) {
 	options = append(options, OptionDontCloseFile())
 	return WriteSequence(iterator, os.Stdout, options...)
 }
 
-func WriteSequencesToFile(iterator obiiter.IBioSequenceBatch,
+func WriteSequencesToFile(iterator obiiter.IBioSequence,
 	filename string,
-	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+	options ...WithOption) (obiiter.IBioSequence, error) {
 
 	file, err := os.Create(filename)
 
 	if err != nil {
 		log.Fatalf("open file error: %v", err)
-		return obiiter.NilIBioSequenceBatch, err
+		return obiiter.NilIBioSequence, err
 	}
 
 	options = append(options, OptionCloseFile())

pkg/obiiter/batchiterator.go

@@ -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 {
+type IBioSequence struct {
-	pointer *_IBioSequenceBatch
+	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,
+func (iterator IBioSequence) DivideOn(predicate obiseq.SequencePredicate,
-	size int, sizes ...int) (IBioSequenceBatch, IBioSequenceBatch) {
+	size int, sizes ...int) (IBioSequence, IBioSequence) {
 	buffsize := iterator.BufferSize()
 
 	if len(sizes) > 0 {
 		buffsize = sizes[0]
 	}
 
-	trueIter := MakeIBioSequenceBatch(buffsize)
+	trueIter := MakeIBioSequence(buffsize)
-	falseIter := MakeIBioSequenceBatch(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,
+func (iterator IBioSequence) FilterOn(predicate obiseq.SequencePredicate,
-	size int, sizes ...int) IBioSequenceBatch {
+	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)
 

pkg/obiiter/distribute.go

@@ -8,19 +8,19 @@ import (
 )
 
 type IDistribute struct {
-	outputs    map[int]IBioSequenceBatch
+	outputs    map[int]IBioSequence
 	news       chan int
 	classifier *obiseq.BioSequenceClassifier
 	lock       *sync.Mutex
 }
 
-func (dist *IDistribute) Outputs(key int) (IBioSequenceBatch, error) {
+func (dist *IDistribute) Outputs(key int) (IBioSequence, error) {
 	dist.lock.Lock()
 	iter, ok := dist.outputs[key]
 	dist.lock.Unlock()
 
 	if !ok {
-		return NilIBioSequenceBatch, fmt.Errorf("code %d unknown", key)
+		return NilIBioSequence, fmt.Errorf("code %d unknown", key)
 	}
 
 	return iter, nil
@@ -34,11 +34,11 @@ func (dist *IDistribute) Classifier() *obiseq.BioSequenceClassifier {
 	return dist.classifier
 }
 
-func (iterator IBioSequenceBatch) Distribute(class *obiseq.BioSequenceClassifier, sizes ...int) IDistribute {
+func (iterator IBioSequence) Distribute(class *obiseq.BioSequenceClassifier, sizes ...int) IDistribute {
 	batchsize := 5000
 	buffsize := 2
 
-	outputs := make(map[int]IBioSequenceBatch, 100)
+	outputs := make(map[int]IBioSequence, 100)
 	slices := make(map[int]*obiseq.BioSequenceSlice, 100)
 	orders := make(map[int]int, 100)
 	news := make(chan int)
@@ -80,7 +80,7 @@ func (iterator IBioSequenceBatch) Distribute(class *obiseq.BioSequenceClassifier
 					orders[key] = 0
 
 					lock.Lock()
-					outputs[key] = MakeIBioSequenceBatch(buffsize)
+					outputs[key] = MakeIBioSequence(buffsize)
 					lock.Unlock()
 
 					news <- key

pkg/obiiter/merge.go

@@ -2,7 +2,7 @@ package obiiter
 
 import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 
-func (iterator IBioSequenceBatch) IMergeSequenceBatch(na string, statsOn []string, sizes ...int) IBioSequenceBatch {
+func (iterator IBioSequence) IMergeSequenceBatch(na string, statsOn []string, sizes ...int) IBioSequence {
 	batchsize := 100
 	buffsize := iterator.BufferSize()
 
@@ -13,7 +13,7 @@ func (iterator IBioSequenceBatch) IMergeSequenceBatch(na string, statsOn []strin
 		buffsize = sizes[1]
 	}
 
-	newIter := MakeIBioSequenceBatch(buffsize)
+	newIter := MakeIBioSequence(buffsize)
 
 	newIter.Add(1)
 
@@ -41,7 +41,7 @@ func (iterator IBioSequenceBatch) IMergeSequenceBatch(na string, statsOn []strin
 }
 
 func MergePipe(na string, statsOn []string, sizes ...int) Pipeable {
-	f := func(iterator IBioSequenceBatch) IBioSequenceBatch {
+	f := func(iterator IBioSequence) IBioSequence {
 		return iterator.IMergeSequenceBatch(na, statsOn, sizes...)
 	}
 

pkg/obiiter/pipe.go

@@ -1,12 +1,11 @@
 package obiiter
 
+type Pipeable func(input IBioSequence) IBioSequence
 
-type Pipeable func(input IBioSequenceBatch) IBioSequenceBatch
+func Pipeline(start Pipeable, parts ...Pipeable) Pipeable {
-
+	p := func(input IBioSequence) IBioSequence {
-func Pipeline(start Pipeable,parts ...Pipeable) Pipeable {
-	p := func (input IBioSequenceBatch) IBioSequenceBatch {
 		data := start(input)
-		for _,part := range parts {
+		for _, part := range parts {
 			data = part(data)
 		}
 		return data
@@ -15,17 +14,16 @@ func Pipeline(start Pipeable,parts ...Pipeable) Pipeable {
 	return p
 }
 
-func (input IBioSequenceBatch) Pipe(start Pipeable, parts ...Pipeable) IBioSequenceBatch {
+func (input IBioSequence) Pipe(start Pipeable, parts ...Pipeable) IBioSequence {
-	p := Pipeline(start,parts...)
+	p := Pipeline(start, parts...)
 	return p(input)
 }
 
+type Teeable func(input IBioSequence) (IBioSequence, IBioSequence)
 
-type Teeable func(input IBioSequenceBatch) (IBioSequenceBatch,IBioSequenceBatch) 
+func (input IBioSequence) CopyTee() (IBioSequence, IBioSequence) {
-
+	first := MakeIBioSequence()
-func (input IBioSequenceBatch) CopyTee() (IBioSequenceBatch,IBioSequenceBatch) {
+	second := MakeIBioSequence()
-	first := MakeIBioSequenceBatch()
-	second:= MakeIBioSequenceBatch()
 
 	first.Add(1)
 
@@ -36,11 +34,11 @@ func (input IBioSequenceBatch) CopyTee() (IBioSequenceBatch,IBioSequenceBatch) {
 
 	go func() {
 		for input.Next() {
-			b:=input.Get()
+			b := input.Get()
 			first.Push(b)
 			second.Push(b)
 		}
 	}()
 
-	return first,second 
+	return first, second
 }

pkg/obiiter/speed.go

@@ -6,8 +6,8 @@ import (
 	"github.com/schollz/progressbar/v3"
 )
 
-func (iterator IBioSequenceBatch) Speed(message ...string) IBioSequenceBatch {
+func (iterator IBioSequence) Speed(message ...string) IBioSequence {
-	newIter := MakeIBioSequenceBatch()
+	newIter := MakeIBioSequence()
 
 	newIter.Add(1)
 
@@ -51,7 +51,7 @@ func (iterator IBioSequenceBatch) Speed(message ...string) IBioSequenceBatch {
 }
 
 func SpeedPipe(message ...string) Pipeable {
-	f := func(iterator IBioSequenceBatch) IBioSequenceBatch {
+	f := func(iterator IBioSequence) IBioSequence {
 		return iterator.Speed(message...)
 	}
 

pkg/obiiter/workers.go

@@ -27,7 +27,7 @@ func AnnotatorToSeqWorker(function SeqAnnotator) SeqWorker {
 // Moreover the SeqWorker function, the method accepted two optional integer parameters.
 //   - First is allowing to indicates the number of workers running in parallele (default 4)
 //   - The second the size of the chanel buffer. By default set to the same value than the input buffer.
-func (iterator IBioSequenceBatch) MakeIWorker(worker SeqWorker, sizes ...int) IBioSequenceBatch {
+func (iterator IBioSequence) MakeIWorker(worker SeqWorker, sizes ...int) IBioSequence {
 	nworkers := 4
 	buffsize := iterator.BufferSize()
 
@@ -39,7 +39,7 @@ func (iterator IBioSequenceBatch) MakeIWorker(worker SeqWorker, sizes ...int) IB
 		buffsize = sizes[1]
 	}
 
-	newIter := MakeIBioSequenceBatch(buffsize)
+	newIter := MakeIBioSequence(buffsize)
 
 	newIter.Add(nworkers)
 
@@ -49,7 +49,7 @@ func (iterator IBioSequenceBatch) MakeIWorker(worker SeqWorker, sizes ...int) IB
 
 	}()
 
-	f := func(iterator IBioSequenceBatch) {
+	f := func(iterator IBioSequence) {
 		for iterator.Next() {
 			batch := iterator.Get()
 			for i, seq := range batch.slice {
@@ -69,8 +69,8 @@ func (iterator IBioSequenceBatch) MakeIWorker(worker SeqWorker, sizes ...int) IB
 	return newIter
 }
 
-func (iterator IBioSequenceBatch) MakeIConditionalWorker(predicate obiseq.SequencePredicate,
+func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePredicate,
-	worker SeqWorker, sizes ...int) IBioSequenceBatch {
+	worker SeqWorker, sizes ...int) IBioSequence {
 	nworkers := 4
 	buffsize := iterator.BufferSize()
 
@@ -82,7 +82,7 @@ func (iterator IBioSequenceBatch) MakeIConditionalWorker(predicate obiseq.Sequen
 		buffsize = sizes[1]
 	}
 
-	newIter := MakeIBioSequenceBatch(buffsize)
+	newIter := MakeIBioSequence(buffsize)
 
 	newIter.Add(nworkers)
 
@@ -92,7 +92,7 @@ func (iterator IBioSequenceBatch) MakeIConditionalWorker(predicate obiseq.Sequen
 
 	}()
 
-	f := func(iterator IBioSequenceBatch) {
+	f := func(iterator IBioSequence) {
 		for iterator.Next() {
 			batch := iterator.Get()
 			for i, seq := range batch.slice {
@@ -114,7 +114,7 @@ func (iterator IBioSequenceBatch) MakeIConditionalWorker(predicate obiseq.Sequen
 	return newIter
 }
 
-func (iterator IBioSequenceBatch) MakeISliceWorker(worker SeqSliceWorker, sizes ...int) IBioSequenceBatch {
+func (iterator IBioSequence) MakeISliceWorker(worker SeqSliceWorker, sizes ...int) IBioSequence {
 	nworkers := 4
 	buffsize := iterator.BufferSize()
 
@@ -126,7 +126,7 @@ func (iterator IBioSequenceBatch) MakeISliceWorker(worker SeqSliceWorker, sizes
 		buffsize = sizes[1]
 	}
 
-	newIter := MakeIBioSequenceBatch(buffsize)
+	newIter := MakeIBioSequence(buffsize)
 
 	newIter.Add(nworkers)
 
@@ -135,7 +135,7 @@ func (iterator IBioSequenceBatch) MakeISliceWorker(worker SeqSliceWorker, sizes
 		log.Println("End of the batch slice workers")
 	}()
 
-	f := func(iterator IBioSequenceBatch) {
+	f := func(iterator IBioSequence) {
 		for iterator.Next() {
 			batch := iterator.Get()
 			batch.slice = worker(batch.slice)
@@ -154,7 +154,7 @@ func (iterator IBioSequenceBatch) MakeISliceWorker(worker SeqSliceWorker, sizes
 }
 
 func WorkerPipe(worker SeqWorker, sizes ...int) Pipeable {
-	f := func(iterator IBioSequenceBatch) IBioSequenceBatch {
+	f := func(iterator IBioSequence) IBioSequence {
 		return iterator.MakeIWorker(worker, sizes...)
 	}
 
@@ -162,7 +162,7 @@ func WorkerPipe(worker SeqWorker, sizes ...int) Pipeable {
 }
 
 func SliceWorkerPipe(worker SeqSliceWorker, sizes ...int) Pipeable {
-	f := func(iterator IBioSequenceBatch) IBioSequenceBatch {
+	f := func(iterator IBioSequence) IBioSequence {
 		return iterator.MakeISliceWorker(worker, sizes...)
 	}
 

pkg/obiseq/attributes.go

@@ -0,0 +1,193 @@
+package obiseq
+
+import (
+	"fmt"
+	"strconv"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	log "github.com/sirupsen/logrus"
+)
+
+// A method that returns the value of the key in the annotation map.
+func (s *BioSequence) GetAttribute(key string) (interface{}, bool) {
+	var val interface{}
+	ok := s.annotations != nil
+
+	if ok {
+		val, ok = s.annotations[key]
+	}
+
+	return val, ok
+}
+
+// A method that sets the value of the key in the annotation map.
+func (s *BioSequence) SetAttribute(key string, value interface{}) {
+	annot := s.Annotations()
+	annot[key] = value
+}
+
+// A method that returns the value of the key in the annotation map.
+func (s *BioSequence) GetIntAttribute(key string) (int, bool) {
+	var val int
+	var err error
+
+	v, ok := s.GetAttribute(key)
+
+	if ok {
+		val, err = goutils.InterfaceToInt(v)
+		ok = err == nil
+	}
+
+	return val, ok
+}
+
+// Deleting the key from the annotation map.
+func (s *BioSequence) DeleteAttribute(key string) {
+	delete(s.Annotations(),key)
+}
+ 
+// Renaming the key in the annotation map.
+func (s *BioSequence) RenameAttribute(newName, oldName string) {
+	val,ok := s.GetAttribute(oldName)
+
+	if (ok) {
+		s.SetAttribute(newName,val)
+		s.DeleteAttribute(oldName)
+	}
+}
+
+// A method that returns the value of the key in the annotation map.
+func (s *BioSequence) GetNumericAttribute(key string) (float64, bool) {
+	var val float64
+	var err error
+
+	v, ok := s.GetAttribute(key)
+
+	if ok {
+		val, err = goutils.InterfaceToFloat64(v)
+		ok = err == nil
+	}
+
+	return val, ok
+}
+
+
+// A method that returns the value of the key in the annotation map.
+func (s *BioSequence) GetStringAttribute(key string) (string, bool) {
+	var val string
+	v, ok := s.GetAttribute(key)
+
+	if ok {
+		val = fmt.Sprint(v)
+	}
+
+	return val, ok
+}
+
+// A method that returns the value of the key in the annotation map.
+func (s *BioSequence) GetBoolAttribute(key string) (bool, bool) {
+	var val bool
+	var err error
+
+	v, ok := s.GetAttribute(key)
+
+	if ok {
+		val, err = goutils.InterfaceToBool(v)
+		ok = err == nil
+	}
+
+	return val, ok
+}
+
+func (s *BioSequence) GetIntMap(key string) (map[string]int, bool) {
+	var val map[string]int
+	var err error
+
+	v, ok := s.GetAttribute(key)
+
+	if ok {
+		val, err = goutils.InterfaceToIntMap(v)
+		ok = err == nil
+	}
+
+	return val, ok
+}
+
+// Returning the number of times the sequence has been observed.
+func (s *BioSequence) Count() int {
+	count, ok := s.GetIntAttribute("count")
+
+	if !ok {
+		count = 1
+	}
+
+	return count
+}
+
+// Setting the number of times the sequence has been observed.
+func (s *BioSequence) SetCount(count int) {
+	annot := s.Annotations()
+	annot["count"] = count
+}
+
+
+// Returning the taxid of the sequence.
+func (s *BioSequence) Taxid() int {
+	taxid, ok := s.GetIntAttribute("taxid")
+
+	if !ok {
+		taxid = 1
+	}
+
+	return taxid
+}
+
+// Setting the taxid of the sequence.
+func (s *BioSequence) SetTaxid(taxid int) {
+	annot := s.Annotations()
+	annot["taxid"] = taxid
+}
+
+
+func (s *BioSequence) OBITagRefIndex() map[int]string {
+
+	var val map[int]string
+
+	i, ok := s.GetAttribute("obitag_ref_index")
+
+	if !ok {
+		return nil
+	}
+
+	switch i := i.(type) {
+	case map[int]string:
+		val = i
+	case map[string]interface{}:
+		val = make(map[int]string, len(i))
+		for k, v := range i {
+			score, err := strconv.Atoi(k)
+			if err != nil {
+				log.Panicln(err)
+			}
+
+			val[score], err = goutils.InterfaceToString(v)
+			if err != nil {
+				log.Panicln(err)
+			}
+		}
+	case map[string]string:
+		val = make(map[int]string, len(i))
+		for k, v := range i {
+			score, err := strconv.Atoi(k)
+			if err != nil {
+				log.Panicln(err)
+			}
+			val[score] = v
+
+		}
+	default:
+		log.Panicln("value of attribute obitag_ref_index cannot be casted to a map[int]string")
+	}
+
+	return val
+}

pkg/obiseq/biosequence.go

@@ -13,20 +13,17 @@ package obiseq
 import (
 	"bytes"
 	"crypto/md5"
-	"fmt"
-	"strconv"
 	"sync/atomic"
 
 	log "github.com/sirupsen/logrus"
-
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 )
 
 var _NewSeq = int32(0)
 var _RecycleSeq = int32(0)
 var _InMemSeq = int32(0)
-var _MaxInMemSeq = int32(0)
+
-var _BioLogRate = int(100000)
+// var _MaxInMemSeq = int32(0)
+// var _BioLogRate = int(100000)
 
 func LogBioSeqStatus() {
 	log.Debugf("Created seq : %d Destroyed : %d  In Memory : %d", _NewSeq, _RecycleSeq, _InMemSeq)
@@ -200,154 +197,11 @@ func (s *BioSequence) Annotations() Annotation {
 	return s.annotations
 }
 
-// A method that returns the value of the key in the annotation map.
-func (s *BioSequence) GetAttribute(key string) (interface{}, bool) {
-	var val interface{}
-	ok := s.annotations != nil
-
-	if ok {
-		val, ok = s.annotations[key]
-	}
-
-	return val, ok
-}
-
-func (s *BioSequence) SetAttribute(key string, value interface{}) {
-	annot := s.Annotations()
-	annot[key] = value
-}
-
-// A method that returns the value of the key in the annotation map.
-func (s *BioSequence) GetIntAttribute(key string) (int, bool) {
-	var val int
-	var err error
-
-	v, ok := s.GetAttribute(key)
-
-	if ok {
-		val, err = goutils.InterfaceToInt(v)
-		ok = err == nil
-	}
-
-	return val, ok
-}
-
-// A method that returns the value of the key in the annotation map.
-func (s *BioSequence) GetStringAttribute(key string) (string, bool) {
-	var val string
-	v, ok := s.GetAttribute(key)
-
-	if ok {
-		val = fmt.Sprint(v)
-	}
-
-	return val, ok
-}
-
-// A method that returns the value of the key in the annotation map.
-func (s *BioSequence) GetBool(key string) (bool, bool) {
-	var val bool
-	var err error
-
-	v, ok := s.GetAttribute(key)
-
-	if ok {
-		val, err = goutils.InterfaceToBool(v)
-		ok = err == nil
-	}
-
-	return val, ok
-}
-
-func (s *BioSequence) GetIntMap(key string) (map[string]int, bool) {
-	var val map[string]int
-	var err error
-
-	v, ok := s.GetAttribute(key)
-
-	if ok {
-		val, err = goutils.InterfaceToIntMap(v)
-		ok = err == nil
-	}
-
-	return val, ok
-}
-
 // Returning the MD5 hash of the sequence.
 func (s *BioSequence) MD5() [16]byte {
 	return md5.Sum(s.sequence)
 }
 
-// Returning the number of times the sequence has been observed.
-func (s *BioSequence) Count() int {
-	count, ok := s.GetIntAttribute("count")
-
-	if !ok {
-		count = 1
-	}
-
-	return count
-}
-
-// Returning the taxid of the sequence.
-func (s *BioSequence) Taxid() int {
-	taxid, ok := s.GetIntAttribute("taxid")
-
-	if !ok {
-		taxid = 1
-	}
-
-	return taxid
-}
-
-func (s *BioSequence) OBITagRefIndex() map[int]string {
-
-	var val map[int]string
-
-	i, ok := s.GetAttribute("obitag_ref_index")
-
-	if !ok {
-		return nil
-	}
-
-	switch i := i.(type) {
-	case map[int]string:
-		val = i
-	case map[string]interface{}:
-		val = make(map[int]string, len(i))
-		for k, v := range i {
-			score, err := strconv.Atoi(k)
-			if err != nil {
-				log.Panicln(err)
-			}
-
-			val[score], err = goutils.InterfaceToString(v)
-			if err != nil {
-				log.Panicln(err)
-			}
-		}
-	case map[string]string:
-		val = make(map[int]string, len(i))
-		for k, v := range i {
-			score, err := strconv.Atoi(k)
-			if err != nil {
-				log.Panicln(err)
-			}
-			val[score] = v
-
-		}
-	default:
-		log.Panicln("value of attribute obitag_ref_index cannot be casted to a map[int]string")
-	}
-
-	return val
-}
-
-func (s *BioSequence) SetTaxid(taxid int) {
-	annot := s.Annotations()
-	annot["taxid"] = taxid
-}
-
 // Setting the id of the BioSequence.
 func (s *BioSequence) SetId(id string) {
 	s.id = id

pkg/obitools/obiannotate/obiannotate.go

@@ -0,0 +1,2 @@
+package obiannotate
+

pkg/obitools/obiclean/obiclean.go

@@ -19,7 +19,7 @@ type seqPCR struct {
 	SonCount  int
 	AddedSons int
 	Edges     []Edge
-	Cluster   map[int]bool        // used as the set of head sequences associated to that sequence 
+	Cluster   map[int]bool // used as the set of head sequences associated to that sequence
 }
 
 // buildSamples sorts the sequences by samples
@@ -58,7 +58,7 @@ func buildSamples(dataset obiseq.BioSequenceSlice,
 
 func annotateOBIClean(dataset obiseq.BioSequenceSlice,
 	sample map[string]*([]*seqPCR),
-	tag, NAValue string) obiiter.IBioSequenceBatch {
+	tag, NAValue string) obiiter.IBioSequence {
 	batchsize := 1000
 	var annot = func(data obiseq.BioSequenceSlice) obiseq.BioSequenceSlice {
 
@@ -207,7 +207,6 @@ func GetCluster(sequence *obiseq.BioSequence) map[string]string {
 	return cluster
 }
 
-
 // func Cluster(sample map[string]*([]*seqPCR)) {
 // 	for _, graph := range sample {
 // 		for _, s := range *graph {
@@ -215,7 +214,7 @@ func GetCluster(sequence *obiseq.BioSequence) map[string]string {
 // 			if len(s.Edges) > 0 {
 // 				for _, f := range s.Edges {
 
-// 				}	
+// 				}
 // 			} else {
 // 				cluster
 // 			}
@@ -286,7 +285,7 @@ func Weight(sequence *obiseq.BioSequence) map[string]int {
 	return weight
 }
 
-func IOBIClean(itertator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
+func IOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 
 	db := itertator.Load()
 
@@ -318,7 +317,6 @@ func IOBIClean(itertator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
 		}
 	}
 
-
 	Mutation(samples)
 
 	pbopt := make([]progressbar.Option, 0, 5)
@@ -352,7 +350,6 @@ func IOBIClean(itertator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
 		EmpiricalDistCsv(RatioTableFilename(), all_ratio)
 	}
 
-
 	iter := annotateOBIClean(db, samples, SampleAttribute(), "NA")
 
 	if OnlyHead() {

pkg/obitools/obiconvert/sequence_reader.go

@@ -67,9 +67,9 @@ func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
 	return list_of_files, nil
 }
 
-func ReadBioSequences(filenames ...string) (obiiter.IBioSequenceBatch, error) {
+func ReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
-	var iterator obiiter.IBioSequenceBatch
+	var iterator obiiter.IBioSequence
-	var reader func(string, ...obiformats.WithOption) (obiiter.IBioSequenceBatch, error)
+	var reader func(string, ...obiformats.WithOption) (obiiter.IBioSequence, error)
 
 	opts := make([]obiformats.WithOption, 0, 10)
 
@@ -109,7 +109,7 @@ func ReadBioSequences(filenames ...string) (obiiter.IBioSequenceBatch, error) {
 
 		list_of_files, err := _ExpandListOfFiles(false, filenames...)
 		if err != nil {
-			return obiiter.NilIBioSequenceBatch, err
+			return obiiter.NilIBioSequence, err
 		}
 
 		switch CLIInputFormat() {
@@ -140,7 +140,7 @@ func ReadBioSequences(filenames ...string) (obiiter.IBioSequenceBatch, error) {
 			iterator, err = reader(list_of_files[0], opts...)
 
 			if err != nil {
-				return obiiter.NilIBioSequenceBatch, err
+				return obiiter.NilIBioSequence, err
 			}
 		}
 

pkg/obitools/obiconvert/sequence_writer.go

@@ -8,10 +8,10 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 )
 
-func WriteBioSequences(iterator obiiter.IBioSequenceBatch,
+func WriteBioSequences(iterator obiiter.IBioSequence,
-	terminalAction bool, filenames ...string) (obiiter.IBioSequenceBatch, error) {
+	terminalAction bool, filenames ...string) (obiiter.IBioSequence, error) {
 
-	var newIter obiiter.IBioSequenceBatch
+	var newIter obiiter.IBioSequence
 
 	opts := make([]obiformats.WithOption, 0, 10)
 
@@ -62,12 +62,12 @@ func WriteBioSequences(iterator obiiter.IBioSequenceBatch,
 
 	if err != nil {
 		log.Fatalf("Write file error: %v", err)
-		return obiiter.NilIBioSequenceBatch, err
+		return obiiter.NilIBioSequence, err
 	}
 
 	if terminalAction {
 		newIter.Recycle()
-		return obiiter.NilIBioSequenceBatch, nil
+		return obiiter.NilIBioSequence, nil
 	}
 
 	return newIter, nil

pkg/obitools/obidistribute/distribute.go

@@ -9,7 +9,7 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
 )
 
-func DistributeSequence(sequences obiiter.IBioSequenceBatch) {
+func DistributeSequence(sequences obiiter.IBioSequence) {
 
 	opts := make([]obiformats.WithOption, 0, 10)
 

pkg/obitools/obigrep/grep.go

@@ -8,14 +8,14 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
 )
 
-func IFilterSequence(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
+func IFilterSequence(iterator obiiter.IBioSequence) obiiter.IBioSequence {
-	var newIter obiiter.IBioSequenceBatch
+	var newIter obiiter.IBioSequence
 
 	predicate := CLISequenceSelectionPredicate()
 
 	if predicate != nil {
 		if CLISaveDiscardedSequences() {
-			var discarded obiiter.IBioSequenceBatch
+			var discarded obiiter.IBioSequence
 
 			log.Printf("Discarded sequences saved in file: %s\n", CLIDiscardedFileName())
 			newIter, discarded = iterator.DivideOn(predicate,

pkg/obitools/obimultiplex/demultiplex.go

@@ -10,7 +10,7 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
 )
 
-func IExtractBarcode(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSequenceBatch, error) {
+func IExtractBarcode(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
 
 	opts := make([]obingslibrary.WithOption, 0, 10)
 
@@ -37,7 +37,7 @@ func IExtractBarcode(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSequenceBa
 		newIter = newIter.Rebatch(obioptions.CLIBatchSize())
 	}
 
-	var unidentified obiiter.IBioSequenceBatch
+	var unidentified obiiter.IBioSequence
 	if CLIUnidentifiedFileName() != "" {
 		log.Printf("Unassigned sequences saved in file: %s\n", CLIUnidentifiedFileName())
 		unidentified, newIter = newIter.DivideOn(obiseq.HasAttribute("demultiplex_error"),

pkg/obitools/obipairing/pairing.go

@@ -206,7 +206,7 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 func IAssemblePESequencesBatch(iterator obiiter.IPairedBioSequenceBatch,
 	gap float64, delta, minOverlap int,
 	minIdentity float64,
-	withStats bool, sizes ...int) obiiter.IBioSequenceBatch {
+	withStats bool, sizes ...int) obiiter.IBioSequence {
 
 	nworkers := runtime.NumCPU() * 3 / 2
 	buffsize := iterator.BufferSize()
@@ -219,7 +219,7 @@ func IAssemblePESequencesBatch(iterator obiiter.IPairedBioSequenceBatch,
 		buffsize = sizes[1]
 	}
 
-	newIter := obiiter.MakeIBioSequenceBatch(buffsize)
+	newIter := obiiter.MakeIBioSequence(buffsize)
 
 	newIter.Add(nworkers)
 

pkg/obitools/obipcr/pcr.go

@@ -9,7 +9,7 @@ import (
 // PCR iterates over sequences provided by a obiseq.IBioSequenceBatch
 // and returns an other obiseq.IBioSequenceBatch distributing
 // obiseq.BioSequenceBatch containing the selected amplicon sequences.
-func PCR(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSequenceBatch, error) {
+func PCR(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
 
 	opts := make([]obiapat.WithOption, 0, 10)
 

pkg/obitools/obirefidx/obirefidx.go

@@ -32,7 +32,7 @@ func IndexSequence(seqidx int,
 	// r := 0
 	// w := 0
 	for i, ref := range references {
-		lcs, alilength := obialign.FastLCSScore(sequence, ref, -1 , &matrix)
+		lcs, alilength := obialign.FastLCSScore(sequence, ref, -1, &matrix)
 		score[i] = alilength - lcs
 	}
 
@@ -88,7 +88,7 @@ func IndexSequence(seqidx int,
 	return obitag_index
 }
 
-func IndexReferenceDB(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
+func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 
 	references := iterator.Load()
 	refcounts := make(
@@ -118,7 +118,7 @@ func IndexReferenceDB(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBa
 	bar := progressbar.NewOptions(len(references), pbopt...)
 
 	limits := make(chan [2]int)
-	indexed := obiiter.MakeIBioSequenceBatch()
+	indexed := obiiter.MakeIBioSequence()
 	go func() {
 		for i := 0; i < len(references); i += 10 {
 			limits <- [2]int{i, goutils.MinInt(i+10, len(references))}

pkg/obitools/obitag/obitag.go

@@ -171,7 +171,7 @@ func IdentifySeqWorker(references obiseq.BioSequenceSlice,
 	}
 }
 
-func AssignTaxonomy(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
+func AssignTaxonomy(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 
 	references := CLIRefDB()
 	refcounts := make(

pkg/obitools/obiuniq/unique.go

@@ -8,7 +8,7 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 )
 
-func Unique(sequences obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
+func Unique(sequences obiiter.IBioSequence) obiiter.IBioSequence {
 
 	options := make([]obichunk.WithOption, 0, 30)