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rename the iterator class

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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
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8
pkg/obichunk/chunk_on_disk.go
View File

@ -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)

9
pkg/obichunk/chunks.go
View File

@ -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)

8
pkg/obichunk/subchunks.go
View File

@ -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)

18
pkg/obichunk/unique.go
View File

@ -12,14 +12,14 @@ import (
// Runs dereplication algorithm on a obiiter.IBioSequenceBatch
// iterator.
func IUniqueSequence(iterator obiiter.IBioSequenceBatch,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
func IUniqueSequence(iterator obiiter.IBioSequence,
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)