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move the worker class to the obiseq package

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This commit is contained in:
Eric Coissac
2023-01-22 22:39:13 +01:00
parent f97f92df72
commit 2d375df94f
12 changed files with 153 additions and 43 deletions
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2
pkg/obiiter/batchiterator.go
View File

@ -1,3 +1,5 @@
// It takes a slice of BioSequence objects, and returns an iterator that will return batches of
// BioSequence objects
package obiiter
import (

29
pkg/obiiter/workers.go
View File

@ -6,18 +6,6 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
type SeqAnnotator func(*obiseq.BioSequence)
type SeqWorker func(*obiseq.BioSequence) *obiseq.BioSequence
type SeqSliceWorker func(obiseq.BioSequenceSlice) obiseq.BioSequenceSlice
func AnnotatorToSeqWorker(function SeqAnnotator) SeqWorker {
f := func(seq *obiseq.BioSequence) *obiseq.BioSequence {
function(seq)
return seq
}
return f
}
// That method allows for applying a SeqWorker function on every sequences.
//
@ -27,7 +15,7 @@ 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 IBioSequence) MakeIWorker(worker SeqWorker, sizes ...int) IBioSequence {
func (iterator IBioSequence) MakeIWorker(worker obiseq.SeqWorker, sizes ...int) IBioSequence {
nworkers := 4
buffsize := iterator.BufferSize()
@ -70,7 +58,7 @@ func (iterator IBioSequence) MakeIWorker(worker SeqWorker, sizes ...int) IBioSeq
}
func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePredicate,
worker SeqWorker, sizes ...int) IBioSequence {
worker obiseq.SeqWorker, sizes ...int) IBioSequence {
nworkers := 4
buffsize := iterator.BufferSize()
@ -114,7 +102,7 @@ func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePre
return newIter
}
func (iterator IBioSequence) MakeISliceWorker(worker SeqSliceWorker, sizes ...int) IBioSequence {
func (iterator IBioSequence) MakeISliceWorker(worker obiseq.SeqSliceWorker, sizes ...int) IBioSequence {
nworkers := 4
buffsize := iterator.BufferSize()
@ -153,7 +141,7 @@ func (iterator IBioSequence) MakeISliceWorker(worker SeqSliceWorker, sizes ...in
return newIter
}
func WorkerPipe(worker SeqWorker, sizes ...int) Pipeable {
func WorkerPipe(worker obiseq.SeqWorker, sizes ...int) Pipeable {
f := func(iterator IBioSequence) IBioSequence {
return iterator.MakeIWorker(worker, sizes...)
}
@ -161,7 +149,7 @@ func WorkerPipe(worker SeqWorker, sizes ...int) Pipeable {
return f
}
func SliceWorkerPipe(worker SeqSliceWorker, sizes ...int) Pipeable {
func SliceWorkerPipe(worker obiseq.SeqSliceWorker, sizes ...int) Pipeable {
f := func(iterator IBioSequence) IBioSequence {
return iterator.MakeISliceWorker(worker, sizes...)
}
@ -169,10 +157,3 @@ func SliceWorkerPipe(worker SeqSliceWorker, sizes ...int) Pipeable {
return f
}
func ReverseComplementWorker(inplace bool) SeqWorker {
f := func(input *obiseq.BioSequence) *obiseq.BioSequence {
return input.ReverseComplement(inplace)
}
return f
}