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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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11
pkg/obitax/sequence_workers.go
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@ -2,12 +2,11 @@ package obitax
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
log "github.com/sirupsen/logrus"
)
func (taxonomy *Taxonomy) MakeSetTaxonAtRankWorker(rank string) obiiter.SeqWorker {
func (taxonomy *Taxonomy) MakeSetTaxonAtRankWorker(rank string) obiseq.SeqWorker {
if !goutils.Contains(taxonomy.RankList(), rank) {
log.Fatalf("%s is not a valid rank (allowed ranks are %v)",
@ -23,7 +22,7 @@ func (taxonomy *Taxonomy) MakeSetTaxonAtRankWorker(rank string) obiiter.SeqWorke
return w
}
func (taxonomy *Taxonomy) MakeSetSpeciesWorker() obiiter.SeqWorker {
func (taxonomy *Taxonomy) MakeSetSpeciesWorker() obiseq.SeqWorker {
w := func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
taxonomy.SetSpecies(sequence)
@ -33,7 +32,7 @@ func (taxonomy *Taxonomy) MakeSetSpeciesWorker() obiiter.SeqWorker {
return w
}
func (taxonomy *Taxonomy) MakeSetGenusWorker() obiiter.SeqWorker {
func (taxonomy *Taxonomy) MakeSetGenusWorker() obiseq.SeqWorker {
w := func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
taxonomy.SetGenus(sequence)
@ -43,7 +42,7 @@ func (taxonomy *Taxonomy) MakeSetGenusWorker() obiiter.SeqWorker {
return w
}
func (taxonomy *Taxonomy) MakeSetFamilyWorker() obiiter.SeqWorker {
func (taxonomy *Taxonomy) MakeSetFamilyWorker() obiseq.SeqWorker {
w := func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
taxonomy.SetFamily(sequence)
@ -52,5 +51,3 @@ func (taxonomy *Taxonomy) MakeSetFamilyWorker() obiiter.SeqWorker {
return w
}