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Patch a small bug on json write

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This commit is contained in:
Eric Coissac
2024-12-20 19:42:03 +01:00
parent abfa8f357a
commit 5d0f996625
14 changed files with 458 additions and 79 deletions
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32
pkg/obiseq/taxonomy_methods.go
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@ -9,6 +9,7 @@ import (
)
func (s *BioSequence) Taxon(taxonomy *obitax.Taxonomy) *obitax.Taxon {
taxid := s.Taxid()
if taxid == "NA" {
return nil
@ -21,16 +22,39 @@ func (s *BioSequence) Taxon(taxonomy *obitax.Taxonomy) *obitax.Taxon {
// Parameters:
//
// taxid - the taxid to set.
func (s *BioSequence) SetTaxid(taxid string) {
func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
if taxid == "" {
taxid = "NA"
} else {
taxonomy := obitax.DefaultTaxonomy()
taxon := (*obitax.Taxon)(nil)
if taxonomy != nil {
taxon = taxonomy.Taxon(taxid)
}
if taxon != nil {
taxid = taxon.String()
}
}
if len(rank) > 0 {
r := rank[0]
s.SetAttribute(r+"_taxid", taxid)
} else {
s.SetAttribute("taxid", taxid)
}
s.SetAttribute("taxid", taxid)
}
func (s *BioSequence) SetTaxon(taxon *obitax.Taxon) {
func (s *BioSequence) SetTaxon(taxon *obitax.Taxon, rank ...string) {
taxid := taxon.String()
s.SetTaxid(taxid)
if len(rank) > 0 {
r := rank[0]
s.SetAttribute(r+"_taxid", taxid)
} else {
s.SetAttribute("taxid", taxid)
}
}
// Taxid returns the taxonomic ID associated with the BioSequence.