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Changes to be committed:

Browse Source 
modified:   cmd/obitools/obitag/main.go
	modified:   cmd/obitools/obitag2/main.go
	modified:   go.mod
	modified:   go.sum
	modified:   pkg/obiformats/ncbitaxdump/read.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/attributes.go
	modified:   pkg/obiseq/taxonomy_lca.go
	modified:   pkg/obiseq/taxonomy_methods.go
	modified:   pkg/obiseq/taxonomy_predicate.go
	modified:   pkg/obitax/inner.go
	modified:   pkg/obitax/lca.go
	new file:   pkg/obitax/taxid.go
	modified:   pkg/obitax/taxon.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonslice.go
	modified:   pkg/obitools/obicleandb/obicleandb.go
	modified:   pkg/obitools/obigrep/options.go
	modified:   pkg/obitools/obilandmark/obilandmark.go
	modified:   pkg/obitools/obilandmark/options.go
	modified:   pkg/obitools/obirefidx/famlilyindexing.go
	modified:   pkg/obitools/obirefidx/geomindexing.go
	modified:   pkg/obitools/obirefidx/obirefidx.go
	modified:   pkg/obitools/obirefidx/options.go
	modified:   pkg/obitools/obitag/obigeomtag.go
	modified:   pkg/obitools/obitag/obitag.go
	modified:   pkg/obitools/obitag/options.go
	modified:   pkg/obiutils/strings.go
This commit is contained in:
Eric Coissac
2024-12-19 13:36:59 +01:00
parent f41a6fbb60
commit 795df34d1a
28 changed files with 590 additions and 280 deletions
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21
pkg/obitax/taxonslice.go
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@@ -13,6 +13,7 @@ package obitax
import (
"bytes"
"fmt"
"log"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
@@ -59,6 +60,16 @@ func (slice *TaxonSlice) Get(i int) *TaxNode {
return slice.slice[i]
}
func (slice *TaxonSlice) Taxon(i int) *Taxon {
if slice == nil {
return nil
}
return &Taxon{
Node: slice.slice[i],
Taxonomy: slice.taxonomy,
}
}
// Len returns the number of TaxNode instances in the TaxonSlice.
// It provides the count of taxon nodes contained within the slice.
//
@@ -124,3 +135,13 @@ func (slice *TaxonSlice) Reverse(inplace bool) *TaxonSlice {
slice: rep,
}
}
func (slice *TaxonSlice) Set(index int, taxon *Taxon) *TaxonSlice {
if slice.taxonomy != taxon.Taxonomy {
log.Panic("Cannot add taxon from a different taxonomy")
}
slice.slice[index] = taxon.Node
return slice
}