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Changes to be committed:

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modified:   cmd/obitools/obitag/main.go
	modified:   cmd/obitools/obitaxonomy/main.go
	modified:   pkg/obiformats/csvtaxdump_read.go
	modified:   pkg/obiformats/ecopcr_read.go
	modified:   pkg/obiformats/ncbitaxdump_read.go
	modified:   pkg/obiformats/ncbitaxdump_readtar.go
	modified:   pkg/obiformats/newick_write.go
	modified:   pkg/obiformats/options.go
	modified:   pkg/obiformats/taxonomy_read.go
	modified:   pkg/obiformats/universal_read.go
	modified:   pkg/obiiter/extract_taxonomy.go
	modified:   pkg/obioptions/options.go
	modified:   pkg/obioptions/version.go
	new file:   pkg/obiphylo/tree.go
	modified:   pkg/obiseq/biosequenceslice.go
	modified:   pkg/obiseq/taxonomy_methods.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonset.go
	modified:   pkg/obitools/obiconvert/sequence_reader.go
	modified:   pkg/obitools/obitag/obitag.go
	modified:   pkg/obitools/obitaxonomy/obitaxonomy.go
	modified:   pkg/obitools/obitaxonomy/options.go
	deleted:    sample/.DS_Store
This commit is contained in:
Eric Coissac
2025-06-04 09:48:10 +02:00
parent 3424d3057f
commit 6cb7a5a352
23 changed files with 230 additions and 56 deletions
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14
pkg/obiformats/options.go
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@ -42,6 +42,7 @@ type __options__ struct {
with_rank bool
with_taxid bool
with_scientific_name bool
without_root_path bool
raw_taxid bool
with_metadata []string
}
@ -88,6 +89,7 @@ func MakeOptions(setters []WithOption) Options {
with_rank: true,
with_taxid: true,
with_scientific_name: false,
without_root_path: false,
raw_taxid: false,
}
@ -250,6 +252,11 @@ func (o *Options) WithScientificName() bool {
return o.pointer.with_scientific_name
}
// WithoutRootPath returns whether the root path option is enabled.
func (o *Options) WithoutRootPath() bool {
return o.pointer.without_root_path
}
// RawTaxid returns whether the raw taxid option is enabled.
// It retrieves the setting from the underlying options.
func (o *Options) RawTaxid() bool {
@ -576,6 +583,13 @@ func OptionsWithScientificName(value bool) WithOption {
return f
}
func OptionWithoutRootPath(value bool) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.without_root_path = value
})
return f
}
func OptionsRawTaxid(value bool) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.raw_taxid = value