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update documentation

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This commit is contained in:
Eric Coissac
2024-11-16 06:00:27 +01:00
parent f5d79d0bc4
commit 7633fc4d23
1 changed files with 14 additions and 0 deletions
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14
pkg/obiformats/ncbitaxdump/read.go
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@ -90,6 +90,17 @@ func loadMergedTable(reader io.Reader, taxonomy *obitax.Taxonomy) int {
return n
}
// LoadNCBITaxDump loads the NCBI taxonomy data from the specified directory.
// It reads the taxonomy nodes, taxon names, and merged taxa from the corresponding files
// and constructs a Taxonomy object.
//
// Parameters:
// - directory: A string representing the path to the directory containing the NCBI taxonomy dump files.
// - onlysn: A boolean indicating whether to load only scientific names (true) or all names (false).
//
// Returns:
// - A pointer to the obitax.Taxonomy object containing the loaded taxonomy data, or an error
// if any of the files cannot be opened or read.
func LoadNCBITaxDump(directory string, onlysn bool) (*obitax.Taxonomy, error) {
taxonomy := obitax.NewTaxonomy("NCBI Taxonomy", "taxon", "[[:digit:]]")
@ -144,5 +155,8 @@ func LoadNCBITaxDump(directory string, onlysn bool) (*obitax.Taxonomy, error) {
n = loadMergedTable(buffered, taxonomy)
log.Printf("%d merged taxa read\n", n)
root := taxonomy.Taxon("1")
taxonomy.SetRoot(root)
return taxonomy, nil
}