obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Patch a bug in the embl reader and adds some doc

Browse Source 
Former-commit-id: 9b5f75fb14bcc3043da1647055279987a295d271
This commit is contained in:
Eric Coissac
2024-01-31 15:43:02 +01:00
parent f2f7b4574e
commit 23758b00f6
7 changed files with 105 additions and 4 deletions
Download Patch File Download Diff File Expand all files Collapse all files

28
pkg/obitax/path.go
View File

@ -6,6 +6,11 @@ import (
log "github.com/sirupsen/logrus"
)
// Path generates the lineage path from the current taxon up to the root.
//
// This method does not take parameters as it is called on a TaxNode receiver.
// It returns a pointer to a TaxonSlice containing the path and an error if
// the taxonomy needs reindexing.
func (taxon *TaxNode) Path() (*TaxonSlice, error) {
path := make(TaxonSlice, 0, 30)
@ -24,6 +29,18 @@ func (taxon *TaxNode) Path() (*TaxonSlice, error) {
return &path, nil
}
// TaxonAtRank traverses up the taxonomy tree starting from the current
// node until it finds a node that matches the specified rank.
//
// If a node with the given rank is not found in the path to the root,
// or if the taxonomy tree is not properly indexed (i.e., a node's parent
// is itself), the function will return nil. In case the taxonomy needs
// reindexing, the function will panic.
//
// rank: the taxonomic rank to search for (e.g., "species", "genus").
//
// Returns a pointer to a TaxNode representing the node at the
// specified rank, or nil if no such node exists in the path.
func (taxon *TaxNode) TaxonAtRank(rank string) *TaxNode {
for taxon.rank != rank && taxon != taxon.pparent {
taxon = taxon.pparent
@ -33,13 +50,20 @@ func (taxon *TaxNode) TaxonAtRank(rank string) *TaxNode {
}
}
if taxon == taxon.pparent && taxon.rank != rank {
if taxon == taxon.pparent && taxon.rank != rank {
taxon = nil
}
return taxon
}
// Species retrieves the TaxNode corresponding to the species rank.
//
// This method does not take any parameters. It is a convenience
// wrapper around the TaxonAtRank method, specifically retrieving
// the species-level taxonomic classification for the calling TaxNode.
//
// Returns a pointer to the TaxNode representing the species.
func (taxon *TaxNode) Species() *TaxNode {
return taxon.TaxonAtRank("species")
}
@ -52,8 +76,6 @@ func (taxon *TaxNode) Family() *TaxNode {
return taxon.TaxonAtRank("family")
}
// Returns a TaxonSet listing the requested taxon and all
// its ancestors in the taxonomy down to the root.
func (taxonomy *Taxonomy) Path(taxid int) (*TaxonSlice, error) {
taxon, err := taxonomy.Taxon(taxid)