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update api documentation

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This commit is contained in:
Eric Coissac
2024-11-16 05:59:41 +01:00
parent 03f4e88a17
commit f5d79d0bc4
13 changed files with 372 additions and 62 deletions
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55
pkg/obitax/taxon.go
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@@ -11,8 +11,8 @@ import (
// it belongs to and the specific taxon node information.
//
// Fields:
// - Taxonomy: A pointer to the Taxonomy[T] instance that this taxon is part of.
// - Node: A pointer to the TaxNode[T] instance representing the specific taxon.
// - Taxonomy: A pointer to the Taxonomy instance that this taxon is part of.
// - Node: A pointer to the TaxNode instance representing the specific taxon.
type Taxon struct {
Taxonomy *Taxonomy
Node *TaxNode
@@ -42,6 +42,14 @@ func (taxon *Taxon) ScientificName() string {
return taxon.Node.ScientificName()
}
// Name retrieves the name of the Taxon based on the specified class.
// It uses the taxonomy's name classes to format the name appropriately.
//
// Parameters:
// - class: A string representing the name class to use for retrieval.
//
// Returns:
// - The name of the taxon as a string.
func (taxon *Taxon) Name(class string) string {
if taxon == nil {
return "NA"
@@ -50,6 +58,14 @@ func (taxon *Taxon) Name(class string) string {
return taxon.Node.Name(pclass)
}
// IsNameEqual checks if the given name is equal to the name of the Taxon.
// It compares the provided name with the name stored in the TaxNode.
//
// Parameters:
// - name: A string representing the name to compare against.
//
// Returns:
// - A boolean indicating whether the names are equal.
func (taxon *Taxon) IsNameEqual(name string) bool {
if taxon == nil {
return false
@@ -58,6 +74,13 @@ func (taxon *Taxon) IsNameEqual(name string) bool {
return taxon.Node.IsNameEqual(name)
}
// IsNameMatching checks if the name of the Taxon matches the given regular expression pattern.
//
// Parameters:
// - pattern: A pointer to a compiled regular expression to match against the taxon's name.
//
// Returns:
// - A boolean indicating whether the taxon's name matches the specified pattern.
func (taxon *Taxon) IsNameMatching(pattern *regexp.Regexp) bool {
if taxon == nil {
return false
@@ -66,6 +89,12 @@ func (taxon *Taxon) IsNameMatching(pattern *regexp.Regexp) bool {
return taxon.Node.IsNameMatching(pattern)
}
// SetName sets the name of the Taxon based on the provided name and class.
// It logs a panic if the taxon pointer is nil.
//
// Parameters:
// - name: A string representing the new name to set for the taxon.
// - class: A string representing the name class to associate with the taxon.
func (taxon *Taxon) SetName(name, class string) {
if taxon == nil {
log.Panicf("nil taxon pointer for name %s [%s]", name, class)
@@ -76,6 +105,11 @@ func (taxon *Taxon) SetName(name, class string) {
taxon.Node.SetName(pname, pclass)
}
// IsRoot checks if the Taxon is the root of the taxonomy.
// It returns true if the taxon is nil or if it matches the root node of the taxonomy.
//
// Returns:
// - A boolean indicating whether the Taxon is the root of the taxonomy.
func (taxon *Taxon) IsRoot() bool {
if taxon == nil {
return true
@@ -101,7 +135,7 @@ func (taxon *Taxon) Rank() string {
// to create a new Taxon instance representing the parent taxon.
//
// Returns:
// - A pointer to the parent Taxon[T]. If the parent does not exist, it returns
// - A pointer to the parent Taxon. If the parent does not exist, it returns
// a Taxon with a nil Node.
func (taxon *Taxon) Parent() *Taxon {
if taxon == nil {
@@ -120,7 +154,6 @@ func (taxon *Taxon) Parent() *Taxon {
// is called with each Taxon in the path from the current taxon to the root. If the
// taxonomy has no root node, the method logs a fatal error and terminates the program.
func (taxon *Taxon) IPath() iter.Seq[*Taxon] {
if taxon.Taxonomy.root == nil {
log.Fatalf("Taxon[%v].IPath(): Taxonomy has no root node", taxon.Taxonomy.name)
}
@@ -140,13 +173,13 @@ func (taxon *Taxon) IPath() iter.Seq[*Taxon] {
}
}
// Path returns a slice of TaxNode[T] representing the path from the current Taxon
// Path returns a slice of TaxNode representing the path from the current Taxon
// to the root Taxon in the associated Taxonomy. It collects all the nodes in the path
// using the IPath method and returns them as a TaxonSlice.
//
// Returns:
// - A pointer to a TaxonSlice[T] containing the TaxNode[T] instances in the path
// from the current taxon to the root.
// - A pointer to a TaxonSlice containing the TaxNode instances in the path
// from the current taxon to the root. If the taxon is nil, it returns nil.
func (taxon *Taxon) Path() *TaxonSlice {
if taxon == nil {
return nil
@@ -196,7 +229,7 @@ func (taxon *Taxon) HasRankDefined(rank string) bool {
// - rank: A string representing the rank to search for (e.g., "species", "genus").
//
// Returns:
// - A pointer to the Taxon[T] that matches the specified rank, or nil if no such taxon exists
// - A pointer to the Taxon that matches the specified rank, or nil if no such taxon exists
// in the path to the root.
func (taxon *Taxon) TaxonAtRank(rank string) *Taxon {
if taxon == nil {
@@ -219,7 +252,7 @@ func (taxon *Taxon) TaxonAtRank(rank string) *Taxon {
// the matching Taxon.
//
// Returns:
// - A pointer to the Taxon[T] that matches the "species" rank, or nil if no such taxon
// - A pointer to the Taxon that matches the "species" rank, or nil if no such taxon
// exists in the path to the root.
func (taxon *Taxon) Species() *Taxon {
return taxon.TaxonAtRank("species")
@@ -230,7 +263,7 @@ func (taxon *Taxon) Species() *Taxon {
// the matching Taxon.
//
// Returns:
// - A pointer to the Taxon[T] that matches the "genus" rank, or nil if no such taxon
// - A pointer to the Taxon that matches the "genus" rank, or nil if no such taxon
// exists in the path to the root.
func (taxon *Taxon) Genus() *Taxon {
return taxon.TaxonAtRank("genus")
@@ -241,7 +274,7 @@ func (taxon *Taxon) Genus() *Taxon {
// the matching Taxon.
//
// Returns:
// - A pointer to the Taxon[T] that matches the "family" rank, or nil if no such taxon
// - A pointer to the Taxon that matches the "family" rank, or nil if no such taxon
// exists in the path to the root.
func (taxon *Taxon) Family() *Taxon {
return taxon.TaxonAtRank("family")