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Changes to be committed:

Browse Source 
modified:   .gitignore
	new file:   pkg/obitax/default_taxonomy.go
	modified:   pkg/obitax/taxon.go
	modified:   pkg/obitax/taxonnode.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonset.go
	modified:   pkg/obitax/taxonslice.go
	modified:   pkg/obitools/obifind/iterator.go
	modified:   pkg/obitools/obifind/options.go
This commit is contained in:
Eric Coissac
2024-11-16 10:01:49 +01:00
parent f3d8707c08
commit 36327c79c8
9 changed files with 153 additions and 87 deletions
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29
pkg/obitax/taxonset.go
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@ -32,7 +32,7 @@ func (taxonomy *Taxonomy) NewTaxonSet() *TaxonSet {
return &TaxonSet{
set: make(map[*string]*TaxNode),
nalias: 0,
taxonomy: taxonomy,
taxonomy: taxonomy.OrDefault(true),
}
}
@ -68,6 +68,9 @@ func (set *TaxonSet) Get(id *string) *Taxon {
// Returns:
// - An integer representing the count of unique taxa in the TaxonSet.
func (set *TaxonSet) Len() int {
if set == nil {
return 0
}
return len(set.set) - set.nalias
}
@ -81,11 +84,17 @@ func (set *TaxonSet) Len() int {
// Behavior:
// - If a taxon with the same identifier already exists and is different from the
// new taxon, the alias count is decremented.
func (set *TaxonSet) Insert(node *TaxNode) {
func (set *TaxonSet) Insert(node *TaxNode) *TaxonSet {
if set == nil {
log.Panic("Cannot insert node into nil TaxonSet")
}
if old := set.set[node.id]; old != nil && old.id != node.id {
set.nalias--
}
set.set[node.id] = node
return set
}
// InsertTaxon adds a Taxon to the TaxonSet. It verifies that the Taxon belongs
@ -94,7 +103,11 @@ func (set *TaxonSet) Insert(node *TaxNode) {
//
// Parameters:
// - taxon: A pointer to the Taxon instance to be added to the TaxonSet.
func (set *TaxonSet) InsertTaxon(taxon *Taxon) {
func (set *TaxonSet) InsertTaxon(taxon *Taxon) *TaxonSet {
if set == nil {
set = taxon.Taxonomy.NewTaxonSet()
}
if set.taxonomy != taxon.Taxonomy {
log.Fatalf(
"Cannot insert taxon %s into taxon set belonging to %s taxonomy",
@ -102,6 +115,8 @@ func (set *TaxonSet) InsertTaxon(taxon *Taxon) {
set.taxonomy.name,
)
}
return set.Insert(taxon.Node)
}
// Taxonomy returns a pointer to the Taxonomy instance that this TaxonSet belongs to.
@ -109,6 +124,10 @@ func (set *TaxonSet) InsertTaxon(taxon *Taxon) {
// Returns:
// - A pointer to the Taxonomy instance that this TaxonSet belongs to.
func (set *TaxonSet) Taxonomy() *Taxonomy {
if set == nil {
return nil
}
return set.taxonomy
}
@ -124,6 +143,10 @@ func (set *TaxonSet) Taxonomy() *Taxonomy {
// - If the original taxon corresponding to the alias is not part of the taxon set,
// the method will log a fatal error and terminate the program.
func (set *TaxonSet) Alias(id *string, taxon *Taxon) {
if set == nil {
log.Panic("Cannot add alias to a nil TaxonSet")
}
original := set.Get(taxon.Node.id)
if original == nil {
log.Fatalf("Original taxon %v is not part of taxon set", id)