First commit

pkg/obitax/taxonomy.go

@@ -0,0 +1,135 @@
+package obitax
+
+import (
+	"errors"
+	"fmt"
+	"log"
+)
+
+type TaxName struct {
+	name      *string
+	nameclass *string
+}
+
+type Taxonomy struct {
+	nodes *TaxonSet
+	alias map[int]*TaxNode
+	index map[string]*TaxonSet
+}
+
+func NewTaxonomy() *Taxonomy {
+	set := make(TaxonSet)
+	taxonomy := Taxonomy{
+		nodes: &set,
+		alias: make(TaxonSet),
+		index: make(map[string]*TaxonSet)}
+	return &taxonomy
+}
+
+func (taxonomy *Taxonomy) TaxonSet() *TaxonSet {
+	return taxonomy.nodes
+}
+
+func (taxonomy *Taxonomy) Alias() *map[int]*TaxNode {
+	return &(taxonomy.alias)
+}
+
+func (taxonomy *Taxonomy) Index() *map[string]*TaxonSet {
+	return &(taxonomy.index)
+}
+
+func (taxonomy *Taxonomy) Length() int {
+	return len(*taxonomy.nodes)
+}
+
+func (taxonomy *Taxonomy) Iterator() *ITaxonSet {
+	return taxonomy.nodes.Iterator()
+}
+
+func (taxonomy *Taxonomy) AddNewTaxa(taxid, parent int, rank string, replace bool, init bool) (*TaxNode, error) {
+	if !replace {
+		_, ok := (*taxonomy.nodes)[taxid]
+		if ok {
+			return nil, errors.New(fmt.Sprintf("Trying to add taxoon %d already present in the taxonomy", taxid))
+		}
+	}
+
+	n := NewTaxNode(taxid, parent, rank)
+	(*taxonomy.nodes)[taxid] = n
+
+	return n, nil
+}
+
+func (taxonomy *Taxonomy) Taxon(taxid int) (*TaxNode, error) {
+	t, ok := (*taxonomy.nodes)[taxid]
+
+	if !ok {
+		a, aok := taxonomy.alias[taxid]
+		if !aok {
+			return nil, errors.New(fmt.Sprintf("Taxid %d is not part of the taxonomy", taxid))
+		}
+		log.Printf("Taxid %d is deprecated and must be replaced by %d", taxid, a.taxid)
+		t = a
+	}
+	return t, nil
+}
+
+func (taxonomy *Taxonomy) AddNewName(taxid int, name, nameclass *string) error {
+	node, node_err := taxonomy.Taxon(taxid)
+	if node_err != nil {
+		return node_err
+	}
+
+	if *nameclass == "scientific name" {
+		node.scientificname = name
+	} else {
+		names := node.alternatenames
+		if names == nil {
+			n := make(map[string]*string)
+			names = &n
+			node.alternatenames = names
+		} else {
+			(*names)[*name] = nameclass
+		}
+	}
+
+	i, ok := taxonomy.index[*name]
+	if !ok {
+		tnm := make(TaxonSet)
+		i = &tnm
+		taxonomy.index[*name] = i
+	}
+	(*i)[taxid] = node
+
+	return nil
+}
+
+func (taxonomy *Taxonomy) ReindexParent() error {
+	var ok bool
+	for _, taxon := range *taxonomy.nodes {
+		taxon.pparent, ok = (*taxonomy.nodes)[taxon.parent]
+		if !ok {
+			return errors.New(fmt.Sprintf("Parent %d of taxon %d is not defined in taxonomy",
+				taxon.taxid,
+				taxon.parent))
+		}
+	}
+
+	return nil
+}
+
+func MakeTaxName(name, nameclass *string) *TaxName {
+	tn := TaxName{name, nameclass}
+	return &tn
+}
+
+func (taxonomy *Taxonomy) AddNewAlias(newtaxid, oldtaxid int) error {
+	n, node_err := taxonomy.Taxon(newtaxid)
+	if node_err != nil {
+		return node_err
+	}
+
+	taxonomy.alias[oldtaxid] = n
+
+	return nil
+}