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Fisrt functional version

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This commit is contained in:
Eric Coissac
2024-11-14 19:10:23 +01:00
parent 9471fedfa1
commit 03f4e88a17
26 changed files with 908 additions and 307 deletions
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55
pkg/obiseq/attributes.go
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@ -9,17 +9,18 @@ import (
)
// AttributeKeys returns the keys of the attributes in the BioSequence.
// It optionally skips keys associated with container values based on the skip_container parameter.
//
// It does not take any parameters.
// Parameters:
// - skip_container: A boolean indicating whether to skip keys associated with a container value.
//
// Returns:
//
// []string: The keys of the BioSequence.
func (s *BioSequence) AttributeKeys(skip_map bool) obiutils.Set[string] {
// - A set of strings containing the keys of the BioSequence attributes.
func (s *BioSequence) AttributeKeys(skip_container bool) obiutils.Set[string] {
keys := obiutils.MakeSet[string]()
for k, v := range s.Annotations() {
if !skip_map || !obiutils.IsAMap(v) {
if !skip_container || !obiutils.IsAContainer(v) {
keys.Add(k)
}
}
@ -27,17 +28,18 @@ func (s *BioSequence) AttributeKeys(skip_map bool) obiutils.Set[string] {
return keys
}
// Keys returns the keys of the BioSequence.
// Keys returns the keys of the BioSequence, including standard keys and attribute keys.
//
// It returns a slice of strings containing the keys of the BioSequence.
// The keys include "id", "sequence", "qualities", and the attribute keys
// of the BioSequence.
// It returns a set of strings containing the keys of the BioSequence.
// The keys include "id", "sequence", "qualities", and the attribute keys of the BioSequence.
//
// Parameters:
// - skip_container: A boolean indicating whether to skip keys associated with container values.
//
// Returns:
//
// []string: The keys of the BioSequence.
func (s *BioSequence) Keys(skip_map bool) obiutils.Set[string] {
keys := s.AttributeKeys(skip_map)
// - A set of strings containing the keys of the BioSequence.
func (s *BioSequence) Keys(skip_container bool) obiutils.Set[string] {
keys := s.AttributeKeys(skip_container)
keys.Add("id")
if s.HasSequence() {
@ -53,10 +55,10 @@ func (s *BioSequence) Keys(skip_map bool) obiutils.Set[string] {
// HasAttribute checks if the BioSequence has the specified attribute.
//
// Parameters:
// - key: a string representing the attribute key to check.
// - key: A string representing the attribute key to check.
//
// Returns:
// - a boolean indicating whether the BioSequence has the attribute.
// - A boolean indicating whether the BioSequence has the attribute.
func (s *BioSequence) HasAttribute(key string) bool {
if key == "id" {
return true
@ -386,31 +388,14 @@ func (s *BioSequence) SetCount(count int) {
s.SetAttribute("count", count)
}
// Taxid returns the taxonomic ID associated with the BioSequence.
//
// It retrieves the "taxid" attribute from the BioSequence's attributes map.
// If the attribute is not found, the function returns 1 as the default taxonomic ID.
// The taxid 1 corresponds to the root taxonomic level.
//
// The function returns an integer representing the taxonomic ID.
func (s *BioSequence) Taxid() int {
taxid, ok := s.GetIntAttribute("taxid")
if !ok {
taxid = 1
}
return taxid
}
// SetTaxid sets the taxid for the BioSequence.
//
// Parameters:
//
// taxid - the taxid to set.
func (s *BioSequence) SetTaxid(taxid int) {
if taxid < 1 {
taxid = 1
func (s *BioSequence) SetTaxid(taxid string) {
if taxid == "" {
taxid = "NA"
}
s.SetAttribute("taxid", taxid)
}