From 2002299b7ff9a798de28552cd9ef0f513b8213e6 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Thu, 2 Feb 2023 23:09:16 +0100
Subject: [PATCH] reorder some edits

---
 pkg/obitools/obiannotate/obiannotate.go | 31 +++++++++++++++++++++----
 1 file changed, 27 insertions(+), 4 deletions(-)

diff --git a/pkg/obitools/obiannotate/obiannotate.go b/pkg/obitools/obiannotate/obiannotate.go
index aefab8a..41c5b10 100644
--- a/pkg/obitools/obiannotate/obiannotate.go
+++ b/pkg/obitools/obiannotate/obiannotate.go
@@ -18,12 +18,18 @@ func DeleteAttributesWorker(toBeDeleted []string) obiseq.SeqWorker {
 	return f
 }
 
-func ToBeKeptAttributesWorker(toBeKept map[string]bool) obiseq.SeqWorker {
+func ToBeKeptAttributesWorker(toBeKept []string) obiseq.SeqWorker {
+
+	d := make(map[string]bool, len(_keepOnly))
+
+	for _, v := range _keepOnly {
+		d[v] = true
+	}
 
 	f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
 		annot := s.Annotations()
 		for key := range annot {
-			if _, ok := toBeKept[key]; !ok {
+			if _, ok := d[key]; !ok {
 				s.DeleteAttribute(key)
 			}
 		}
@@ -33,6 +39,18 @@ func ToBeKeptAttributesWorker(toBeKept map[string]bool) obiseq.SeqWorker {
 	return f
 }
 
+func ClearAllAttributesWorker() obiseq.SeqWorker {
+	f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
+		annot := s.Annotations()
+		for key := range annot {
+			s.DeleteAttribute(key)
+		}
+		return s
+	}
+
+	return f
+}
+
 func RenameAttributeWorker(toBeRenamed map[string]string) obiseq.SeqWorker {
 	f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
 		for newName, oldName := range toBeRenamed {
@@ -69,8 +87,8 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
 	var annotator obiseq.SeqWorker
 	annotator = nil
 
-	if CLIHasAttributeToBeRenamed() {
-		w := RenameAttributeWorker(CLIAttributeToBeRenamed())
+	if CLIHasClearAllFlag() {
+		w := ClearAllAttributesWorker()
 		annotator = annotator.ChainWorkers(w)
 	}
 
@@ -84,6 +102,11 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
 		annotator = annotator.ChainWorkers(w)
 	}
 
+	if CLIHasAttributeToBeRenamed() {
+		w := RenameAttributeWorker(CLIAttributeToBeRenamed())
+		annotator = annotator.ChainWorkers(w)
+	}
+
 	if CLIHasTaxonAtRank() {
 		taxo := obigrep.CLILoadSelectedTaxonomy()
 		w := AddTaxonAtRankWorker(taxo, CLITaxonAtRank()...)