From 8f08959ebba7fe51c1e8f285ade2a2063b2f6b78 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Mon, 22 Apr 2024 12:01:43 +0200
Subject: [PATCH] Make the --no-progressbar option effective on graph building
 progress too.

Former-commit-id: 3fabecfc9de69ad406d6840c8f821c16eebaef46
---
 pkg/obitools/obiclean/obiclean.go | 57 +++++++++++++++++++------------
 1 file changed, 36 insertions(+), 21 deletions(-)

diff --git a/pkg/obitools/obiclean/obiclean.go b/pkg/obitools/obiclean/obiclean.go
index 4804aa6..8ee93e7 100644
--- a/pkg/obitools/obiclean/obiclean.go
+++ b/pkg/obitools/obiclean/obiclean.go
@@ -7,6 +7,7 @@ import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	"github.com/schollz/progressbar/v3"
 	log "github.com/sirupsen/logrus"
@@ -300,36 +301,47 @@ func CLIOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 		obioptions.CLIParallelWorkers())
 
 	if RatioMax() < 1.0 {
+		bar := (*progressbar.ProgressBar)(nil)
+
+		if obiconvert.CLIProgressBar() {
+
+			pbopt := make([]progressbar.Option, 0, 5)
+			pbopt = append(pbopt,
+				progressbar.OptionSetWriter(os.Stderr),
+				progressbar.OptionSetWidth(15),
+				progressbar.OptionShowIts(),
+				progressbar.OptionSetPredictTime(true),
+				progressbar.OptionSetDescription("[Filter graph on abundance ratio]"),
+			)
+
+			bar = progressbar.NewOptions(len(samples), pbopt...)
+		}
+
+		for _, seqs := range samples {
+			FilterGraphOnRatio(seqs, RatioMax())
+			if bar != nil {
+				bar.Add(1)
+			}
+		}
+	}
+
+	Mutation(samples)
+
+	bar := (*progressbar.ProgressBar)(nil)
+
+	if obiconvert.CLIProgressBar() {
 		pbopt := make([]progressbar.Option, 0, 5)
 		pbopt = append(pbopt,
 			progressbar.OptionSetWriter(os.Stderr),
 			progressbar.OptionSetWidth(15),
 			progressbar.OptionShowIts(),
 			progressbar.OptionSetPredictTime(true),
-			progressbar.OptionSetDescription("[Filter graph on abundance ratio]"),
+			progressbar.OptionSetDescription("[Annotate sequence status]"),
 		)
 
-		bar := progressbar.NewOptions(len(samples), pbopt...)
-
-		for _, seqs := range samples {
-			FilterGraphOnRatio(seqs, RatioMax())
-			bar.Add(1)
-		}
+		bar = progressbar.NewOptions(len(samples), pbopt...)
 	}
 
-	Mutation(samples)
-
-	pbopt := make([]progressbar.Option, 0, 5)
-	pbopt = append(pbopt,
-		progressbar.OptionSetWriter(os.Stderr),
-		progressbar.OptionSetWidth(15),
-		progressbar.OptionShowIts(),
-		progressbar.OptionSetPredictTime(true),
-		progressbar.OptionSetDescription("[Annotate sequence status]"),
-	)
-
-	bar := progressbar.NewOptions(len(samples), pbopt...)
-
 	for name, seqs := range samples {
 		for _, pcr := range *seqs {
 			obistatus := Status(pcr.Sequence)
@@ -338,7 +350,10 @@ func CLIOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 			obiweight := Weight(pcr.Sequence)
 			obiweight[name] = pcr.Weight
 		}
-		bar.Add(1)
+
+		if bar != nil {
+			bar.Add(1)
+		}
 	}
 
 	if SaveGraphToFiles() {