From 7b7128196af84b0ce2cde39d3bf9b04c83dbc4a4 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Sun, 27 Aug 2023 15:52:28 +0200
Subject: [PATCH] small refactoring including doc

Former-commit-id: 6d6b527d89d77aa571831f7500f841840e280536
---
 pkg/obiseq/class.go               | 4 ++--
 pkg/obitax/lca.go                 | 4 ++--
 pkg/obitools/obiclean/obiclean.go | 8 ++++----
 pkg/obiutils/array.go             | 9 +++++++++
 4 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/pkg/obiseq/class.go b/pkg/obiseq/class.go
index c2a6ae4..21c722b 100644
--- a/pkg/obiseq/class.go
+++ b/pkg/obiseq/class.go
@@ -71,7 +71,7 @@ func AnnotationClassifier(key string, na string) *BioSequenceClassifier {
 		locke.RLock()
 		defer locke.RUnlock()
 		if k >= maxcode {
-			log.Fatalf("value %d not register")
+			log.Fatalf("value %d not register", k)
 		}
 		return decode[k]
 	}
@@ -154,7 +154,7 @@ func DualAnnotationClassifier(key1, key2 string, na string) *BioSequenceClassifi
 		locke.RLock()
 		defer locke.RUnlock()
 		if k >= maxcode {
-			log.Fatalf("value %d not register")
+			log.Fatalf("value %d not register", k)
 		}
 		return decode[k]
 	}
diff --git a/pkg/obitax/lca.go b/pkg/obitax/lca.go
index 725700b..b3a6292 100644
--- a/pkg/obitax/lca.go
+++ b/pkg/obitax/lca.go
@@ -43,7 +43,7 @@ func (taxonomy *Taxonomy) TaxonomicDistribution(sequence *obiseq.BioSequence) ma
 
 		t, et := taxonomy.Taxon(taxid)
 		if et != nil {
-			log.Panic("Taxid %d not defined in taxonomy : %v", k, et)
+			log.Panicf("Taxid %d not defined in taxonomy : %v", k, et)
 		}
 		taxons[t] = v
 	}
@@ -60,7 +60,7 @@ func (taxonomy *Taxonomy) LCA(sequence *obiseq.BioSequence, threshold float64) (
 	for t, w := range taxons {
 		p, ep := t.Path()
 		if ep != nil {
-			log.Panic("Taxonomic path cannot be retreived from Taxid %d : %v", t.Taxid(), ep)
+			log.Panicf("Taxonomic path cannot be retreived from Taxid %d : %v", t.Taxid(), ep)
 		}
 
 		obiutils.Reverse(*p, true)
diff --git a/pkg/obitools/obiclean/obiclean.go b/pkg/obitools/obiclean/obiclean.go
index 65be6b3..f3cb685 100644
--- a/pkg/obitools/obiclean/obiclean.go
+++ b/pkg/obitools/obiclean/obiclean.go
@@ -106,7 +106,7 @@ func IsHead(sequence *obiseq.BioSequence) bool {
 		case bool:
 			ishead = iishead
 		default:
-			log.Panic("obiclean_head attribute of sequence %s must be a boolean not : %v", sequence.Id(), iishead)
+			log.Panicf("obiclean_head attribute of sequence %s must be a boolean not : %v", sequence.Id(), iishead)
 		}
 	}
 
@@ -122,7 +122,7 @@ func HeadCount(sequence *obiseq.BioSequence) int {
 	if ok {
 		value, err = obiutils.InterfaceToInt(value)
 		if err != nil {
-			log.Panic("obiclean_headcount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
+			log.Panicf("obiclean_headcount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
 		}
 	}
 
@@ -138,7 +138,7 @@ func InternalCount(sequence *obiseq.BioSequence) int {
 	if ok {
 		value, err = obiutils.InterfaceToInt(value)
 		if err != nil {
-			log.Panic("obiclean_internalcount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
+			log.Panicf("obiclean_internalcount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
 		}
 	}
 
@@ -154,7 +154,7 @@ func SingletonCount(sequence *obiseq.BioSequence) int {
 	if ok {
 		value, err = obiutils.InterfaceToInt(value)
 		if err != nil {
-			log.Panic("obiclean_samplecount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
+			log.Panicf("obiclean_samplecount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
 		}
 	}
 
diff --git a/pkg/obiutils/array.go b/pkg/obiutils/array.go
index cc20f80..b616f31 100644
--- a/pkg/obiutils/array.go
+++ b/pkg/obiutils/array.go
@@ -33,6 +33,15 @@ func Make2DArray[T any](rows, cols int) Matrix[T] {
 	return matrix
 }
 
+// Make2DNumericArray generates a 2D numeric array with the specified number of rows and columns.
+//
+// Parameters:
+//   - rows: the number of rows in the array.
+//   - cols: the number of columns in the array.
+//   - zeroed: a boolean indicating whether the array should be initialized with zeros.
+//
+// Returns:
+//   - matrix: a 2D numeric array with the specified dimensions.
 func Make2DNumericArray[T Numeric](rows, cols int, zeroed bool) Matrix[T] {
 	matrix := make(Matrix[T], rows)
 	data := make([]T, cols*rows)