From 402d54cb628be6180fa3263389484216e3a315ac Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Fri, 14 Jan 2022 15:30:01 +0100
Subject: [PATCH] Code refactoring

---
 pkg/obialign/backtracking.go |  4 +--
 pkg/obialign/dnamatrix.go    | 48 ++++++++++++++++++------------------
 2 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/pkg/obialign/backtracking.go b/pkg/obialign/backtracking.go
index 17128ca..44be309 100644
--- a/pkg/obialign/backtracking.go
+++ b/pkg/obialign/backtracking.go
@@ -1,6 +1,6 @@
 package obialign
 
-func __backtracking__(path_matrix []int, lseqA, lseqB int, path *[]int) []int {
+func _Backtracking(pathMatrix []int, lseqA, lseqB int, path *[]int) []int {
 
 	needed := (lseqA + lseqB) * 2
 
@@ -19,7 +19,7 @@ func __backtracking__(path_matrix []int, lseqA, lseqB int, path *[]int) []int {
 	lleft := 0
 
 	for i > -1 || j > -1 {
-		step := __get_matrix__(&path_matrix, lseqA, i, j)
+		step := __get_matrix__(&pathMatrix, lseqA, i, j)
 		// log.Printf("I: %d J:%d -> %d\n", i, j, step)
 
 		switch {
diff --git a/pkg/obialign/dnamatrix.go b/pkg/obialign/dnamatrix.go
index a3b9a22..ca9de19 100644
--- a/pkg/obialign/dnamatrix.go
+++ b/pkg/obialign/dnamatrix.go
@@ -4,7 +4,7 @@ import (
 	"math"
 )
 
-var __four_bits_count__ = []float64{
+var _FourBitsCount = []float64{
 	0, // 0000
 	1, // 0001
 	1, // 0010
@@ -23,18 +23,18 @@ var __four_bits_count__ = []float64{
 	4, // 1111
 }
 
-var __initialized_dna_score__ = false
+var _InitializedDnaScore = false
 
-var __nuc_part_match__ [32][32]float64
-var __nuc_score_part_match_match__ [100][100]int
-var __nuc_score_part_match_mismatch__ [100][100]int
+var _NucPartMatch [32][32]float64
+var _NucScorePartMatchMatch [100][100]int
+var _NucScorePartMatchMismatch [100][100]int
 
-func __match_ratio__(a, b byte) float64 {
+func _MatchRatio(a, b byte) float64 {
 	// count of common bits
-	cm := __four_bits_count__[a&b&15]
+	cm := _FourBitsCount[a&b&15]
 
-	ca := __four_bits_count__[a&15]
-	cb := __four_bits_count__[b&15]
+	ca := _FourBitsCount[a&15]
+	cb := _FourBitsCount[b&15]
 
 	if cm == 0 || ca == 0 || cb == 0 {
 		return float64(0)
@@ -43,7 +43,7 @@ func __match_ratio__(a, b byte) float64 {
 	return float64(cm) / float64(ca) / float64(cb)
 }
 
-func __logaddexp__(a, b float64) float64 {
+func _Logaddexp(a, b float64) float64 {
 	if a > b {
 		a, b = b, a
 	}
@@ -51,7 +51,7 @@ func __logaddexp__(a, b float64) float64 {
 	return b + math.Log1p(math.Exp(a-b))
 }
 
-func __match_score_ratio__(a, b byte) (float64, float64) {
+func _MatchScoreRatio(a, b byte) (float64, float64) {
 
 	l2 := math.Log(2)
 	l3 := math.Log(3)
@@ -66,35 +66,35 @@ func __match_score_ratio__(a, b byte) (float64, float64) {
 	lO1E2 := lO1 + lE2
 	lO2E1 := lO2 + lE1
 
-	MM := __logaddexp__(lO1O2, lE1E2+l3) + l4
-	Mm := __logaddexp__(__logaddexp__(lO1E2, lO2E1), lE1E2+l2) + l4
+	MM := _Logaddexp(lO1O2, lE1E2+l3) + l4
+	Mm := _Logaddexp(_Logaddexp(lO1E2, lO2E1), lE1E2+l2) + l4
 
 	return MM, Mm
 }
 
-func __init_nuc_part_match__() {
+func _InitNucPartMatch() {
 
 	for i, a := range __four_bits_base_code__ {
 		for j, b := range __four_bits_base_code__ {
-			__nuc_part_match__[i][j] = __match_ratio__(a, b)
+			_NucPartMatch[i][j] = _MatchRatio(a, b)
 		}
 	}
 }
 
-func __init_nuc_score_part_match__() {
+func _InitNucScorePartMatch() {
 	for i := 0; i < 100; i++ {
 		for j := 0; j < 100; j++ {
-			MM, Mm := __match_score_ratio__(byte(i), byte(j))
-			__nuc_score_part_match_match__[i][j] = int(MM*10 + 0.5)
-			__nuc_score_part_match_mismatch__[i][j] = int(Mm*10 + 0.5)
+			MM, Mm := _MatchScoreRatio(byte(i), byte(j))
+			_NucScorePartMatchMatch[i][j] = int(MM*10 + 0.5)
+			_NucScorePartMatchMismatch[i][j] = int(Mm*10 + 0.5)
 		}
 	}
 }
 
-func InitDNAScoreMatrix() {
-	if !__initialized_dna_score__ {
-		__init_nuc_part_match__()
-		__init_nuc_score_part_match__()
-		__initialized_dna_score__ = true
+func _InitDNAScoreMatrix() {
+	if !_InitializedDnaScore {
+		_InitNucPartMatch()
+		_InitNucScorePartMatch()
+		_InitializedDnaScore = true
 	}
 }