From 9a9fb383ad82022b6f230970c899e9937391dd72 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 24 May 2024 14:26:22 +0200
Subject: [PATCH] standardize uint type names

---
 src/libecoPCR/ecoPCR.h         |  6 +++---
 src/libecoprimer/PrimerSets.c  | 14 +++++++-------
 src/libecoprimer/apat_search.c |  4 ++--
 src/libthermo/nnparams.c       |  4 ++--
 src/libthermo/nnparams.h       |  6 ++++--
 5 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/src/libecoPCR/ecoPCR.h b/src/libecoPCR/ecoPCR.h
index c736167..51c8f4a 100644
--- a/src/libecoPCR/ecoPCR.h
+++ b/src/libecoPCR/ecoPCR.h
@@ -21,8 +21,8 @@ typedef struct {
 	int32_t  taxid;
 	char     AC[20];
 	int32_t  DE_length;
-	u_int32_t  SQ_length;
-	u_int32_t  CSQ_length; /*what is this CSQ_length ? */
+	uint32_t  SQ_length;
+	uint32_t  CSQ_length; /*what is this CSQ_length ? */
 
 	char     data[1];
 
@@ -30,7 +30,7 @@ typedef struct {
 
 typedef struct {
 	int32_t taxid;
-	u_int32_t SQ_length;
+	uint32_t SQ_length;
 	int32_t isexample;
 	char    *AC;
 	char    *DE;
diff --git a/src/libecoprimer/PrimerSets.c b/src/libecoprimer/PrimerSets.c
index 9725f9f..00e42f1 100644
--- a/src/libecoprimer/PrimerSets.c
+++ b/src/libecoprimer/PrimerSets.c
@@ -1567,7 +1567,7 @@ size_t primers_changeSortedArray (ppair_t ** pairs,
 		size_t sorted_count, poptions_t options)
 {
 	int32_t i, k, total_links;
-	u_int32_t j;
+	uint32_t j;
 	int *owi;
 	int *iwi;
 	int allowedtaxa;
@@ -1580,14 +1580,14 @@ size_t primers_changeSortedArray (ppair_t ** pairs,
 	idx_set = ECOMALLOC(slots*sizeof (int32_t),
 		            "Could not allocate memory for index set.");
 
-	for (i=0; ((u_int32_t)i)<sorted_count; i++)
+	for (i=0; ((uint32_t)i)<sorted_count; i++)
 	{
 		owi = sortedpairs[i]->wellIdentifiedSeqs;
 		passed = FALSE;
 
 		for (j=0; j<sorted_count; j++)
 		{
-			if ((u_int32_t)i == j) continue;
+			if ((uint32_t)i == j) continue;
 
 			iwi = sortedpairs[j]->wellIdentifiedSeqs;
 			total_links = 0;
@@ -1632,7 +1632,7 @@ size_t primers_changeSortedArray (ppair_t ** pairs,
 	for (j=0; j<sorted_count; j++)
 	{
 		for (k=0; k<index; k++)
-			if (j == (u_int32_t)(idx_set[k])) break;
+			if (j == (uint32_t)(idx_set[k])) break;
 		//need to remove this element
 		if (k == index)
 		{
@@ -1714,7 +1714,7 @@ size_t primers_filterWithGivenLinks (ppair_t ** pairs,
 		size_t sorted_count, poptions_t options)
 {
 	int32_t i,  k;
-	u_int32_t j;
+	uint32_t j;
 	ppair_t *sortedpairs = *pairs;
 
 	int32_t *idx_set = NULL;
@@ -1734,7 +1734,7 @@ size_t primers_filterWithGivenLinks (ppair_t ** pairs,
 	for (j=0; j<sorted_count; j++)
 	{
 		for (k=0; k<index; k++)
-			if (j == (u_int32_t) (idx_set[k])) break;
+			if (j == (uint32_t) (idx_set[k])) break;
 		//need to remove this element
 		if (k == index)
 		{
@@ -1757,7 +1757,7 @@ size_t primers_filterWithGivenLinks (ppair_t ** pairs,
 	else i=sorted_count;
 
 
-	for (j=0; j<(u_int32_t)i; j++)
+	for (j=0; j<(uint32_t)i; j++)
 		for (k=0; k<options->dbsize; k++)
 			if ((*pairs)[j]->coveredSeqs[k] == 1)
 				cov[k] = 1;
diff --git a/src/libecoprimer/apat_search.c b/src/libecoprimer/apat_search.c
index 3da4070..87b5e6e 100644
--- a/src/libecoprimer/apat_search.c
+++ b/src/libecoprimer/apat_search.c
@@ -36,7 +36,7 @@ int32_t ManberNoErr(pecoseq_t pseq,ppattern_t pat,
         ppatternParam_t param,
         StackiPtr stkpos)
 {
-        u_int32_t     pos;
+        uint32_t     pos;
         uint32_t    smask, r;
         uint8_t     *data;
         uint32_t    end;
@@ -84,7 +84,7 @@ int32_t ManberSub(pecoseq_t pseq,ppattern_t pat,
         StackiPtr stkpos)
 {
         int       e, found;
-        u_int32_t     pos;
+        uint32_t     pos;
         uint32_t    smask, cmask, sindx;
         uint32_t    *pr, r[2 * MAX_PAT_ERR + 2];
         uint8_t     *data;
diff --git a/src/libthermo/nnparams.c b/src/libthermo/nnparams.c
index ab74604..2cfdb56 100644
--- a/src/libthermo/nnparams.c
+++ b/src/libthermo/nnparams.c
@@ -542,7 +542,7 @@ double nparam_CalcSelfTM(PNNParams nparm, const char* seq, size_t len)
 		c4 = GETNUMCODE(useq[i]);
 
 
-		thedH += nparm->dH[(u_int8_t) c3][(u_int8_t)c4][(u_int8_t)c1][(u_int8_t)c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
+		thedH += nparm->dH[(uint8_t) c3][(uint8_t)c4][(uint8_t)c1][(uint8_t)c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
 		thedS += nparam_GetEntropy(nparm, c3,c4,c1,c2);
 	}
 	//printf("------------------\n");
@@ -584,7 +584,7 @@ double nparam_CalcTwoTM(PNNParams nparm, const char* seq1, const char* seq2, siz
 
 		//fprintf (stderr,"Primer : %s %f %f %d %d, %d %d %f\n",useq,thedH,thedS,(int)c3,(int)c4,(int)c1,(int)c2,nparam_GetEnthalpy(nparm, c3,c4,c1,c2));
 
-		thedH += nparm->dH[(u_int8_t)c3][(u_int8_t)c4][(u_int8_t)c1][(u_int8_t)c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
+		thedH += nparm->dH[(uint8_t)c3][(uint8_t)c4][(uint8_t)c1][(uint8_t)c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
 		thedS += nparam_GetEntropy(nparm, c3,c4,c1,c2);
 	}
 	//fprintf(stderr,"------------------\n");
diff --git a/src/libthermo/nnparams.h b/src/libthermo/nnparams.h
index b88825e..9154a19 100644
--- a/src/libthermo/nnparams.h
+++ b/src/libthermo/nnparams.h
@@ -13,11 +13,13 @@
 
 #include <math.h>
 #include <string.h>
+#include <stdint.h>
+
 //#include "../libecoprimer/ecoprimer.h"
 
 // following defines to simplify coding...
-#define ndH(a,b,c,d) nparm->dH[(u_int8_t) a][(u_int8_t) b][(u_int8_t) c][(u_int8_t) d]
-#define ndS(a,b,c,d) nparm->dS[(u_int8_t) a][(u_int8_t) b][(u_int8_t) c][(u_int8_t) d]
+#define ndH(a,b,c,d) nparm->dH[(uint8_t) a][(uint8_t) b][(uint8_t) c][(uint8_t) d]
+#define ndS(a,b,c,d) nparm->dS[(uint8_t) a][(uint8_t) b][(uint8_t) c][(uint8_t) d]
 #define forbidden_enthalpy 1000000000000000000.0f
 #define	R 1.987f
 #define	SALT_METHOD_SANTALUCIA 1