From 50c26e81b9f30c759520ced461281da3fbbf4710 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Tue, 14 Jul 2009 22:23:18 +0000
Subject: [PATCH] Added command line options for: a. 'salt method' like "-m 1"
 or "-m 2" here 1 is for SANTALUCIA and 2 is for OWCZARZY b. 'salt
 concentration' "-a 0.01" valid range is from 0.01 to 0.3. if not specified
 then we use default 0.05

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@224 60f365c0-8329-0410-b2a4-ec073aeeaa1d
---
 src/ecoprimer.c              | 28 +++++++++++++++++++++++++---
 src/libecoprimer/ecoprimer.h |  2 ++
 src/libthermo/nnparams.c     |  8 --------
 3 files changed, 27 insertions(+), 11 deletions(-)

diff --git a/src/ecoprimer.c b/src/ecoprimer.c
index 75ed821..9651d67 100644
--- a/src/ecoprimer.c
+++ b/src/ecoprimer.c
@@ -157,6 +157,8 @@ void initoptions(poptions_t options)
 	options->no_multi_match=FALSE;
 	options->pnparm = NULL;
 	strcpy(options->taxonrank, DEFAULTTAXONRANK);			/*taxon level for results, species by default*/
+	options->saltmethod = SALT_METHOD_SANTALUCIA; 
+	options->salt = DEF_SALT;
 }
 
 void printapair(int32_t index,ppair_t pair, poptions_t options)
@@ -540,11 +542,10 @@ int main(int argc, char **argv)
 	//printf ("\nGETREVCODE: A=%d, C=%d, G=%d, T=%d\n", GETREVCODE(t[0]), GETREVCODE('C'), GETREVCODE('G'), GETREVCODE('T'));
 	//return 0;
 	CNNParams nnparams;
-	nparam_InitParams(&nnparams, DEF_CONC_PRIMERS,DEF_CONC_SEQUENCES,DEF_SALT,SALT_METHOD_SANTALUCIA);
 	
 	initoptions(&options);
 
-    while ((carg = getopt(argc, argv, "hfvcUDSd:l:L:e:i:r:R:q:3:s:x:t:O:")) != -1) {
+    while ((carg = getopt(argc, argv, "hfvcUDSd:l:L:e:i:r:R:q:3:s:x:t:O:m:a:")) != -1) {
 
      switch (carg) {
 								 /* ---------------------------- */
@@ -674,7 +675,19 @@ int main(int argc, char **argv)
 			sscanf(optarg,"%d",&(options.primer_length));
 			break;
 
-                                /* -------------------- */
+								/* --------------------------------- */
+        case 'm':               /* set salt method                   */
+								/* --------------------------------- */
+        	sscanf(optarg,"%d",&(options.saltmethod));
+        	break;
+
+        						/* --------------------------------- */
+        case 'a':               /* set salt 	                     */
+								/* --------------------------------- */
+        	sscanf(optarg,"%f",&(options.salt));
+        	break;
+
+        						/* -------------------- */
         case 'c':               /* sequences are circular */
         						/* --------------------------------- */
 		  options.circular = 1;
@@ -687,6 +700,15 @@ int main(int argc, char **argv)
 
 	}
     options.pnparm = &nnparams;
+    if (options.saltmethod != 2) //if not SALT_METHOD_OWCZARZY
+    	options.saltmethod = SALT_METHOD_SANTALUCIA; //then force SALT_METHOD_SANTALUCIA
+    
+    
+    if (options.salt < 0.01 || options.salt > 0.3) //if salt value out of literature values
+    	options.salt = DEF_SALT; //set to default
+    
+	nparam_InitParams(&nnparams, DEF_CONC_PRIMERS,DEF_CONC_SEQUENCES,options.salt,options.saltmethod);
+
     fprintf(stderr,"Reading taxonomy database ...");
     taxonomy = read_taxonomy(options.prefix,0);
     fprintf(stderr,"Ok\n");
diff --git a/src/libecoprimer/ecoprimer.h b/src/libecoprimer/ecoprimer.h
index f226a01..68b774e 100644
--- a/src/libecoprimer/ecoprimer.h
+++ b/src/libecoprimer/ecoprimer.h
@@ -278,6 +278,8 @@ typedef struct {
 	int32_t		  outsamples;
 	int32_t       intaxa;
 	int32_t       outtaxa;
+	int			  saltmethod;
+	float		  salt;
 	PNNParams	  pnparm;
 } options_t, *poptions_t;
 
diff --git a/src/libthermo/nnparams.c b/src/libthermo/nnparams.c
index a7ed186..047498c 100644
--- a/src/libthermo/nnparams.c
+++ b/src/libthermo/nnparams.c
@@ -89,14 +89,6 @@ float nparam_CalcTM(float entropy,float enthalpy)
 	return tm;
 }
 
-/* PURPOSE:    Initialize nearest neighbor parameters. 
-*
-*  PARAMETERS:
-*      none
-*
-*  RETURN VALUE:
-*      void
-*/
 
 void nparam_InitParams(PNNParams nparm, float c1, float c2, float kp, int sm)
 {