added compare function for amplifias

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/branches/eric-test@193 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/libecoprimer/ecoprimer.h

@@ -104,7 +104,7 @@ typedef struct {
  * on all sequences as a list of primer_t
  */
 typedef struct {
-	pprimer_t   primers;
+	pprimer_t   primers; 
 	uint32_t    size;
 } primercount_t, *pprimercount_t;
 
@@ -300,6 +300,6 @@ int32_t getrankdbstats(pecodnadb_t seqdb,
 					   ecotaxonomy_t *taxonomy,
 					   poptions_t options);
 float taxonomycoverage(ppair_t pair, poptions_t options);
-
+char ecoComplementChar(char base);
 
 #endif /* EPSORT_H_ */

src/libecoprimer/hashsequence.c

@@ -201,3 +201,13 @@ uint32_t ecoFindWord(pwordcount_t table,word_t word)
 		return ~0;
 }
 
+char ecoComplementChar(char base)
+{
+	switch(base){
+		case 'A': return T; 
+		case 'C': return G;
+		case 'G': return C; 
+		case 'T': return A; 
+	}
+}
+

src/libecoprimer/pairs.c

@@ -296,6 +296,7 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
 		    		   current.asdirect1=current.asdirect2;
 		    		   current.asdirect2=bswp;
 		    	   }
+		    	   
 
 		    	   // Look for the new pair in already seen pairs
 

src/libecoprimer/taxstats.c

@@ -121,3 +121,45 @@ float taxonomycoverage(ppair_t pair, poptions_t options)
 	pair->outtaxa=outcount;
 	return (float)incount/options->intaxa;
 }
+
+
+
+static int cmpamp(const void *ampf1, const void* ampf2)
+{
+	int i;
+	int j = 0;
+	int incr = 1;
+	char cd1;
+	char cd2;
+	int chd = 0;
+	
+	pamplifia_t pampf1 = (pamplifia_t) ampf1;
+	pamplifia_t pampf2 = (pamplifia_t) ampf2;
+	
+	
+	if (pampf1->strand != pampf2->strand)
+	{
+		incr = -1;
+		j = pampf1->length - 1;
+		if (pampf2->strand)
+		{
+			pampf1 = (pamplifia_t) ampf2;
+			pampf2 = (pamplifia_t) ampf1;
+			chd = 1;
+		}
+	}
+	
+	for (i = 0; i < pampf1->length; i++, j += incr;)
+	{
+		cd1 = pampf1->amplifia[i];
+		if (incr == -1)
+			cd2 = ecoComplementChar(pampf2->amplifia[j]);
+		else
+			cd2 = pampf2->amplifia[j];
+		
+		if (cd1 < cd2) (chd)? return 1: return -1;
+		if (cd2 < cd1) (chd)? return -1: return 1;
+	}
+	return 0;
+}
+