Backup with sets and ahocorasick

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/branches/ecoPrimers-2.1@298 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/libecoprimer/readdnadb.c

@@ -0,0 +1,59 @@
+/*
+ * readdnadb.c
+ *
+ *  Created on: 7 nov. 2008
+ *      Author: coissac
+ */
+
+#include "ecoprimer.h"
+
+pecodnadb_t readdnadb(const char *name, ecotaxonomy_t *taxonomy, uint32_t *size,poptions_t options)
+{
+	ecoseq_t      *seq;
+	uint32_t       buffsize=100;
+	pecodnadb_t db;
+
+	db = ECOMALLOC(buffsize*sizeof(ecoseq_t*),"I cannot allocate db memory");
+
+
+	for(seq=ecoseq_iterator(name), *size=0;
+	    seq;
+	    seq=ecoseq_iterator(NULL)
+	   )
+	{
+	  if (isExampleTaxon(taxonomy,seq->taxid,options) ||
+		  isCounterExampleTaxon(taxonomy,seq->taxid,options))
+	  {
+			if (*size==buffsize)
+			{
+				buffsize*=2;
+				db = ECOREALLOC(db,buffsize*sizeof(ecoseq_t*),"I cannot allocate db memory");
+			}
+			db[*size]=seq;
+			(*size)++;
+	  }
+	  else
+	  {
+		  delete_ecoseq(seq);
+	  }
+	};
+
+	db = ECOREALLOC(db,(*size)*sizeof(ecoseq_t*),"I cannot allocate db memory");
+
+	return db;
+}
+
+
+void printSeqTest(pecodnadb_t seqdb,uint32_t seqdbsize)
+{
+	uint32_t i;
+	char ch[11];
+	ch [10] = '\0';
+	
+	for (i=0; i < seqdbsize; i++)
+	{
+		strncpy (ch, seqdb[i]->SQ, 10);
+		fprintf (stderr, "seq %d = %s\n", i, ch);
+	}
+	exit (0);
+}