Implemented the retrieval of values with groups of AVLs

python/obitools3/obiimport.py

@@ -134,9 +134,10 @@ if __name__ == '__main__':
 # #                 #print("header", line)
 # # 
             id = line.split(" ", 1)[0][1:]
-# #                 #print(id)
+            print(id)
 # #                 #rest = (line[:-1].split(" ", 1)[1]).split(";")
             view[i].set_id(id)
+            #print(view[i]["ID"])
 # 
             i+=1
         

src/obiavl.c

@@ -1528,6 +1528,18 @@ int obi_close_avl(OBIDMS_avl_p avl)
 }
 
 
+byte_t* obi_avl_group_get(OBIDMS_avl_group_p avl_group, index_t idx)
+{
+	int32_t avl_idx;
+	index_t idx_in_avl;
+
+	avl_idx = (int32_t) (idx >> 32);
+	idx_in_avl = idx & 0x00000000FFFFFFFF;
+
+	return obi_avl_get((avl_group->sub_avls)[avl_idx], idx_in_avl);
+}
+
+
 byte_t* obi_avl_get(OBIDMS_avl_p avl, index_t idx)
 {
 	return (((avl->data)->data)+idx);
@@ -1540,45 +1552,57 @@ int maybe_in_avl(OBIDMS_avl_p avl, byte_t* value)
 }
 
 
-index_t insert_in_avl_group(OBIDMS_avl_group_p avl_group, byte_t* value)	// TODO won't be index_t
+int64_t insert_in_avl_group(OBIDMS_avl_group_p avl_group, byte_t* value)	// TODO won't be index_t
 {
-	index_t index_if_already_in;
+	int32_t index_in_avl;
-	int i;
+	int64_t index_with_avl;
+	int     i;
 
 	if (maybe_in_avl((avl_group->sub_avls)[avl_group->current_avl_idx], value))
 	{
-		//fprintf(stderr, "\nyah maybe");
+		index_in_avl = (int32_t) obi_avl_find((avl_group->sub_avls)[avl_group->current_avl_idx], value);
-		index_if_already_in = obi_avl_find((avl_group->sub_avls)[avl_group->current_avl_idx], value);
+		if (index_in_avl >= 0)
-		if (index_if_already_in >= 0)
+		{
-			return index_if_already_in;
+			index_with_avl = avl_group->current_avl_idx;
+			index_with_avl = index_with_avl << 32;
+			index_with_avl = index_with_avl + index_in_avl;
+			return index_with_avl;
+		}
 	}
-//	else
-//		fprintf(stderr, "\nnah");
 	for (i=0; i < (avl_group->current_avl_idx); i++)
 	{
 		if (maybe_in_avl((avl_group->sub_avls)[i], value))
 		{
-			//fprintf(stderr, "\nyah maybe");
 			if (remap_an_avl((avl_group->sub_avls)[i]) < 0)
 				return -1;
-			index_if_already_in = obi_avl_find((avl_group->sub_avls)[i], value);
+			index_in_avl = (int32_t) obi_avl_find((avl_group->sub_avls)[i], value);
 			if (unmap_an_avl((avl_group->sub_avls)[i]) < 0)
 				return -1;
-			if (index_if_already_in >= 0)
+			if (index_in_avl >= 0)
-				return index_if_already_in;
+			{
+				index_with_avl = i;
+				index_with_avl = index_with_avl << 32;
+				index_with_avl = index_with_avl + index_in_avl;
+				return index_with_avl;
+			}
 		}
-//		else
-//			fprintf(stderr, "\nnah");
 	}
 
-	// not found in any avl: add in current
+	// Not found in any AVL: add in current
-	// first, check if make new one
+	// First, check if make new AVL
 	if ((((avl_group->sub_avls)[avl_group->current_avl_idx])->header)->nb_items == NODE_COUNT_PER_AVL)		// TODO add condition with data size
 		obi_add_new_avl_in_group(avl_group);
 
+	// Add in the current AVL
 	bloom_add(&((((avl_group->sub_avls)[avl_group->current_avl_idx])->header)->bloom_filter), value, BYTE_ARRAY_HEADER_SIZE + *((int32_t*)(value+1)));
 
-	return obi_avl_add((avl_group->sub_avls)[avl_group->current_avl_idx], value);
+	// Build the index containing the AVL index
+	index_in_avl = (int32_t) obi_avl_add((avl_group->sub_avls)[avl_group->current_avl_idx], value);
+	index_with_avl = avl_group->current_avl_idx;
+	index_with_avl = index_with_avl << 32;
+	index_with_avl = index_with_avl + index_in_avl;
+
+	return index_with_avl;
 }
 
 

src/obiavl.h

@@ -365,7 +365,11 @@ byte_t* obi_seq_to_obibytes(char* seq);
  * @since November 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-const char* obi_obibytes_to_seq(byte_t* value_b);
+const char* obi_obibytes_to_seq(byte_t* value_b);		// TODO move to encode source files
+
+
+// TODO
+byte_t* obi_avl_group_get(OBIDMS_avl_group_p avl_group, index_t idx);
 
 
 #endif /* OBIAVL_H_ */

src/obidmscolumn_seq.c

@@ -135,7 +135,8 @@ const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t l
 	if (idx == OBIIdx_NA)
 		return OBISeq_NA;
 
-	//value_b = obi_avl_get((column->avl)[crc(value)], idx);
+	value_b = obi_avl_group_get(column->avl, idx);
+
 	return obi_obibytes_to_seq(value_b);
 }
 

src/obidmscolumn_str.c

@@ -129,7 +129,8 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
 	if (idx == OBIIdx_NA)
 		return OBIStr_NA;
 
-	//value_b = obi_avl_get(column->avl, idx);
+	value_b = obi_avl_group_get(column->avl, idx);
+
 	return obi_obibytes_to_str(value_b);
 }