Committing minor comments before merging branch with master

doc/conf.py

@@ -33,7 +33,7 @@ extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
-    'sphinx.ext.pngmath',
+    'sphinx.ext.imgmath',
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
     'breathe',

src/linked_list.h

@@ -90,7 +90,7 @@ Linked_list_node_p ll_get(Linked_list_node_p head, int idx);
  * @param idx The index of the node to delete.
  *
  * @returns A pointer on the new head node of the linked list.
- * @retval NULL if an error occurred.
+ * @retval NULL if an error occurred.	// TODO or if list is now empty...
  *
  * @since February 2017
  * @author Celine Mercier (celine.mercier@metabarcoding.org)

src/obi_align.c

@@ -883,6 +883,10 @@ int obi_lcs_align_two_columns(OBIDMS_p dms,
 		return -1;
 	}
 
+	// TODO check this
+	if (!similarity_mode && normalize && (threshold > 0))
+		threshold = 1.0 - threshold;
+
 	seq1_count = (seq1_view->infos)->line_count;
 	seq2_count = (seq2_view->infos)->line_count;
 
@@ -932,6 +936,11 @@ int obi_lcs_align_two_columns(OBIDMS_p dms,
 				// Compute alignment score
 				if ((threshold == 0) || (score == -1.0))	// no threshold, or filter passed: align
 					score = obiblob_sse_banded_lcs_align(blob1, blob2, threshold, normalize, reference, similarity_mode, &lcs_length, &ali_length);
+
+				// TODO check this
+//				if (print && !lcsmode && normalize)
+//					score = 1.0 - score;
+
 			}
 
 			if ((score >= 0) && (((normalize || similarity_mode) && (score >= threshold)) || ((!similarity_mode && !normalize) && (score <= threshold))))

src/obiview.c

@@ -1188,6 +1188,8 @@ static int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* colum
 		}
 	}
 
+	// TODO add line_max
+
 	if (((*line_nb_p)+1) > (view->infos)->line_count)
 	{
 		if (update_lines(view, ((*line_nb_p)+1)) < 0)

src/upperband.c

@@ -230,7 +230,7 @@ int thresholdLCS4(int32_t reflen, int32_t lcs)
 }
 
 
-Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col, index_t seq_idx)
+Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col, index_t seq_idx)		// TODO move in another file (obi_align.c)
 {
 	size_t       i;
 	size_t       seq_count;