From 3e6aecc63591ad3ea2c20943f91938b9b583e4c4 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Tue, 11 Jul 2017 16:44:23 +0200
Subject: [PATCH] Added a C function to add a COUNT column to a view with all
 lines set to 1

---
 src/obiview.c | 44 ++++++++++++++++++++++++++++++++++++++++++--
 src/obiview.h | 20 ++++++++++++++++++++
 2 files changed, 62 insertions(+), 2 deletions(-)

diff --git a/src/obiview.c b/src/obiview.c
index e2d7543..e84d506 100644
--- a/src/obiview.c
+++ b/src/obiview.c
@@ -1188,8 +1188,6 @@ 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)
@@ -2160,6 +2158,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
 }
 
 
+// TODO return a pointer on the column?
 int obi_view_add_column(Obiview_p    view,
 						const char*  column_name,
 						obiversion_t version_number,
@@ -2458,6 +2457,47 @@ int obi_save_and_close_view(Obiview_p view)
 }
 
 
+int obi_create_auto_count_column(Obiview_p view)
+{
+	index_t  i;
+	OBIDMS_p column;
+
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to create an automatic count column in a read-only view");
+		return -1;
+	}
+
+	if (obi_view_add_column(view, COUNT_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, NULL, "Sequence counts", true) < 0)
+	{
+		obidebug(1, "Error adding an automatic count column in a view");
+		return -1;
+	}
+
+	column = obi_view_get_column(view, COUNT_COLUMN);
+	if (column == NULL)
+	{
+		obidebug(1, "Error adding an automatic count column in a view");
+		return -1;
+	}
+
+	// Fill the column with 1s
+	for (i=0; i < (view->infos)->line_count; i++)
+	{
+		if (obi_column_set_obiint_with_elt_idx(column, i, 0, 1) < 0)
+		{
+			obidebug(1, "Error adding an automatic count column in a view");
+			return -1;
+		}
+	}
+
+	return 0;
+}
+
+
+// TODO Move to another file?
 /*********** FOR BLOB COLUMNS ***********/
 
 Obi_blob_p obi_get_blob_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx)
diff --git a/src/obiview.h b/src/obiview.h
index 0a1c447..7a4bef8 100644
--- a/src/obiview.h
+++ b/src/obiview.h
@@ -51,6 +51,9 @@
                                 	 	  	  	 */
 #define QUALITY_COLUMN "QUALITY"				/**< The name of the column containing the sequence qualities
  	 	 	 	 	 	 	 	 	 	 	 	 *   in NUC_SEQS_VIEW views.
+                                	 	  	   	 */
+#define COUNT_COLUMN "COUNT"				    /**< The name of the column containing the sequence counts
+ 	 	 	 	 	 	 	 	 	 	 	 	 *   in NUC_SEQS_VIEW views.
                                 	 	  	  	 */
 
 
@@ -507,6 +510,23 @@ int obi_select_lines(Obiview_p view, index_t* line_nbs);
 int obi_save_and_close_view(Obiview_p view);
 
 
+/**
+ * @brief Creates an OBI_INT column with the line count of the view it belongs to, and sets all lines to 1.
+ *
+ * @warning The number of lines set corresponds to the line count of the view.
+ *
+ * @param view A pointer on the view.
+ *
+ * @returns A value indicating the success of the operation.
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since July 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_create_auto_count_column(Obiview_p view);
+
+
 /**
  * @brief Recovers an obiblob from an OBIDMS column containing indices referring to obiblobs,
  *        using the index of the element in the line, and the column pointer, in the context of a view.