Views: Files for unfinished views now have the extension

'.obiview_unfinished', renamed to '.obiview' when the view is finished.

python/obitools3/obidms/_obidms.pyx

@@ -690,7 +690,7 @@ cdef class OBIDMS :
         cdef int                  i, j
         cdef str                  column_name
 
-        view_infos_p = obi_view_map_file(self._pointer, str2bytes(view_name))
+        view_infos_p = obi_view_map_file(self._pointer, str2bytes(view_name), True)
         view_infos_d = {}
         view_infos_d["name"] = bytes2str(view_infos_p.name)
         view_infos_d["comments"] = bytes2str(view_infos_p.comments)

python/obitools3/obidms/capi/obiview.pxd

@@ -68,7 +68,7 @@ cdef extern from "obiview.h" nogil:
 
     Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments, bint quality_column)
               
-    Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name)
+    Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name, bint finished)
 
     int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos)
 
@@ -94,11 +94,7 @@ cdef extern from "obiview.h" nogil:
 
     OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const_char_p column_name)
 
-    int obi_view_create_column_alias(Obiview_p view, const_char_p current_name, const_char_p alias)
-
-    int obi_save_view(Obiview_p view)
-    
-    int obi_close_view(Obiview_p view)
+    int obi_view_create_column_alias(Obiview_p view, const_char_p current_name, const_char_p alias)    
     
     int obi_save_and_close_view(Obiview_p view)
 

src/obi_align.c

@@ -4,7 +4,7 @@
 
 /**
  * @file obi_align.c
- * @author Celine Mercier
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date May 4th 2016
  * @brief Functions handling LCS sequence alignments.
  */
@@ -31,10 +31,6 @@
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
-// TODO
-// use openMP pragmas
-
-
 /**************************************************************************
  *
  * D E C L A R A T I O N   O F   T H E   P R I V A T E   F U N C T I O N S
@@ -618,12 +614,12 @@ int obi_lcs_align_one_column(OBIDMS_p dms, const char* seq_view_name, const char
 	}
 
 	// Close views
-	if (obi_close_view(seq_view) < 0)
+	if (obi_save_and_close_view(seq_view) < 0)
 	{
 		obidebug(1, "\nError closing the input view after aligning");
 		return -1;
 	}
-	if (obi_close_view(output_view) < 0)
+	if (obi_save_and_close_view(output_view) < 0)
 	{
 		obidebug(1, "\nError closing the output view after aligning");
 		return -1;
@@ -963,19 +959,19 @@ int obi_lcs_align_two_columns(OBIDMS_p dms,
 	// Close views
 	if (seq2_view != seq1_view)
 	{
-		if (obi_close_view(seq2_view) < 0)
+		if (obi_save_and_close_view(seq2_view) < 0)
 		{
 			obidebug(1, "\nError closing the second input view after aligning");
 			return -1;
 		}
 	}
-	if (obi_close_view(seq1_view) < 0)
+	if (obi_save_and_close_view(seq1_view) < 0)
 	{
 		obidebug(1, "\nError closing the first input view after aligning");
 		return -1;
 	}
 
-	if (obi_close_view(output_view) < 0)
+	if (obi_save_and_close_view(output_view) < 0)
 	{
 		obidebug(1, "\nError closing the output view after aligning");
 		return -1;

src/obiview.h

@@ -242,6 +242,7 @@ Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_
  *
  * @param dms A pointer on the OBIDMS.
  * @param view_name The unique name identifying the view.
+ * @param finished Whether the view is finished or not.
  *
  * @returns A pointer on the mapped view infos structure.
  * @retval NULL if an error occurred.
@@ -249,7 +250,7 @@ Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_
  * @since June 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name);
+Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name, bool finished);
 
 
 /**
@@ -444,42 +445,6 @@ int obi_select_line(Obiview_p view, index_t line_nb);
 int obi_select_lines(Obiview_p view, index_t* line_nbs);
 
 
-/**
- * @brief Saves a view, writing it in the view file.
- *
- * The view is written at the end of the view file, following the latest written view.
- *
- * @warning The view must be writable.
- *
- * @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 February 2016
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-int obi_save_view(Obiview_p view);
-
-
-/**
- * @brief Closes an opened view.
- *
- * @warning Uses obi_save_and_close_view() to automatically save the view if it's not already saved in the view file.
- *
- * @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 February 2016
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-int obi_close_view(Obiview_p view);
-
-
 /**
  * @brief Closes an opened view, and saves it if it is not read-only (meaning it is not already saved in the view file).
  *