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Added functions to clone views with a simpler API

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This commit is contained in:
Celine Mercier
2017-04-21 11:58:15 +02:00
parent 1725b8b80c
commit 71b1a43df8
2 changed files with 93 additions and 6 deletions
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52
src/obiview.c
View File

@ -1802,6 +1802,11 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
obidebug(1, "Trying to clone a non-NUC SEQS view to create a NUC SEQS view"); obidebug(1, "Trying to clone a non-NUC SEQS view to create a NUC SEQS view");
return NULL; return NULL;
} }
// Check if there is a quality column
if (obi_view_get_column(view_to_clone, QUALITY_COLUMN) != NULL)
quality_column = true;
else
quality_column = false;
} }
view = obi_new_view(dms, view_name, view_to_clone, line_selection, comments); view = obi_new_view(dms, view_name, view_to_clone, line_selection, comments);
@ -1874,7 +1879,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
} }
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments, bool quality_column) Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments)
{ {
Obiview_p view; Obiview_p view;
Obiview_p view_to_clone; Obiview_p view_to_clone;
@ -1882,7 +1887,43 @@ Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_
view_to_clone = obi_open_view(dms, view_to_clone_name); view_to_clone = obi_open_view(dms, view_to_clone_name);
if (view_to_clone == NULL) if (view_to_clone == NULL)
return NULL; return NULL;
view = obi_new_view_nuc_seqs(dms, view_name, view_to_clone, line_selection, comments, quality_column); view = obi_new_view_nuc_seqs(dms, view_name, view_to_clone, line_selection, comments, false);
close_view(view_to_clone);
return view;
}
Obiview_p obi_clone_view(OBIDMS_p dms, Obiview_p view_to_clone, const char* view_name, index_t* line_selection, const char* comments)
{
if (view_to_clone == NULL)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError: pointer on view to clone is NULL");
return NULL;
}
if (strcmp((view_to_clone->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0)
return obi_new_view_nuc_seqs(dms, view_name, view_to_clone, line_selection, comments, false);
else // Non-typed view
return obi_new_view(dms, view_name, view_to_clone, line_selection, comments);
}
Obiview_p obi_clone_view_from_name(OBIDMS_p dms, const char* view_to_clone_name, const char* view_name, index_t* line_selection, const char* comments)
{
Obiview_p view;
Obiview_p view_to_clone;
view_to_clone = obi_open_view(dms, view_to_clone_name);
if (view_to_clone == NULL)
{
obidebug(1, "\nError: could not open view to clone");
return NULL;
}
view = obi_clone_view(dms, view_to_clone, view_name, line_selection, comments);
close_view(view_to_clone); close_view(view_to_clone);
@ -2242,7 +2283,6 @@ int obi_view_add_column(Obiview_p view,
return -1; return -1;
} }
// If an alias is not defined, it's the original name of the column. // TODO discuss // If an alias is not defined, it's the original name of the column. // TODO discuss
if (alias == NULL) if (alias == NULL)
alias = column_name; alias = column_name;
@ -2342,7 +2382,11 @@ int obi_view_delete_column(Obiview_p view, const char* column_name)
OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name) OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name)
{ {
return (OBIDMS_column_p)(*((OBIDMS_column_p*)(ht_get(view->column_dict, column_name)))); OBIDMS_column_p* column_pp;
column_pp = (OBIDMS_column_p*)(ht_get(view->column_dict, column_name));
if (column_pp == NULL)
return NULL;
return (*column_pp);
} }

47
src/obiview.h
View File

@ -227,7 +227,6 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
* @param line_selection Eventually a pointer on a list of indexes corresponding to a line selection to use with the view to clone * @param line_selection Eventually a pointer on a list of indexes corresponding to a line selection to use with the view to clone
* if there is one. NULL if there is no line selection or no view to clone. * if there is one. NULL if there is no line selection or no view to clone.
* @param comments Eventually, comments to associate with the view. NULL if not. * @param comments Eventually, comments to associate with the view. NULL if not.
* @param quality_column Whether or not a sequence quality column is associated with the view.
* *
* @returns A pointer to the newly created view structure. * @returns A pointer to the newly created view structure.
* @retval NULL if an error occurred. * @retval NULL if an error occurred.
@ -235,7 +234,51 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
* @since February 2016 * @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org) * @author Celine Mercier (celine.mercier@metabarcoding.org)
*/ */
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments, bool quality_column); Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments);
/**
* @brief Clones a view using a pointer on the view to clone.
*
* The new view has the same type as the cloned one.
* Fails if a view with the same name already exists.
*
* @param dms A pointer on the OBIDMS.
* @param view_to_clone A pointer on the opened view to clone to create the new one.
* @param view_name The unique name of the new view.
* @param line_selection Eventually a pointer on a list of indexes corresponding to a line selection to use with the view to clone
* if there is one. NULL if there is no line selection or no view to clone.
* @param comments Eventually, comments to associate with the view. NULL if not.
*
* @returns A pointer to the newly created view structure.
* @retval NULL if an error occurred.
*
* @since April 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
Obiview_p obi_clone_view(OBIDMS_p dms, Obiview_p view_to_clone, const char* view_name, index_t* line_selection, const char* comments);
/**
* @brief Clones a view using the name of the view to clone.
*
* The new view has the same type as the cloned one.
* Fails if a view with the same name already exists.
*
* @param dms A pointer on the OBIDMS.
* @param view_to_clone_name The name of the view to clone.
* @param view_name The unique name of the new view.
* @param line_selection Eventually a pointer on a list of indexes corresponding to a line selection to use with the view to clone
* if there is one. NULL if there is no line selection or no view to clone.
* @param comments Eventually, comments to associate with the view. NULL if not.
*
* @returns A pointer to the newly created view structure.
* @retval NULL if an error occurred.
*
* @since April 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
Obiview_p obi_clone_view_from_name(OBIDMS_p dms, const char* view_to_clone_name, const char* view_name, index_t* line_selection, const char* comments);
/** /**