Commit d076ea99 authored by Celine Mercier's avatar Celine Mercier

Alignment: updated functions to align columns (LCS)

parent 6b1c41f3
This diff is collapsed.
......@@ -3,15 +3,15 @@
****************************************************************************/
/**
* @file obi_align.h
* @file obi_lcs.h
* @author Celine Mercier (celine.mercier@metabarcoding.org)
* @date May 11th 2016
* @brief Header file for the functions handling the LCS alignment of DNA sequences.
*/
#ifndef OBI_ALIGN_H_
#define OBI_ALIGN_H_
#ifndef OBI_LCS_H_
#define OBI_LCS_H_
#include <stdlib.h>
......@@ -59,7 +59,7 @@
*
* Note: The columns where the results are written are automatically named and created.
*
* @param dms A pointer on an OBIDMS.
* @param dms_name The path of the DMS.
* @param seq_view_name The name of the view where the column to align is.
* @param seq_column_name The name of the OBI_SEQ column in the input view to align.
* If "" (empty string), and the input view is of type NUC_SEQS_VIEW, the associated "NUC_SEQ" column is aligned.
......@@ -87,10 +87,13 @@
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_lcs_align_one_column(OBIDMS_p dms,
const char* seq_view_name, const char* seq_column_name, const char* seq_elt_name,
int obi_lcs_align_one_column(const char* dms_name,
const char* seq_view_name,
const char* seq_column_name,
const char* seq_elt_name,
const char* id_column_name,
const char* output_view_name, const char* output_view_comments,
const char* output_view_name,
const char* output_view_comments,
bool print_seq, bool print_count,
double threshold, bool normalize, int reference, bool similarity_mode,
int thread_count);
......@@ -103,7 +106,7 @@ int obi_lcs_align_one_column(OBIDMS_p dms,
*
* Note: The columns where the results are written are automatically named and created.
*
* @param dms A pointer on an OBIDMS.
* @param dms_name The path of the DMS.
* @param seq1_view_name The name of the view where the first column to align is.
* @param seq2_view_name The name of the view where the second column to align is ("" if it is the same view as the first one).
* @param seq1_column_name The name of the first OBI_SEQ column in the input view to align.
......@@ -138,7 +141,7 @@ int obi_lcs_align_one_column(OBIDMS_p dms,
* @since December 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_lcs_align_two_columns(OBIDMS_p dms,
int obi_lcs_align_two_columns(const char* dms_name,
const char* seq1_view_name,
const char* seq2_view_name,
const char* seq1_column_name,
......@@ -147,10 +150,11 @@ int obi_lcs_align_two_columns(OBIDMS_p dms,
const char* seq2_elt_name,
const char* id1_column_name,
const char* id2_column_name,
const char* output_view_name, const char* output_view_comments,
const char* output_view_name,
const char* output_view_comments,
bool print_seq, bool print_count,
double threshold, bool normalize, int reference, bool similarity_mode);
#endif /* OBI_ALIGN_H_ */
#endif /* OBI_LCS_H_ */
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