From 857a5198e4dc33c46c1abf33b819cc10dd1c01a2 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Fri, 16 Dec 2016 19:40:36 +0100
Subject: [PATCH] Updated ``obi lcs`` for the LCS alignment of two columns

---
 python/obitools3/commands/lcs.pyx         | 45 ++++++++++++++++-------
 python/obitools3/obidms/capi/obialign.pxd | 18 +++++++++
 2 files changed, 49 insertions(+), 14 deletions(-)

diff --git a/python/obitools3/commands/lcs.pyx b/python/obitools3/commands/lcs.pyx
index 0a8b3b0..8a8bea9 100644
--- a/python/obitools3/commands/lcs.pyx
+++ b/python/obitools3/commands/lcs.pyx
@@ -4,7 +4,8 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.obidms._obidms cimport OBIDMS    # TODO cimport doesn't work
 from obitools3.utils cimport str2bytes
 
-from obitools3.obidms.capi.obialign cimport obi_lcs_align_one_column
+from obitools3.obidms.capi.obialign cimport obi_lcs_align_one_column, \
+                                            obi_lcs_align_two_columns
 
 
 import time
@@ -161,19 +162,35 @@ cpdef align(str dms_n,
     cdef OBIDMS d         
     d = OBIDMS(dms_n)
 
-    # Align 1 column (2 columns not implemented yet)
-    if obi_lcs_align_one_column(d._pointer, \
-                                str2bytes(input_view_1_n), \
-                                str2bytes(input_column_1_n), \
-                                str2bytes(input_elt_1_n), \
-                                str2bytes(id_column_1_n), \
-                                str2bytes(output_view_n), \
-                                str2bytes(comments), \
-                                print_seq, \
-                                print_count, \
-                                threshold, normalize, reference, similarity_mode) < 0 :
-        raise Exception("Error aligning sequences")
-
+    if input_view_2_n == "" and input_column_2_n == "" :
+        if obi_lcs_align_one_column(d._pointer, \
+                                    str2bytes(input_view_1_n), \
+                                    str2bytes(input_column_1_n), \
+                                    str2bytes(input_elt_1_n), \
+                                    str2bytes(id_column_1_n), \
+                                    str2bytes(output_view_n), \
+                                    str2bytes(comments), \
+                                    print_seq, \
+                                    print_count, \
+                                    threshold, normalize, reference, similarity_mode) < 0 :
+            raise Exception("Error aligning sequences")
+    else :
+        if obi_lcs_align_two_columns(d._pointer, \
+                                     str2bytes(input_view_1_n), \
+                                     str2bytes(input_view_2_n), \
+                                     str2bytes(input_column_1_n), \
+                                     str2bytes(input_column_2_n), \
+                                     str2bytes(input_elt_1_n), \
+                                     str2bytes(input_elt_2_n), \
+                                     str2bytes(id_column_1_n), \
+                                     str2bytes(id_column_2_n), \
+                                     str2bytes(output_view_n), \
+                                     str2bytes(comments), \
+                                     print_seq, \
+                                     print_count, \
+                                     threshold, normalize, reference, similarity_mode) < 0 :
+            raise Exception("Error aligning sequences")        
+        
     d.close()
 
 
diff --git a/python/obitools3/obidms/capi/obialign.pxd b/python/obitools3/obidms/capi/obialign.pxd
index e9c105c..e76cabe 100644
--- a/python/obitools3/obidms/capi/obialign.pxd
+++ b/python/obitools3/obidms/capi/obialign.pxd
@@ -20,3 +20,21 @@ cdef extern from "obi_align.h" nogil:
                                  int reference, 
                                  bint similarity_mode)
 
+
+    int obi_lcs_align_two_columns(OBIDMS_p dms,
+                                  const_char_p seq1_view_name,
+                                  const_char_p seq2_view_name,
+                                  const_char_p seq1_column_name,
+                                  const_char_p seq2_column_name,
+                                  const_char_p seq1_elt_name,
+                                  const_char_p seq2_elt_name,
+                                  const_char_p id1_column_name,
+                                  const_char_p id2_column_name,
+                                  const_char_p output_view_name, 
+                                  const_char_p output_view_comments,
+                                  bint print_seq, 
+                                  bint print_count,
+                                  double threshold, 
+                                  bint normalize, 
+                                  int reference, 
+                                  bint similarity_mode);