Merged master fixed conflict.

python/obitools3/commands/lcs.cfiles

@@ -0,0 +1,65 @@
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obi_align.h
+../../../src/obi_align.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/obilittlebigman.h
+../../../src/obilittlebigman.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/uint8_indexer.h
+../../../src/uint8_indexer.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/utils.h
+../../../src/utils.c

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
@@ -146,6 +147,13 @@ def addOptions(parser):
                        default=False,
                        help="Sequence counts are written in the output view. Default: they are not written.")
 
+    group.add_argument('--thread-count','-p',   # TODO should probably be in a specific option group
+                       action="store", dest="align:threadcount",
+                       metavar='<THREAD COUNT>',
+                       default=1,
+                       type=int,
+                       help="Number of threads to use for the computation. Default: one.")
+
 
 cpdef align(str dms_n, 
             str input_view_1_n, str output_view_n,
@@ -156,12 +164,13 @@ cpdef align(str dms_n,
             double threshold=0.0, bint normalize=True, 
             int reference=0, bint similarity_mode=True,
             bint print_seq=False, bint print_count=False,
-            comments="") :
+            comments="",
+            int thread_count=1) :
                  
     cdef OBIDMS d         
     d = OBIDMS(dms_n)
 
-    # Align 1 column (2 columns not implemented yet)
+    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), \
@@ -171,6 +180,23 @@ cpdef align(str dms_n,
                                     str2bytes(comments), \
                                     print_seq, \
                                     print_count, \
+                                    threshold, normalize, reference, similarity_mode,
+                                    thread_count) < 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")        
         
@@ -199,7 +225,8 @@ def run(config):
           similarity_mode  = config['align']['similarity'],  \
           print_seq        = config['align']['printseq'],  \
           print_count      = config['align']['printcount'], \
-          comments         = comments)
+          comments         = comments, \
+          thread_count     = config['align']['threadcount'])
 
     print("Done.")
 

python/obitools3/commands/test.pyx

@@ -97,8 +97,7 @@ def test_set_and_get(config, infos):
         return
     idx = random_int(config)
     value = infos['random_generator'][data_type](config)
-    
+    if col.nb_elements_per_line > 1 :
-    if len(element_names) > 1 :
         elt = random.choice(element_names)
         col[idx][elt] = value
         assert col[idx][elt] == value, "Set value != gotten value "+str(col[idx][elt])+" != "+str(value)
@@ -187,6 +186,7 @@ def create_random_column(config, infos) :
     elements_names = []
     for i in range(nb_elements_per_line) :
         elements_names.append(random_unique_element_name(config, infos))
+    elements_names = random.choice([None, elements_names])
     name = random_unique_name(infos)
     infos['view'].add_column(name, 
                              alias=alias, 
@@ -359,6 +359,8 @@ def run(config):
 
     print("Initializing the DMS and the first view...")
     
+    shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
+
     ini_dms_and_first_view(config, infos)
     print_test(config, repr(infos['view']))
     

python/obitools3/obidms/_obidms.pyx

@@ -7,7 +7,8 @@ from .capi.obidms cimport obi_dms, \
                           
 from .capi.obidmscolumn cimport obi_close_column, \
                                 OBIDMS_column_p, \
-                                OBIDMS_column_header_p
+                                OBIDMS_column_header_p, \
+                                obi_get_elements_names
 
 from .capi.obiutils cimport obi_format_date
                    
@@ -73,7 +74,7 @@ from .capi.obiview cimport Obiview_p, \
                            DEFINITION_COLUMN, \
                            QUALITY_COLUMN
                            
-from libc.stdlib cimport malloc
+from libc.stdlib cimport malloc, free
 
 
 
@@ -100,17 +101,17 @@ cdef class OBIDMS_column :
     def __getitem__(self, index_t line_nb):
         return self.get_line(line_nb)
 
-    def __len__(self):
+    def __len__(self):        # TODO discuss
-        return self.lines_used
+        return self._view.line_count
     
     def __sizeof__(self):
         return ((self._pointer)[0].header.header_size + (self._pointer)[0].header.data_size)
     
-    def __iter__(self):
+    def __iter__(self):      # TODO discuss
         # Declarations
         cdef index_t line_nb  
         # Yield each line
-        for line_nb in range(self.lines_used):
+        for line_nb in range(self._view.line_count): 
             yield self.get_line(line_nb)
                 
     def __str__(self) :
@@ -138,7 +139,12 @@ cdef class OBIDMS_column :
     # elements_names property getter
     @property
     def elements_names(self):
-        return (bytes2str(((self._pointer)[0].header).elements_names)).split(';')
+        cdef char* elts_names_b
+        cdef str   elts_names
+        elts_names_b = obi_get_elements_names((self._pointer)[0])
+        elts_names = bytes2str(elts_names_b)
+        free(<char*>elts_names_b)
+        return elts_names.split(';')
 
     # nb_elements_per_line property getter
     @property
@@ -160,11 +166,6 @@ cdef class OBIDMS_column :
     def version(self):
         return ((self._pointer)[0].header).version
 
-    # lines_used property getter
-    @property
-    def lines_used(self):
-        return (self._pointer)[0].header.lines_used
-
     # comments property getter
     @property
     def comments(self):
@@ -268,15 +269,6 @@ cdef class OBIDMS_column_line :
 ######################################################################################################
 
 
-
-
-######################################################################################################
-
-
-
-######################################################################################################
-
-
 cdef class OBIView_line :
 
     def __init__(self, OBIView view, index_t line_nb) :
@@ -424,7 +416,7 @@ 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/_obidmscolumn_str.pyx

@@ -22,7 +22,7 @@ cdef class OBIDMS_column_str(OBIDMS_column):
             result = None
         else :
             result = bytes2str(value)
-        # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
+        # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
@@ -46,7 +46,7 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
             result = None
         else :
             result = bytes2str(value)
-        # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
+        # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
         return result
 
     cpdef object get_line(self, index_t line_nb) :
@@ -65,7 +65,7 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
                 value_in_result = None
             else :
                 value_in_result = bytes2str(value)
-            # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
+            # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
             result[self.elements_names[i]] = value_in_result
             if all_NA and (value_in_result is not None) :
                 all_NA = False

python/obitools3/obidms/_obitaxo.pxd

@@ -18,3 +18,4 @@ cdef class OBI_Taxonomy :
 cdef class OBI_Taxon :
 
     cdef ecotx_t*      _pointer
+    cdef OBI_Taxonomy  _tax

python/obitools3/obidms/_obitaxo.pyx

@@ -7,10 +7,10 @@ from .capi.obitaxonomy cimport obi_read_taxonomy, \
                                obi_write_taxonomy, \
                                obi_close_taxonomy, \
                                obi_taxo_get_taxon_with_taxid, \
-                               obi_taxonomy_add_local_taxon, \
+                               obi_taxo_add_local_taxon, \
+                               obi_taxo_add_preferred_name_with_taxon, \
                                ecotx_t                            
 
-
 from ._obidms cimport OBIDMS
 
 from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
@@ -42,7 +42,7 @@ cdef class OBI_Taxonomy :
             if taxon_p == NULL :
                 raise Exception("Taxon not found")
             taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
-            return OBI_Taxon(taxon_capsule)
+            return OBI_Taxon(taxon_capsule, self)
         else :
             raise Exception("Not implemented")
 
@@ -60,7 +60,7 @@ cdef class OBI_Taxonomy :
         for t in range(self._pointer.taxa.count):
             taxon_p = <ecotx_t*> (taxa+t)
             taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
-            yield OBI_Taxon(taxon_capsule)
+            yield OBI_Taxon(taxon_capsule, self)
 
 
     cpdef write(self, str prefix) :
@@ -70,7 +70,7 @@ cdef class OBI_Taxonomy :
     
     cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=10000000) :
         cdef int taxid
-        taxid = obi_taxonomy_add_local_taxon(self._pointer, str2bytes(name), str2bytes(rank_name), parent_taxid, min_taxid)
+        taxid = obi_taxo_add_local_taxon(self._pointer, str2bytes(name), str2bytes(rank_name), parent_taxid, min_taxid)
         if taxid < 0 :
             raise Exception("Error adding a new taxon to the taxonomy")
         else :
@@ -85,10 +85,11 @@ cdef class OBI_Taxonomy :
 
 cdef class OBI_Taxon :    # TODO dict subclass?
 
-    def __init__(self, object taxon_capsule) :
+    def __init__(self, object taxon_capsule, OBI_Taxonomy tax) :
         self._pointer = <ecotx_t*> PyCapsule_GetPointer(taxon_capsule, NULL)
         if self._pointer == NULL :
-            raise Exception("Error reading the taxonomy")
+            raise Exception("Error reading a taxon (NULL pointer)")
+        self._tax = tax
 
     # name property getter
     @property
@@ -115,12 +116,23 @@ cdef class OBI_Taxon :    # TODO dict subclass?
     def parent(self):
         cdef object parent_capsule
         parent_capsule = PyCapsule_New(self._pointer.parent, NULL, NULL)
-        return OBI_Taxon(parent_capsule)
+        return OBI_Taxon(parent_capsule, self._tax)
+
+    # preferred name property getter and setter
+    @property
+    def preferred_name(self):
+        if self._pointer.preferred_name != NULL :
+            return bytes2str(self._pointer.preferred_name)
+    @preferred_name.setter
+    def preferred_name(self, str new_preferred_name) :  # @DuplicatedSignature
+        if (obi_taxo_add_preferred_name_with_taxon(self._tax._pointer, self._pointer, str2bytes(new_preferred_name)) < 0) :
+            raise Exception("Error adding a new preferred name to a taxon")
 
     def __repr__(self):
         d = {}
         d['taxid']          = self.taxid
         d['name']           = self.name
+        d['preferred name'] = self.preferred_name
         d['parent']         = self.parent.taxid
         d['farest']         = self.farest
         return str(d)

python/obitools3/obidms/capi/obialign.cfiles

@@ -0,0 +1,65 @@
+../../../../src/bloom.h
+../../../../src/bloom.c
+../../../../src/char_str_indexer.h
+../../../../src/char_str_indexer.c
+../../../../src/crc64.h
+../../../../src/crc64.c
+../../../../src/dna_seq_indexer.h
+../../../../src/dna_seq_indexer.c
+../../../../src/encode.h
+../../../../src/encode.c
+../../../../src/hashtable.h
+../../../../src/hashtable.c
+../../../../src/murmurhash2.h
+../../../../src/murmurhash2.c
+../../../../src/obi_align.h
+../../../../src/obi_align.c
+../../../../src/obiavl.h
+../../../../src/obiavl.c
+../../../../src/obiblob_indexer.h
+../../../../src/obiblob_indexer.c
+../../../../src/obiblob.h
+../../../../src/obiblob.c
+../../../../src/obidebug.h
+../../../../src/obidms_taxonomy.h
+../../../../src/obidms_taxonomy.c
+../../../../src/obidms.h
+../../../../src/obidms.c
+../../../../src/obidmscolumn_blob.c
+../../../../src/obidmscolumn_blob.h
+../../../../src/obidmscolumn_bool.c
+../../../../src/obidmscolumn_bool.h
+../../../../src/obidmscolumn_char.c
+../../../../src/obidmscolumn_char.h
+../../../../src/obidmscolumn_float.c
+../../../../src/obidmscolumn_float.h
+../../../../src/obidmscolumn_idx.h
+../../../../src/obidmscolumn_idx.c
+../../../../src/obidmscolumn_int.c
+../../../../src/obidmscolumn_int.h
+../../../../src/obidmscolumn_qual.h
+../../../../src/obidmscolumn_qual.c
+../../../../src/obidmscolumn_seq.c
+../../../../src/obidmscolumn_seq.h
+../../../../src/obidmscolumn_str.c
+../../../../src/obidmscolumn_str.h
+../../../../src/obidmscolumn.h
+../../../../src/obidmscolumn.c
+../../../../src/obidmscolumndir.h
+../../../../src/obidmscolumndir.c
+../../../../src/obierrno.h
+../../../../src/obierrno.c
+../../../../src/obilittlebigman.h
+../../../../src/obilittlebigman.c
+../../../../src/obitypes.h
+../../../../src/obitypes.c
+../../../../src/obiview.h
+../../../../src/obiview.c
+../../../../src/sse_banded_LCS_alignment.h
+../../../../src/sse_banded_LCS_alignment.c
+../../../../src/uint8_indexer.h
+../../../../src/uint8_indexer.c
+../../../../src/upperband.h
+../../../../src/upperband.c
+../../../../src/utils.h
+../../../../src/utils.c

python/obitools3/obidms/capi/obialign.pxd

@@ -18,5 +18,24 @@ cdef extern from "obi_align.h" nogil:
                                  double threshold, 
                                  bint normalize, 
                                  int reference, 
-                                 bint similarity_mode)
+                                 bint similarity_mode,
+                                 int thread_count)
 
+
+    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);

python/obitools3/obidms/capi/obidms.cfiles

@@ -0,0 +1,65 @@
+../../../../src/bloom.h
+../../../../src/bloom.c
+../../../../src/char_str_indexer.h
+../../../../src/char_str_indexer.c
+../../../../src/crc64.h
+../../../../src/crc64.c
+../../../../src/dna_seq_indexer.h
+../../../../src/dna_seq_indexer.c
+../../../../src/encode.h
+../../../../src/encode.c
+../../../../src/hashtable.h
+../../../../src/hashtable.c
+../../../../src/murmurhash2.h
+../../../../src/murmurhash2.c
+../../../../src/obi_align.h
+../../../../src/obi_align.c
+../../../../src/obiavl.h
+../../../../src/obiavl.c
+../../../../src/obiblob_indexer.h
+../../../../src/obiblob_indexer.c
+../../../../src/obiblob.h
+../../../../src/obiblob.c
+../../../../src/obidebug.h
+../../../../src/obidms_taxonomy.h
+../../../../src/obidms_taxonomy.c
+../../../../src/obidms.h
+../../../../src/obidms.c
+../../../../src/obidmscolumn_blob.c
+../../../../src/obidmscolumn_blob.h
+../../../../src/obidmscolumn_bool.c
+../../../../src/obidmscolumn_bool.h
+../../../../src/obidmscolumn_char.c
+../../../../src/obidmscolumn_char.h
+../../../../src/obidmscolumn_float.c
+../../../../src/obidmscolumn_float.h
+../../../../src/obidmscolumn_idx.h
+../../../../src/obidmscolumn_idx.c
+../../../../src/obidmscolumn_int.c
+../../../../src/obidmscolumn_int.h
+../../../../src/obidmscolumn_qual.h
+../../../../src/obidmscolumn_qual.c
+../../../../src/obidmscolumn_seq.c
+../../../../src/obidmscolumn_seq.h
+../../../../src/obidmscolumn_str.c
+../../../../src/obidmscolumn_str.h
+../../../../src/obidmscolumn.h
+../../../../src/obidmscolumn.c
+../../../../src/obidmscolumndir.h
+../../../../src/obidmscolumndir.c
+../../../../src/obierrno.h
+../../../../src/obierrno.c
+../../../../src/obilittlebigman.h
+../../../../src/obilittlebigman.c
+../../../../src/obitypes.h
+../../../../src/obitypes.c
+../../../../src/obiview.h
+../../../../src/obiview.c
+../../../../src/sse_banded_LCS_alignment.h
+../../../../src/sse_banded_LCS_alignment.c
+../../../../src/uint8_indexer.h
+../../../../src/uint8_indexer.c
+../../../../src/upperband.h
+../../../../src/upperband.c
+../../../../src/utils.h
+../../../../src/utils.c

python/obitools3/obidms/capi/obidmscolumn.cfiles

@@ -0,0 +1,65 @@
+../../../../src/bloom.h
+../../../../src/bloom.c
+../../../../src/char_str_indexer.h
+../../../../src/char_str_indexer.c
+../../../../src/crc64.h
+../../../../src/crc64.c
+../../../../src/dna_seq_indexer.h
+../../../../src/dna_seq_indexer.c
+../../../../src/encode.h
+../../../../src/encode.c
+../../../../src/hashtable.h
+../../../../src/hashtable.c
+../../../../src/murmurhash2.h
+../../../../src/murmurhash2.c
+../../../../src/obi_align.h
+../../../../src/obi_align.c
+../../../../src/obiavl.h
+../../../../src/obiavl.c
+../../../../src/obiblob_indexer.h
+../../../../src/obiblob_indexer.c
+../../../../src/obiblob.h
+../../../../src/obiblob.c
+../../../../src/obidebug.h
+../../../../src/obidms_taxonomy.h
+../../../../src/obidms_taxonomy.c
+../../../../src/obidms.h
+../../../../src/obidms.c
+../../../../src/obidmscolumn_blob.c
+../../../../src/obidmscolumn_blob.h
+../../../../src/obidmscolumn_bool.c
+../../../../src/obidmscolumn_bool.h
+../../../../src/obidmscolumn_char.c
+../../../../src/obidmscolumn_char.h
+../../../../src/obidmscolumn_float.c
+../../../../src/obidmscolumn_float.h
+../../../../src/obidmscolumn_idx.h
+../../../../src/obidmscolumn_idx.c
+../../../../src/obidmscolumn_int.c
+../../../../src/obidmscolumn_int.h
+../../../../src/obidmscolumn_qual.h
+../../../../src/obidmscolumn_qual.c
+../../../../src/obidmscolumn_seq.c
+../../../../src/obidmscolumn_seq.h
+../../../../src/obidmscolumn_str.c
+../../../../src/obidmscolumn_str.h
+../../../../src/obidmscolumn.h
+../../../../src/obidmscolumn.c
+../../../../src/obidmscolumndir.h
+../../../../src/obidmscolumndir.c
+../../../../src/obierrno.h
+../../../../src/obierrno.c
+../../../../src/obilittlebigman.h
+../../../../src/obilittlebigman.c
+../../../../src/obitypes.h
+../../../../src/obitypes.c
+../../../../src/obiview.h
+../../../../src/obiview.c
+../../../../src/sse_banded_LCS_alignment.h
+../../../../src/sse_banded_LCS_alignment.c
+../../../../src/uint8_indexer.h
+../../../../src/uint8_indexer.c
+../../../../src/upperband.h
+../../../../src/upperband.c
+../../../../src/utils.h
+../../../../src/utils.c

python/obitools3/obidms/capi/obidmscolumn.pxd

@@ -48,29 +48,6 @@ cdef extern from "obidmscolumn.h" nogil:
         
     ctypedef OBIDMS_column_t* OBIDMS_column_p
         
-    OBIDMS_column_p obi_create_column(OBIDMS_p dms, 
-                                      const_char_p column_name, 
-                                      OBIType_t type, 
-                                      index_t nb_lines, 
-                                      index_t nb_elements_per_line, 
-                                      const_char_p elements_names,
-                                      const_char_p indexer_name,
-                                      const_char_p associated_colum_name,
-                                      obiversion_t associated_colum_version,
-                                      const_char_p comments)
-                
-    OBIDMS_column_p obi_open_column(OBIDMS_p dms, 
-                                    const_char_p column_name, 
-                                    obiversion_t version_number)
-        
-    int obi_close_column(OBIDMS_column_p column)
-        
-    OBIDMS_column_p obi_clone_column(OBIDMS_p dms, 
-                                     OBIDMS_column_p line_selection,
-                                     const_char_p column_name, 
-                                     obiversion_t version_number, 
-                                     bint clone_data)
-    
     int obi_close_column(OBIDMS_column_p column)
     
     obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, 
@@ -82,7 +59,7 @@ cdef extern from "obidmscolumn.h" nogil:
     
     int obi_close_header(OBIDMS_column_header_p header)
     
-    int obi_select(OBIDMS_column_p line_selection_column, index_t line_to_grep)
+    char* obi_get_elements_names(OBIDMS_column_p column)
     
 
 cdef extern from "obidmscolumn_int.h" nogil:

python/obitools3/obidms/capi/obierrno.cfiles

@@ -0,0 +1,65 @@
+../../../../src/bloom.h
+../../../../src/bloom.c
+../../../../src/char_str_indexer.h
+../../../../src/char_str_indexer.c
+../../../../src/crc64.h
+../../../../src/crc64.c
+../../../../src/dna_seq_indexer.h
+../../../../src/dna_seq_indexer.c
+../../../../src/encode.h
+../../../../src/encode.c
+../../../../src/hashtable.h
+../../../../src/hashtable.c
+../../../../src/murmurhash2.h
+../../../../src/murmurhash2.c
+../../../../src/obi_align.h
+../../../../src/obi_align.c
+../../../../src/obiavl.h
+../../../../src/obiavl.c
+../../../../src/obiblob_indexer.h
+../../../../src/obiblob_indexer.c
+../../../../src/obiblob.h
+../../../../src/obiblob.c
+../../../../src/obidebug.h
+../../../../src/obidms_taxonomy.h
+../../../../src/obidms_taxonomy.c
+../../../../src/obidms.h
+../../../../src/obidms.c
+../../../../src/obidmscolumn_blob.c
+../../../../src/obidmscolumn_blob.h
+../../../../src/obidmscolumn_bool.c
+../../../../src/obidmscolumn_bool.h
+../../../../src/obidmscolumn_char.c
+../../../../src/obidmscolumn_char.h
+../../../../src/obidmscolumn_float.c
+../../../../src/obidmscolumn_float.h
+../../../../src/obidmscolumn_idx.h
+../../../../src/obidmscolumn_idx.c
+../../../../src/obidmscolumn_int.c
+../../../../src/obidmscolumn_int.h
+../../../../src/obidmscolumn_qual.h
+../../../../src/obidmscolumn_qual.c
+../../../../src/obidmscolumn_seq.c
+../../../../src/obidmscolumn_seq.h
+../../../../src/obidmscolumn_str.c
+../../../../src/obidmscolumn_str.h
+../../../../src/obidmscolumn.h
+../../../../src/obidmscolumn.c
+../../../../src/obidmscolumndir.h
+../../../../src/obidmscolumndir.c
+../../../../src/obierrno.h
+../../../../src/obierrno.c
+../../../../src/obilittlebigman.h
+../../../../src/obilittlebigman.c
+../../../../src/obitypes.h
+../../../../src/obitypes.c
+../../../../src/obiview.h
+../../../../src/obiview.c
+../../../../src/sse_banded_LCS_alignment.h
+../../../../src/sse_banded_LCS_alignment.c
+../../../../src/uint8_indexer.h
+../../../../src/uint8_indexer.c
+../../../../src/upperband.h
+../../../../src/upperband.c
+../../../../src/utils.h
+../../../../src/utils.c

python/obitools3/obidms/capi/obitaxonomy.cfiles

@@ -0,0 +1,65 @@
+../../../../src/bloom.h
+../../../../src/bloom.c
+../../../../src/char_str_indexer.h
+../../../../src/char_str_indexer.c
+../../../../src/crc64.h
+../../../../src/crc64.c
+../../../../src/dna_seq_indexer.h
+../../../../src/dna_seq_indexer.c
+../../../../src/encode.h
+../../../../src/encode.c
+../../../../src/hashtable.h
+../../../../src/hashtable.c
+../../../../src/murmurhash2.h
+../../../../src/murmurhash2.c
+../../../../src/obi_align.h
+../../../../src/obi_align.c
+../../../../src/obiavl.h
+../../../../src/obiavl.c
+../../../../src/obiblob_indexer.h
+../../../../src/obiblob_indexer.c
+../../../../src/obiblob.h
+../../../../src/obiblob.c
+../../../../src/obidebug.h
+../../../../src/obidms_taxonomy.h
+../../../../src/obidms_taxonomy.c
+../../../../src/obidms.h
+../../../../src/obidms.c
+../../../../src/obidmscolumn_blob.c
+../../../../src/obidmscolumn_blob.h
+../../../../src/obidmscolumn_bool.c
+../../../../src/obidmscolumn_bool.h
+../../../../src/obidmscolumn_char.c
+../../../../src/obidmscolumn_char.h
+../../../../src/obidmscolumn_float.c
+../../../../src/obidmscolumn_float.h
+../../../../src/obidmscolumn_idx.h
+../../../../src/obidmscolumn_idx.c
+../../../../src/obidmscolumn_int.c
+../../../../src/obidmscolumn_int.h
+../../../../src/obidmscolumn_qual.h
+../../../../src/obidmscolumn_qual.c
+../../../../src/obidmscolumn_seq.c
+../../../../src/obidmscolumn_seq.h
+../../../../src/obidmscolumn_str.c
+../../../../src/obidmscolumn_str.h
+../../../../src/obidmscolumn.h
+../../../../src/obidmscolumn.c
+../../../../src/obidmscolumndir.h
+../../../../src/obidmscolumndir.c
+../../../../src/obierrno.h
+../../../../src/obierrno.c
+../../../../src/obilittlebigman.h
+../../../../src/obilittlebigman.c
+../../../../src/obitypes.h
+../../../../src/obitypes.c
+../../../../src/obiview.h
+../../../../src/obiview.c
+../../../../src/sse_banded_LCS_alignment.h
+../../../../src/sse_banded_LCS_alignment.c
+../../../../src/uint8_indexer.h
+../../../../src/uint8_indexer.c
+../../../../src/upperband.h
+../../../../src/upperband.c
+../../../../src/utils.h
+../../../../src/utils.c

python/obitools3/obidms/capi/obitaxonomy.pxd

@@ -13,6 +13,7 @@ cdef extern from "obidms_taxonomy.h" nogil:
         int32_t           farest
         ecotxnode*        parent
         char*             name
+        char*             preferred_name
 
     ctypedef ecotxnode ecotx_t
 
@@ -56,4 +57,9 @@ cdef extern from "obidms_taxonomy.h" nogil:
     
     ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
     
-    int obi_taxonomy_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid)
+    int obi_taxo_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid)
+
+    int obi_taxo_add_preferred_name_with_taxid(OBIDMS_taxonomy_p tax, int32_t taxid, const char* preferred_name)
+
+    int obi_taxo_add_preferred_name_with_taxon(OBIDMS_taxonomy_p tax, ecotx_t* taxon, const char* preferred_name)
+

python/obitools3/obidms/capi/obitypes.cfiles

@@ -0,0 +1,65 @@
+../../../../src/bloom.h
+../../../../src/bloom.c
+../../../../src/char_str_indexer.h
+../../../../src/char_str_indexer.c
+../../../../src/crc64.h
+../../../../src/crc64.c
+../../../../src/dna_seq_indexer.h
+../../../../src/dna_seq_indexer.c
+../../../../src/encode.h
+../../../../src/encode.c
+../../../../src/hashtable.h
+../../../../src/hashtable.c
+../../../../src/murmurhash2.h
+../../../../src/murmurhash2.c
+../../../../src/obi_align.h
+../../../../src/obi_align.c
+../../../../src/obiavl.h
+../../../../src/obiavl.c
+../../../../src/obiblob_indexer.h
+../../../../src/obiblob_indexer.c
+../../../../src/obiblob.h
+../../../../src/obiblob.c
+../../../../src/obidebug.h
+../../../../src/obidms_taxonomy.h
+../../../../src/obidms_taxonomy.c
+../../../../src/obidms.h
+../../../../src/obidms.c
+../../../../src/obidmscolumn_blob.c
+../../../../src/obidmscolumn_blob.h
+../../../../src/obidmscolumn_bool.c
+../../../../src/obidmscolumn_bool.h
+../../../../src/obidmscolumn_char.c
+../../../../src/obidmscolumn_char.h
+../../../../src/obidmscolumn_float.c
+../../../../src/obidmscolumn_float.h
+../../../../src/obidmscolumn_idx.h
+../../../../src/obidmscolumn_idx.c
+../../../../src/obidmscolumn_int.c
+../../../../src/obidmscolumn_int.h
+../../../../src/obidmscolumn_qual.h
+../../../../src/obidmscolumn_qual.c
+../../../../src/obidmscolumn_seq.c
+../../../../src/obidmscolumn_seq.h
+../../../../src/obidmscolumn_str.c
+../../../../src/obidmscolumn_str.h
+../../../../src/obidmscolumn.h
+../../../../src/obidmscolumn.c
+../../../../src/obidmscolumndir.h
+../../../../src/obidmscolumndir.c
+../../../../src/obierrno.h
+../../../../src/obierrno.c
+../../../../src/obilittlebigman.h
+../../../../src/obilittlebigman.c
+../../../../src/obitypes.h
+../../../../src/obitypes.c
+../../../../src/obiview.h
+../../../../src/obiview.c
+../../../../src/sse_banded_LCS_alignment.h
+../../../../src/sse_banded_LCS_alignment.c
+../../../../src/uint8_indexer.h
+../../../../src/uint8_indexer.c
+../../../../src/upperband.h
+../../../../src/upperband.c
+../../../../src/utils.h
+../../../../src/utils.c

python/obitools3/obidms/capi/obiutils.cfiles

@@ -0,0 +1,65 @@
+../../../../src/bloom.h
+../../../../src/bloom.c
+../../../../src/char_str_indexer.h
+../../../../src/char_str_indexer.c
+../../../../src/crc64.h
+../../../../src/crc64.c
+../../../../src/dna_seq_indexer.h
+../../../../src/dna_seq_indexer.c
+../../../../src/encode.h
+../../../../src/encode.c
+../../../../src/hashtable.h
+../../../../src/hashtable.c
+../../../../src/murmurhash2.h
+../../../../src/murmurhash2.c
+../../../../src/obi_align.h
+../../../../src/obi_align.c
+../../../../src/obiavl.h
+../../../../src/obiavl.c
+../../../../src/obiblob_indexer.h
+../../../../src/obiblob_indexer.c
+../../../../src/obiblob.h
+../../../../src/obiblob.c
+../../../../src/obidebug.h
+../../../../src/obidms_taxonomy.h
+../../../../src/obidms_taxonomy.c
+../../../../src/obidms.h
+../../../../src/obidms.c
+../../../../src/obidmscolumn_blob.c
+../../../../src/obidmscolumn_blob.h
+../../../../src/obidmscolumn_bool.c
+../../../../src/obidmscolumn_bool.h
+../../../../src/obidmscolumn_char.c
+../../../../src/obidmscolumn_char.h
+../../../../src/obidmscolumn_float.c
+../../../../src/obidmscolumn_float.h
+../../../../src/obidmscolumn_idx.h
+../../../../src/obidmscolumn_idx.c
+../../../../src/obidmscolumn_int.c
+../../../../src/obidmscolumn_int.h
+../../../../src/obidmscolumn_qual.h
+../../../../src/obidmscolumn_qual.c
+../../../../src/obidmscolumn_seq.c
+../../../../src/obidmscolumn_seq.h
+../../../../src/obidmscolumn_str.c
+../../../../src/obidmscolumn_str.h
+../../../../src/obidmscolumn.h
+../../../../src/obidmscolumn.c
+../../../../src/obidmscolumndir.h
+../../../../src/obidmscolumndir.c
+../../../../src/obierrno.h
+../../../../src/obierrno.c
+../../../../src/obilittlebigman.h
+../../../../src/obilittlebigman.c
+../../../../src/obitypes.h
+../../../../src/obitypes.c
+../../../../src/obiview.h
+../../../../src/obiview.c
+../../../../src/sse_banded_LCS_alignment.h
+../../../../src/sse_banded_LCS_alignment.c
+../../../../src/uint8_indexer.h
+../../../../src/uint8_indexer.c
+../../../../src/upperband.h
+../../../../src/upperband.c
+../../../../src/utils.h
+../../../../src/utils.c

python/obitools3/obidms/capi/obiview.cfiles

@@ -0,0 +1,65 @@
+../../../../src/bloom.h
+../../../../src/bloom.c
+../../../../src/char_str_indexer.h
+../../../../src/char_str_indexer.c
+../../../../src/crc64.h
+../../../../src/crc64.c
+../../../../src/dna_seq_indexer.h
+../../../../src/dna_seq_indexer.c
+../../../../src/encode.h
+../../../../src/encode.c
+../../../../src/hashtable.h
+../../../../src/hashtable.c
+../../../../src/murmurhash2.h
+../../../../src/murmurhash2.c
+../../../../src/obi_align.h
+../../../../src/obi_align.c
+../../../../src/obiavl.h
+../../../../src/obiavl.c
+../../../../src/obiblob_indexer.h
+../../../../src/obiblob_indexer.c
+../../../../src/obiblob.h
+../../../../src/obiblob.c
+../../../../src/obidebug.h
+../../../../src/obidms_taxonomy.h
+../../../../src/obidms_taxonomy.c
+../../../../src/obidms.h
+../../../../src/obidms.c
+../../../../src/obidmscolumn_blob.c
+../../../../src/obidmscolumn_blob.h
+../../../../src/obidmscolumn_bool.c
+../../../../src/obidmscolumn_bool.h
+../../../../src/obidmscolumn_char.c
+../../../../src/obidmscolumn_char.h
+../../../../src/obidmscolumn_float.c
+../../../../src/obidmscolumn_float.h
+../../../../src/obidmscolumn_idx.h
+../../../../src/obidmscolumn_idx.c
+../../../../src/obidmscolumn_int.c
+../../../../src/obidmscolumn_int.h
+../../../../src/obidmscolumn_qual.h
+../../../../src/obidmscolumn_qual.c
+../../../../src/obidmscolumn_seq.c
+../../../../src/obidmscolumn_seq.h
+../../../../src/obidmscolumn_str.c
+../../../../src/obidmscolumn_str.h
+../../../../src/obidmscolumn.h
+../../../../src/obidmscolumn.c
+../../../../src/obidmscolumndir.h
+../../../../src/obidmscolumndir.c
+../../../../src/obierrno.h
+../../../../src/obierrno.c
+../../../../src/obilittlebigman.h
+../../../../src/obilittlebigman.c
+../../../../src/obitypes.h
+../../../../src/obitypes.c
+../../../../src/obiview.h
+../../../../src/obiview.c
+../../../../src/sse_banded_LCS_alignment.h
+../../../../src/sse_banded_LCS_alignment.c
+../../../../src/uint8_indexer.h
+../../../../src/uint8_indexer.c
+../../../../src/upperband.h
+../../../../src/upperband.c
+../../../../src/utils.h
+../../../../src/utils.c

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)
 
@@ -96,10 +96,6 @@ cdef extern from "obiview.h" nogil:
 
     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_save_and_close_view(Obiview_p view)
 
 

src/obi_align.h

@@ -1,12 +1,12 @@
 /****************************************************************************
- * Sequence alignment functions header file	                                *
+ * LCS sequence alignment functions header file	                            *
  ****************************************************************************/
 
 /**
  * @file obi_align.h
- * @author Celine Mercier
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date May 11th 2016
- * @brief Header file for the functions handling the alignment of DNA sequences.
+ * @brief Header file for the functions handling the LCS alignment of DNA sequences.
  */
 
 
@@ -55,7 +55,7 @@
 
 
 /**
- * @brief Aligns a NUC_SEQ column with itself.
+ * @brief Aligns an OBI_SEQ column with itself.
  *
  * Note: The columns where the results are written are automatically named and created.
  *
@@ -77,7 +77,7 @@
  * 					the length of the Longest Common Subsequence. If the score is not normalized and expressed in distance,
  *                  it is (reference length - LCS length). Only sequence pairs with a similarity above the threshold are printed.
  * @param normalize Whether the score should be normalized with the reference sequence length.
- * @param reference The reference length. 0: The alignement length; 1: The longest sequence's length; 2: The shortest sequence's length.
+ * @param reference The reference length. 0: The alignment length; 1: The longest sequence's length; 2: The shortest sequence's length.
  * @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false).
  *
  * @returns A value indicating the success of the operation.
@@ -92,18 +92,64 @@ int obi_lcs_align_one_column(OBIDMS_p dms,
 							 const char* id_column_name,
 					         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);
+						     double threshold, bool normalize, int reference, bool similarity_mode,
+							 int thread_count);
 
 
 /**
- * @brief
+ * @brief Aligns two OBI_SEQ columns.
  *
- * TODO
+ * The columns must belong to the same OBIDMS, but can belong to different views.
  *
+ * Note: The columns where the results are written are automatically named and created.
+ *
+ * @param dms A pointer on an OBIDMS.
+ * @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.
+ *                         If "" (empty string), and the input view is of type NUC_SEQS_VIEW, the associated "NUC_SEQ" column is aligned.
+ * @param seq2_column_name The name of the second 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.
+ * @param seq1_elt_name The name of the element in the first column corresponding to the sequence to align, if the column has multiple
+ *                      elements per line.
+ * @param seq2_elt_name The name of the element in the second column corresponding to the sequence to align, if the column has multiple
+ *                      elements per line.
+ * @param id1_column_name The name of the column in the first input view containing the identifiers of the first sequence to align.
+ *                        If "" (empty string), and the input view is of type NUC_SEQS_VIEW, the associated "ID" column is aligned.
+ * @param id2_column_name The name of the column in the second input view containing the identifiers of the second sequence to align.
+ *                        If "" (empty string), and the input view is of type NUC_SEQS_VIEW, the associated "ID" column is aligned.
+ * @param output_view_name The name of the output view where the results should be written (should not already exist).
+ * @param output_view_comments The comments that should be associated with the output view.
+ * @param print_seq A boolean indicating whether the aligned sequences should be copied in the output view.
+ * @param print_count A boolean indicating whether the aligned sequence counts should be copied in the output view.
+ * @param threshold Score threshold. If the score is normalized and expressed in similarity, it is an identity, e.g. 0.95
+ * 					for an identity of 95%. If the score is normalized and expressed in distance, it is (1.0 - identity),
+ * 					e.g. 0.05 for an identity of 95%. If the score is not normalized and expressed in similarity, it is
+ * 					the length of the Longest Common Subsequence. If the score is not normalized and expressed in distance,
+ *                  it is (reference length - LCS length). Only sequence pairs with a similarity above the threshold are printed.
+ * @param normalize Whether the score should be normalized with the reference sequence length.
+ * @param reference The reference length. 0: The alignement length; 1: The longest sequence's length; 2: The shortest sequence's length.
+ * @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false).
+ *
+ * @returns A value indicating the success of the operation.
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since December 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-//int obi_align_two_columns(Obiview_p seq_view, OBIDMS_column_p seq_column_1, OBIDMS_column_p seq_column_2,
+int obi_lcs_align_two_columns(OBIDMS_p dms,
-//						  Obiview_p score_view, OBIDMS_column_p score_column,
+							  const char* seq1_view_name,
-//						  double threshold, bool normalize, int reference, bool similarity_mode);
+							  const char* seq2_view_name,
+							  const char* seq1_column_name,
+							  const char* seq2_column_name,
+							  const char* seq1_elt_name,
+							  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,
+							  bool print_seq, bool print_count,
+						      double threshold, bool normalize, int reference, bool similarity_mode);
 
 
 #endif /* OBI_ALIGN_H_ */

src/obidms_taxonomy.h

@@ -6,7 +6,7 @@
  * @file obidms_taxonomy.h
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date March 2nd 2016
- * @brief Header file for the functions handling the reading of binary taxonomy files.
+ * @brief Header file for the functions handling the reading and writing of taxonomy files.
  */
 
 
@@ -17,105 +17,384 @@
 #include "obidms.h"
 
 
-#define MIN_LOCAL_TAXID (10000000)
+#define MIN_LOCAL_TAXID (10000000)     	  /**< The minimum taxid for a taxon added locally (i.e. not an NCBI taxon).
-#define TAX_NAME_LEN (1024)
+                                	       */
+#define TAX_NAME_LEN (1024)				  /**< The maximum length for the taxonomy name.
+                                	       */
 
 
+/**
+ * @brief Structure for a taxon as stored in a .tdx file.
+ */
 typedef struct {
-	int32_t  taxid;
+	int32_t  taxid;        /**< Taxid.
-	int32_t  rank;
+	 	 	    		    */
-	int32_t	 parent;
+	int32_t  rank;         /**< Rank index.
-	int32_t  name_length;
+	    				    */
-	char     name[1];
+	int32_t	 parent;       /**< Index, in the taxid index, of the parent node in the taxonomic tree.
+	    					*/
+	int32_t  name_length;  /**< Length of the taxon scientific name.
+							*/
+	char     name[];	   /**< Scientific name of the taxon.
+							*/
 } ecotxformat_t;
 
 
+/**
+ * @brief Structure for a taxon as stored in a taxonomy structure.
+ */
 typedef struct ecotxnode {
-	int32_t           taxid;
+	int32_t           taxid;		 	/**< Taxid.		// TODO discuss that this is will be the current taxid even if the struct was accessed through a deprecated one
-	int32_t           rank;
+	    								 */
-	int32_t  		  farest;
+	int32_t           rank;		        /**< Rank index in ecorankidx_t structure.
-	int32_t			  idx;
+	 	 	 	 	 	 	 	 	 	 */
-	struct ecotxnode* parent;
+	int32_t  		  farest;		    /**< Longest branch length, used to compute distances between taxa faster.
-	char*			  name;
+	 	 	 	 	 	 	 	 	 	 */
-	bool			  local;
+	int32_t			  idx;			    /**< Index in the ecotxidx_t structure.
+	 	 	 	 	 	 	 	 	 	 */
+	struct ecotxnode* parent;			/**< Pointer on the parent node in the taxonomic tree.
+	 	 	 	 	 	 	 	 	 	 */
+	char*			  name;		   		/**< Scientific name of the taxon.
+										 */
+	char*			  preferred_name;	/**< Preferred name of the taxon if there is one, otherwise NULL.
+										 */
+	bool			  local;			/**< A boolean indicating whether the taxon is local or not.
+	 	 	 	 	 	 	 	 	 	 */
 } ecotx_t;
 
 
+/**
+ * @brief Structure for the taxon index in a taxonomy structure.
+ */
 typedef struct {
-	int32_t count;
+	int32_t count;			/**< Number of taxa.
-	int32_t ncbi_count;
+	 	 	 	 	 	 	 */
-	int32_t local_count;
+	int32_t ncbi_count;		/**< Number of NCBI taxa.
-	int32_t max_taxid;
+	 	 	 	 	 	 	 */
-	int32_t buffer_size;
+	int32_t local_count;	/**< Number of taxa added locally.
-	ecotx_t taxon[1];
+ 	 	 	 	 	 	 	 */
+	int32_t max_taxid;		/**< Maximum taxid existing in the taxon index.
+	 	 	 	 	 	 	 */
+	int32_t buffer_size;	/**< Number of taxa.	// TODO kept this but not sure of its use
+ 	 	 	 	 	 	 	 */
+	ecotx_t taxon[];		/**< Taxon array.
+ 	 	 	 	 	 	 	 */
 } ecotxidx_t;
 
 
+/**
+ * @brief Structure for the rank index in a taxonomy structure.
+ */
 typedef struct {
-	int32_t count;
+	int32_t count;		/**< Number of ranks.
-	char*   label[1];
+ 	 	 	 	 	 	 */
+	char*   label[];	/**< Array of rank names.
+	 	 	 	 	 	 */
 } ecorankidx_t;
 
 
+/**
+ * @brief Structure for a taxon name as stored in a .ndx file.
+ */
 typedef struct {
- 	int32_t  is_scientific_name;
+ 	int32_t  is_scientific_name;	/**< A boolean indicating whether the name is a scientific name or not.
-	int32_t  name_length;
+	 	 	 	 	 	 	 	 	 */
-	int32_t  class_length;
+	int32_t  name_length;			/**< The name length.
-	int32_t  taxid;	// taxid idx
+	 	 	 	 	 	 	 	 	 */
-	char     names[1];
+	int32_t  class_length;			/**< The name class length.
+	 	 	 	 	 	 	 	 	 */
+	int32_t  taxid;       			/**< Index of the taxon in the taxid index.
+									 */
+	char     names[];       		/**< Taxon name and name class concatenated.
+	 	 	 	 	 	 	 	 	 */
 } econameformat_t;
 
 
+/**
+ * @brief Structure for a taxon name as stored in a taxonomy structure.
+ */
 typedef struct {
-	char*   		  name;
+	char*   		  name;					/**< Taxon name.
-	char*   		  class_name;
+	 	 	 	 	 	 	 	 	 	 	 */
-	int32_t 		  is_scientific_name;
+	char*   		  class_name;			/**< Name class.
-	struct ecotxnode* taxon;
+	 	 	 	 	 	 	 	 	 	 	 */
+	int32_t 		  is_scientific_name;	/**< A boolean indicating whether the name is a scientific name or not.
+	 	 	 	 	 	 	 	 	 	 	 */
+	struct ecotxnode* taxon;				/**< Pointer on the taxon in the taxon index.
+	 	 	 	 	 	 	 	 	 	 	 */
 } econame_t;
 
 
+/**
+ * @brief Structure for the name index in a taxonomy structure.
+ */
 typedef struct {
-	int32_t   count;
+	int32_t   count;		/**< Number of names.
-	econame_t names[1];
+	 	 	 	 	 	 	 */
+	econame_t names[];		/**< Array of names.
+	 	 	 	 	 	 	 */
 } econameidx_t;
 
 
+/**
+ * @brief Structure for a taxid/index pair as stored in a taxonomy structure.
+ */
+typedef struct {
+	int32_t taxid;		/**< Taxid.
+	 	 	 	 	 	 */
+	int32_t idx;		/**< Index of the taxid in the taxon index, -1 if the taxid is deprecated.
+	 	 	 	 	 	 */
+} ecomerged_t;
+
+
+/**
+ * @brief Structure for a merged taxid index in a taxonomy structure.
+ *
+ * This index includes all deprecated taxids that now refer to different taxids, and
+ * the deprecated taxids that are deleted.
+ *
+ */
+typedef struct {
+	int32_t     count;		/**< Number of taxid/index pairs.
+ 	 	 	 	 	 	 	 */
+	ecomerged_t merged[];	/**< Array of taxid/index pairs.
+	 	 	 	 	 	 	 */
+} ecomergedidx_t;
+
+
+/**
+ * @brief Structure for a taxonomy.
+ */
 typedef struct OBIDMS_taxonomy_t {
-	char          tax_name[TAX_NAME_LEN];
+	char            tax_name[TAX_NAME_LEN];		/**< Taxonomy name.
-	OBIDMS_p      dms;
+	 	 	 	 	 	 	 	 	 	 	 	 */
-	ecorankidx_t* ranks;
+	OBIDMS_p        dms;						/**< A pointer on the DMS to which the taxonomy belongs.
-	econameidx_t* names;
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
-	ecotxidx_t*   taxa;
+	ecomergedidx_t* merged_idx;					/**< Merged taxid index.
+	 	 	 	 	 	 	 	 	 	 	 	 */
+	ecorankidx_t*   ranks;						/**< Taxonomic ranks.
+	 	 	 	 	 	 	 	 	 	 	 	 */
+	econameidx_t*   names;						/**< Taxon names.
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
+	econameidx_t*   preferred_names;			/**< Taxon preferred names (i.e. added locally).
+	 	 	 	 	 	 	 	 	 	 	 	 */
+	ecotxidx_t*     taxa;						/**< Taxa.
+	 	 	 	 	 	 	 	 	 	 	 	 */
 } OBIDMS_taxonomy_t, *OBIDMS_taxonomy_p;
 
 
-OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, bool read_alternative_names);
+/**
-
+ * @brief Function reading an NCBI taxdump and loading its information into a taxonomy structure.
-int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy);
+ *
-
+ * @param taxdump The path to the taxdump directory.
-ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx);
+ *
-
+ * @returns A pointer on the read taxonomy structure.
-ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid);
+ * @retval NULL if an error occurred.
-
+ *
-bool obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid);
+ * @since 2016
-
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
-ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+ */
-
-ecotx_t* obi_taxo_get_genus(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
-
-ecotx_t* obi_taxo_get_family(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
-
-ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
-
-ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
-
-
-int write_rankidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_name);
-int write_taxonomyidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_name);
-int write_nameidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_name);
-
-int obi_write_taxonomy(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* tax_name);
-
 OBIDMS_taxonomy_p obi_read_taxdump(const char* taxdump);
 
-int obi_taxonomy_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid);
+
+/**
+ * @brief Function reading a binary taxonomy database (i.e. a set of .tdx, .ndx, .rdx, .adx, .ldx, .pdx files)
+ * 		  and loading its information into a taxonomy structure.
+ *
+ * @param dms A pointer on the DMS to which the taxonomy belongs.
+ * @param taxonomy_name The name (prefix) of the taxonomy.
+ * @param read_alternative_names A boolean indicating whether names other than scientific and preferred names should be read.
+ *
+ * @returns A pointer on the read taxonomy structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, bool read_alternative_names);
+
+
+/**
+ * @brief Function writing a binary taxonomy database (i.e. a set of .tdx, .ndx, .rdx, .adx, .ldx, .pdx files).
+ *
+ * @param dms A pointer on the DMS to which the taxonomy belongs.
+ * @param tax A pointer on the taxonomy structure.
+ * @param tax_name The name (prefix) of the taxonomy.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_write_taxonomy(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* tax_name);
+
+
+/**
+ * @brief Function closing a taxonomy structure.
+ *
+ * This function writes all changes to the binary files (local taxa and preferred names) and free all allocated memory for the structure.
+ *
+ * @param taxonomy A pointer on the taxonomy structure.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy);
+
+
+/**
+ * @brief Function adding a local taxon to a taxonomy.
+ *
+ * @param tax A pointer on the taxonomy structure.
+ * @param name The taxon scientific name.
+ * @param rank_name The taxon rank name.
+ * @param parent_taxid The taxid of the parent node in the taxonomic tree.
+ * @param min_taxid The minimum taxid to give to the new taxon (the function will choose a new taxid >= min_taxid and >= MIN_LOCAL_TAXID).
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_taxo_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid);
+
+
+/**
+ * @brief Function adding a preferred name to a taxon in a taxonomy, referred to by its taxid.
+ *
+ * @param tax A pointer on the taxonomy structure.
+ * @param taxid The taxid of the taxon that should have a new preferred name.
+ * @param preferred_name The new preferred name.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since January 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_taxo_add_preferred_name_with_taxid(OBIDMS_taxonomy_p tax, int32_t taxid, const char* preferred_name);
+
+
+/**
+ * @brief Function adding a preferred name to a taxon in a taxonomy, referred to by the taxon pointer.
+ *
+ * @param tax A pointer on the taxonomy structure.
+ * @param taxon A pointer on the taxon that should have a new preferred name.
+ * @param preferred_name The new preferred name.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since January 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_taxo_add_preferred_name_with_taxon(OBIDMS_taxonomy_p tax, ecotx_t* taxon, const char* preferred_name);
+
+
+/**
+ * @brief Function returning the parent of a taxon at a given rank.
+ *
+ * @param taxon A pointer on the taxon.
+ * @param rankidx The index of the rank wanted.
+ *
+ * @returns A pointer on the parent taxon at the wanted rank.
+ * @retval NULL if no parent taxon was found at the wanted rank.
+ */
+ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx);
+
+
+/**
+ * @brief Function returning a taxon given its taxid.
+ *
+ * @param taxonomy A pointer on the taxonomy.
+ * @param taxid The taxid of the taxon.
+ *
+ * @returns A pointer on the wanted taxon.
+ * @retval NULL if no taxon was found with the given taxid.
+ *
+ * @since January 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid);
+
+
+/**
+ * @brief Function checking whether a taxon is under another in the taxonomy tree.
+ *
+ * @param taxon A pointer on the first taxon.
+ * @param other_taxid The taxid of the second taxon.
+ *
+ * @returns A boolean indicating whether the first taxon is under the second taxon in the taxonomy tree.
+ */
+bool obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid);
+
+
+/**
+ * @brief Function returning the parent of a taxon at the species level.
+ *
+ * @param taxon A pointer on the taxon.
+ * @param taxonomy A pointer on the taxonomy structure.
+ *
+ * @returns A pointer on the parent taxon at the species level.
+ * @retval NULL if no parent taxon was found at the wanted rank.
+ */
+ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+
+/**
+ * @brief Function returning the parent of a taxon at the genus level.
+ *
+ * @param taxon A pointer on the taxon.
+ * @param taxonomy A pointer on the taxonomy structure.
+ *
+ * @returns A pointer on the parent taxon at the genus level.
+ * @retval NULL if no parent taxon was found at the wanted rank.
+ */
+ecotx_t* obi_taxo_get_genus(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+
+/**
+ * @brief Function returning the parent of a taxon at the family level.
+ *
+ * @param taxon A pointer on the taxon.
+ * @param taxonomy A pointer on the taxonomy structure.
+ *
+ * @returns A pointer on the parent taxon at the family level.
+ * @retval NULL if no parent taxon was found at the wanted rank.
+ */
+ecotx_t* obi_taxo_get_family(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+
+/**
+ * @brief Function returning the parent of a taxon at the kingdom level.
+ *
+ * @param taxon A pointer on the taxon.
+ * @param taxonomy A pointer on the taxonomy structure.
+ *
+ * @returns A pointer on the parent taxon at the kingdom level.
+ * @retval NULL if no parent taxon was found at the wanted rank.
+ */
+ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+
+/**
+ * @brief Function returning the parent of a taxon at the superkingdom level.
+ *
+ * @param taxon A pointer on the taxon.
+ * @param taxonomy A pointer on the taxonomy structure.
+ *
+ * @returns A pointer on the parent taxon at the superkingdom level.
+ * @retval NULL if no parent taxon was found at the wanted rank.
+ */
+ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+

src/obidmscolumn.c

@@ -119,7 +119,7 @@ static obiversion_t create_version_file(OBIDMS_column_directory_p column_directo
 
 /**
  * @brief Internal function building the default elements names of the lines of a
- *        column (i.e. "0;1;2;...;n").
+ *        column, with ';' as separator (i.e. "0;1;2;...;n\0").
  *
  * @warning The returned pointer has to be freed by the caller.
  *
@@ -134,12 +134,61 @@ static obiversion_t create_version_file(OBIDMS_column_directory_p column_directo
 static char* build_default_elements_names(index_t nb_elements_per_line);
 
 
+/**
+ * @brief Internal function formatting the elements names of the lines of a
+ *        column with '\0' as separator (e.g. "0\01\02\0...\0n\0").
+ *
+ * @param elements_names The character string formatted with ';' as separator (e.g. "0;1;2;...;n\0").
+ * @param elts_names_length A pointer on an integer where the function will store the length of the character string.
+ *
+ * @since January 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static void format_elements_names(char* elements_names, int* elts_names_length);
+
+
+/**
+ * @brief Internal function comparing two element names using their sorted index, using data stored in the column header.
+ *
+ * @param n1_sort_idx A pointer on the sorted index of the first name.
+ * @param n2_sort_idx A pointer on the sorted index of the second name.
+ * @param h A pointer on the column header.
+ *
+ * @returns A value < 0 if name1 < name2,
+ * 			a value > 0 if name1 > name2,
+ * 			and 0 if name1 == name2.
+ *
+ * @since January 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static int cmp_elements_names_with_idx(const void* n1_sort_idx, const void* n2_sort_idx, const void* h);
+
+
+/**
+ * @brief Internal function comparing two element names using a pointer on the first name and the sorted index of the second name,
+ * 		  using data stored in the column header.
+ *
+ * @param name1 A pointer on the first name.
+ * @param n2_sort_idx A pointer on the sorted index of the second name.
+ * @param h A pointer on the column header.
+ *
+ * @returns A value < 0 if name1 < name2,
+ * 			a value > 0 if name1 > name2,
+ * 			and 0 if name1 == name2.
+ *
+ * @since January 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static int cmp_elements_names_with_name_and_idx(const void* name1, const void* n2_sort_idx, const void* h);
+
+
 /**
  * @brief Internal function setting the elements names of the lines of a
  *        column in the header of the OBIDMS column structure.
  *
  * @param column A pointer as returned by obi_create_column().
- * @param elements_names The names of the elements with ';' as separator.
+ * @param elements_names The names of the elements as formatted by format_elements_names().
+ * @param elts_names_length The length of elements_names.
  *
  * @retval 0 if the operation was successfully completed.
  * @retval -1 if an error occurred.
@@ -147,7 +196,35 @@ static char* build_default_elements_names(index_t nb_elements_per_line);
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-static int obi_column_set_elements_names(OBIDMS_column_p column, char* elements_names);
+static int set_elements_names(OBIDMS_column_p column, char* elements_names, int elts_names_length);
+
+
+/**
+ * @brief Internal function counting the number of elements names in a character array.
+ *
+ * @param elements_names A pointer on the character string corresponding to the elements names,
+ *                       formatted with ';' or with '\0' as separator.
+ * @param elt_names_formatted Whether the separator is ';' (false), or '\0' (true, as formatted by format_elements_names()).
+ *
+ * @returns The number of elements names in the character array.
+ *
+ * @since January 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static index_t check_elt_names_count(const char* elements_names, bool elt_names_formatted);
+
+
+/**
+ * @brief Internal function computing the length of a character array containing elements names as formatted by format_elements_names().
+ *
+ * @param elements_names A pointer on the character string corresponding to the elements names as formatted by format_elements_names().
+ *
+ * @returns The length of a character array.
+ *
+ * @since January 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static int get_formatted_elt_names_length(const char* elements_names);
 
 
 /**
@@ -198,6 +275,7 @@ static char* build_column_file_name(const char* column_name, obiversion_t versio
 }
 
 
+
 static char* build_version_file_name(const char* column_name)
 {
 	char* file_name;
@@ -222,6 +300,7 @@ static char* build_version_file_name(const char* column_name)
 }
 
 
+
 static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_directory, bool block)
 {
 	off_t 			loc_size;
@@ -346,6 +425,7 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
 }
 
 
+
 static obiversion_t create_version_file(OBIDMS_column_directory_p column_directory)
 {
 	off_t 			loc_size;
@@ -437,10 +517,12 @@ static obiversion_t create_version_file(OBIDMS_column_directory_p column_directo
 }
 
 
+
 static char* build_default_elements_names(index_t nb_elements_per_line)
 {
 	char* elements_names;
 	int   i;
+	int   len;
 
 	elements_names = (char*) malloc(ELEMENTS_NAMES_MAX * sizeof(char));
 	if (elements_names == NULL)
@@ -457,31 +539,169 @@ static char* build_default_elements_names(index_t nb_elements_per_line)
 		return NULL;
 	}
 
+	len = 0;
 	for (i = 0; i < nb_elements_per_line; i++)
-		sprintf(elements_names, "%d", i);
+		len += sprintf(elements_names+len, "%d;", i);
 
 	// Terminal character
-	elements_names[strlen(elements_names)] = '\0';
+	elements_names[len-1] = '\0';	// -1 to delete last ';'
+	len--;
 
 	return elements_names;
 }
 
 
-int obi_column_set_elements_names(OBIDMS_column_p column, char* elements_names)
+
+static void format_elements_names(char* elements_names, int* elts_names_length)
 {
-	if (strlen(elements_names) > ELEMENTS_NAMES_MAX)
+	int i;
+
+	*elts_names_length = strlen(elements_names);
+
+	// Replace the ';' with '\0'
+	for (i=0; i < *elts_names_length; i++)
+	{
+		if (elements_names[i] == ';')
+			elements_names[i] = '\0';
+	}
+}
+
+
+
+static int cmp_elements_names_with_idx(const void* n1_sort_idx, const void* n2_sort_idx, const void* h)
+{
+	char* name1=NULL;
+	char* name2=NULL;
+
+	int name1_idx;
+	int name2_idx;
+
+	int name1_sort_idx = *((int*)n1_sort_idx);
+	int name2_sort_idx = *((int*)n2_sort_idx);
+	OBIDMS_column_header_p header = (OBIDMS_column_header_p) h;
+
+	name1_idx = (header->elements_names_idx)[name1_sort_idx];
+	name1 = (header->elements_names)+name1_idx;
+
+	name2_idx = (header->elements_names_idx)[name2_sort_idx];
+	name2 = (header->elements_names)+name2_idx;
+
+	return strcmp(name1, name2);
+}
+
+
+
+static int cmp_elements_names_with_name_and_idx(const void* name1, const void* n2_sort_idx, const void* h)
+{
+	char* name2=NULL;
+	int name2_idx;
+
+	int name2_sort_idx = *((int*)n2_sort_idx);
+	OBIDMS_column_header_p header = (OBIDMS_column_header_p) h;
+
+	name2_idx = (header->elements_names_idx)[name2_sort_idx];
+	name2 = (header->elements_names)+name2_idx;
+
+	return strcmp(name1, name2);
+}
+
+
+
+static int set_elements_names(OBIDMS_column_p column, char* elements_names, int elts_names_length)
+{
+	int i, j;
+
+	// Check that the elements names are not too long
+	if (elts_names_length+2 > ELEMENTS_NAMES_MAX)
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
 		obidebug(1, "\nError: element names too long (max: %d)", ELEMENTS_NAMES_MAX);
 		return -1;
 	}
 
-	strcpy((column->header)->elements_names, elements_names);
+	// Copy the elements names in the header
+	memcpy((column->header)->elements_names, elements_names, elts_names_length*sizeof(char));
+
+	// Terminal characters
+	(column->header)->elements_names[elts_names_length] = '\0';
+	(column->header)->elements_names[elts_names_length + 1] = '\0';
+
+	// Store the length of the character array containing the elements names
+	(column->header)->elements_names_length = elts_names_length;
+
+	// Build the elements names index
+	i = 0;
+	j = 0;
+	// Index the first element name
+	((column->header)->elements_names_idx)[j] = i;
+	((column->header)->sorted_elements_idx)[j] = j;
+	i++;
+	j++;
+	while (i < elts_names_length)
+	{
+		if (elements_names[i] == '\0')
+		{	// Index new element name
+			((column->header)->elements_names_idx)[j] = i+1;
+			((column->header)->sorted_elements_idx)[j] = j;
+			j++;
+		}
+		i++;
+	}
+
+	// Build the sorted index
+	qsort_user_data((column->header)->sorted_elements_idx, j, sizeof(int), column->header, cmp_elements_names_with_idx);
+
 	return 0;
 }
 
 
-index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line)
+
+static index_t check_elt_names_count(const char* elements_names, bool elt_names_formatted)
+{
+	char    sep;
+	int     i = 0;
+	bool    stop = false;
+	index_t count = 0;
+
+	if (elt_names_formatted)
+		sep = FORMATTED_ELT_NAMES_SEPARATOR;
+	else
+		sep = NOT_FORMATTED_ELT_NAMES_SEPARATOR;
+
+	while (! stop)
+	{
+		if ((elt_names_formatted && (elements_names[i] == '\0') && (elements_names[i+1] == '\0')) ||
+				((! elt_names_formatted) && (elements_names[i] == '\0')))
+			stop = true;
+		if ((elements_names[i] == sep) || (elements_names[i] == '\0'))
+			count++;
+		i++;
+	}
+
+	return count;
+}
+
+
+
+static int get_formatted_elt_names_length(const char* elements_names)
+{
+	int     i = 0;
+	bool    stop = false;
+
+	while (! stop)
+	{
+		if ((elements_names[i] == '\0') && (elements_names[i+1] == '\0'))
+			stop = true;
+		else
+			i++;
+	}
+
+	return i;
+}
+
+
+
+static index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line)
 {
 	return getpagesize() / (obi_sizeof(data_type) * nb_elements_per_line);
 }
@@ -493,6 +713,7 @@ index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_lin
  *
  **********************************************************************/
 
+
 obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_directory)
 {
 	off_t 			loc_size;
@@ -557,6 +778,7 @@ obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_dire
 }
 
 
+
 obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name)
 {
 	OBIDMS_column_directory_p	column_directory;
@@ -582,6 +804,7 @@ obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* c
 }
 
 
+
 size_t obi_get_platform_header_size()
 {
 	size_t header_size;
@@ -607,7 +830,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 								  const char*  indexer_name,
 								  const char*  associated_column_name,
 								  obiversion_t associated_column_version,
-								  const char*  comments
+								  const char*  comments,
+								  bool		   elt_names_formatted
 								 )
 {
 	OBIDMS_column_p 			new_column;
@@ -623,6 +847,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 	OBIType_t  					returned_data_type;
 	OBIType_t  					stored_data_type;
 	char*			    		final_indexer_name;
+	char*						built_elements_names = NULL;
+	int							elts_names_length;
 
 	new_column = NULL;
 
@@ -695,31 +921,29 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 	else if (nb_lines < minimum_line_count)
 		nb_lines = minimum_line_count;
 
-	// Check and build if needed the element names
+	// Check, format, and build if needed the element names
-	if ((elements_names == NULL) || (strcmp(elements_names, "") == 0))	// Build the default element names: str of the element index
+	if ((elements_names == NULL) || (*elements_names == '\0'))	// Build the default element names: str of the element index
 	{
-		elements_names = build_default_elements_names(nb_elements_per_line);
+		built_elements_names = build_default_elements_names(nb_elements_per_line);
-		if (elements_names == NULL)
+		if (built_elements_names == NULL)
 			return NULL;
+		elements_names = built_elements_names;
 	}
-	else if (((elements_names == NULL) || (strcmp(elements_names, "") != 0)) && (nb_elements_per_line > 1))
+	else
 	{ // The number of elements names should be equal to the number of elements per line
-		char* token;
+		if (check_elt_names_count(elements_names, elt_names_formatted) != nb_elements_per_line)
-		index_t n = 0;
-		token = strdup(elements_names);
-		token = strtok(token, ";");
-		while (token != NULL)
 		{
-			token = strtok(NULL, ";");
+			obidebug(1, "\nCan't create column because the number of elements names given is not equal to the number of elements per line:"
-			n++;
+					"\n%lld elements per line\nelements names:%s\n", nb_elements_per_line, elements_names);
-		}
-		if (n != nb_elements_per_line)
-		{
-			obidebug(1, "\nCan't create column because the number of elements names given is not equal to the number of elements per line");
 			return NULL;
 		}
 	}
-	// TODO what if 1 element and name specified? doc
+
+	// Format the elements names string
+	if (! elt_names_formatted)
+		format_elements_names(elements_names, &elts_names_length);
+	else
+		elts_names_length = get_formatted_elt_names_length(elements_names);
 
 	// Calculate the size needed
 	header_size = obi_get_platform_header_size();
@@ -816,11 +1040,11 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 	header->version       		          = version_number;
 	header->cloned_from    		          = -1;
 
-	obi_column_set_elements_names(new_column, elements_names);
+	set_elements_names(new_column, elements_names, elts_names_length);
 
 	// Free the element names if they were built
-	if ((elements_names == NULL) || (strcmp(elements_names, "") == 0))
+	if (built_elements_names != NULL)
-		free(elements_names);
+		free(built_elements_names);
 
 	strncpy(header->name, column_name, OBIDMS_COLUMN_MAX_NAME);
 
@@ -886,6 +1110,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 }
 
 
+
 OBIDMS_column_p obi_open_column(OBIDMS_p     dms,
 								const char*  column_name,
 								obiversion_t version_number)
@@ -1043,6 +1268,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p     dms,
 }
 
 
+
 OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 								 OBIDMS_column_p  line_selection,
 								 const char*      column_name,
@@ -1083,7 +1309,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 								   (column_to_clone->header)->indexer_name,
 								   ((column_to_clone->header)->associated_column).column_name,
 								   ((column_to_clone->header)->associated_column).version,
-								   (column_to_clone->header)->comments
+								   (column_to_clone->header)->comments,
+								   true
 								  );
 
 	if (new_column == NULL)
@@ -1097,6 +1324,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 		return NULL;
 	}
 
+
+
 	(new_column->header)->cloned_from = (column_to_clone->header)->version;
 
 	if (clone_data && (line_selection == NULL))
@@ -1137,6 +1366,7 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 }
 
 
+
 int obi_close_column(OBIDMS_column_p column)
 {
 	int     ret_val = 0;
@@ -1185,6 +1415,7 @@ int obi_close_column(OBIDMS_column_p column)
 }
 
 
+
 int obi_clone_column_indexer(OBIDMS_column_p column)
 {
 	char* new_indexer_name;
@@ -1208,6 +1439,7 @@ int obi_clone_column_indexer(OBIDMS_column_p column)
 }
 
 
+
 int obi_truncate_column(OBIDMS_column_p column)	// TODO is it necessary to unmap/remap?
 {
 	size_t  file_size;
@@ -1309,6 +1541,7 @@ int obi_truncate_column(OBIDMS_column_p column)	// TODO is it necessary to unmap
 }
 
 
+
 int obi_enlarge_column(OBIDMS_column_p column)
 {
 	size_t  file_size;
@@ -1363,7 +1596,7 @@ int obi_enlarge_column(OBIDMS_column_p column)
 	header_size = (column->header)->header_size;
 	file_size = header_size + new_data_size;
 
-	// Enlarge the file // TODO isn't it possible that this makes the file "move"?
+	// Enlarge the file
 	if (ftruncate(column_file_descriptor, file_size) < 0)
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
@@ -1414,6 +1647,7 @@ int obi_enlarge_column(OBIDMS_column_p column)
 }
 
 
+
 void obi_ini_to_NA_values(OBIDMS_column_p column,
 						  index_t first_line_nb,
 						  index_t nb_lines)
@@ -1479,6 +1713,7 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
 }
 
 
+
 OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name, obiversion_t version_number)
 {
 	OBIDMS_column_header_p 		header;
@@ -1562,6 +1797,7 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
 }
 
 
+
 int obi_close_header(OBIDMS_column_header_p header)
 {
 	if (munmap(header, header->header_size) < 0)
@@ -1574,47 +1810,56 @@ int obi_close_header(OBIDMS_column_header_p header)
 }
 
 
-// TODO to be rewritten in an optimized and safe way if possible
+
 index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name)
 {
-	char*   elements_names;
+	int* elt_names_idx;
-	char*   name;
-	index_t element_index;
 
-	elements_names = strdup((column->header)->elements_names);
+	elt_names_idx = bsearch_user_data(element_name, (column->header)->sorted_elements_idx, (column->header)->nb_elements_per_line, sizeof(int), column->header, cmp_elements_names_with_name_and_idx);
+
+	if (elt_names_idx != NULL)
+		return (index_t)(*elt_names_idx);
+
+	obi_set_errno(OBICOL_UNKNOWN_ERROR);
+	obidebug(1, "\nError: could not find element name %s", element_name);
+	return OBIIdx_NA;
+}
+
+
+// TODO doc, returns elements names with ; as separator (discuss maybe char**)
+char* obi_get_elements_names(OBIDMS_column_p column)
+{
+	char* elements_names;
+	int   i, j;
+	int   elt_idx;
+	int   len;
+
+	elements_names = (char*) malloc(ELEMENTS_NAMES_MAX * sizeof(char));
 	if (elements_names == NULL)
 	{
-		obidebug(1, "\nError strdup-ing the elements names");
+		obi_set_errno(OBI_MALLOC_ERROR);
-		return OBIIdx_NA;
+		obidebug(1, "\nError allocating memory for elements names");
+		return NULL;
 	}
 
-	element_index = 0;
+	j = 0;
-
+	for (i=0; i < (column->header)->nb_elements_per_line; i++)
-	name = strtok(elements_names, ";");	// TODO not thread safe, see strtok_r maybe
-	if (strcmp(element_name, name) == 0)
 	{
-		free(elements_names);
+		elt_idx = ((column->header)->elements_names_idx)[i];
-		return element_index;
+		len = strlen(((column->header)->elements_names)+elt_idx);
-	}
+		memcpy(elements_names+j, ((column->header)->elements_names)+elt_idx, len*sizeof(char));
-	element_index++;
+		j = j + len;
-
+		elements_names[j] = ';';
-	while (name != NULL)
+		j++;
-	{
-		name = strtok(NULL, ";");			// TODO not thread safe, see strtok_r maybe
-		if (strcmp(element_name, name) == 0)
-		{
-			free(elements_names);
-			return element_index;
-		}
-		element_index++;
 	}
 
-	obidebug(1, "\nCan't find an element name");
+	elements_names[j - 1] = '\0';
-	free(elements_names);
+
-	return OBIIdx_NA;
+	return elements_names;
 }
 
 
+
 int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb)
 {
 	// Check if the column is read-only
@@ -1649,6 +1894,7 @@ int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb)
 }
 
 
+
 int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb)
 {
 	if ((line_nb+1) > ((column->header)->line_count))

src/obidmscolumn.h

@@ -31,7 +31,7 @@
 #define ELEMENTS_NAMES_MAX (2048)     	  		/**< The maximum length of the list of elements names.	// TODO Discuss
                                 	       	   	 */
 #define NB_ELTS_MAX_IF_DEFAULT_NAME (539) 		/**< The maximum number of elements per line if the default element names
-										   *   are used ("0;1;2;...;n"), considering ELEMENTS_NAMES_MAX.
+										   	   	 *   are used ("0\01\02\0...\0n"), considering ELEMENTS_NAMES_MAX.
 										   	   	 */
 #define COLUMN_GROWTH_FACTOR (2)	 	  		/**< The growth factor when a column is enlarged.
                                 	   	   	   	 */
@@ -39,6 +39,10 @@
                                 	       	   	 */
 #define COMMENTS_MAX_LENGTH (2048)        		/**< The maximum length for comments.
  	 	 	 	 	 	 	 	 	       	   	 */
+#define FORMATTED_ELT_NAMES_SEPARATOR '\0'		/**< The maximum length for comments.
+ 	 	 	 	 	 	 	 	 	       	   	 */
+#define NOT_FORMATTED_ELT_NAMES_SEPARATOR ';'   /**< The maximum length for comments.
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
 
 
 /**
@@ -66,9 +70,15 @@ typedef struct OBIDMS_column_header {
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	index_t				nb_elements_per_line;   			   				/**< Number of elements per line.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	char				elements_names[ELEMENTS_NAMES_MAX+1];	/**< Names of the line elements with ';' as separator
+	char				elements_names[ELEMENTS_NAMES_MAX+1];				/**< Names of the line elements with '\0' as separator
-																 *   (no terminal ';').
+																 	 	 	 *   and '\0\0' as terminal flag.
-															 	 *	 (default are the indices: "0;1;2;...;n").
+																 	 	 	 *	 (default are the indices: "0\01\02\0...\0n\0\0").
+																 	 	 	 */
+	int					elements_names_length;								/**< Length of the character array where the elements names are stored.
+																			 */
+	int  				elements_names_idx[NB_ELTS_MAX_IF_DEFAULT_NAME];	/**< Index for the start of each element name in elements_names.
+																			 */
+	int  				sorted_elements_idx[NB_ELTS_MAX_IF_DEFAULT_NAME];	/**< Index for the sorted element names in elements_names_idx.
 																			 */
 	OBIType_t			returned_data_type;		    						/**< Type of the data that is returned when getting an
 															 	 	 	 	 *   element from the column.
@@ -184,12 +194,13 @@ size_t obi_get_platform_header_size();
  * @param nb_lines The number of lines to be stored.
  * @param nb_elements_per_line The number of elements per line.								// TODO talk about default values
  * @param elements_names The names of the elements with ';' as separator (no terminal ';'),
- *                       NULL or "" if the default names are to be used ("0;1;2;...;n").
+ *                       NULL or "" if the default names are to be used ("0\01\02\0...\0n").
  * @param indexer_name The name of the indexer if there is one associated with the column.
  *                     If NULL or "", the indexer name is set as the column name.
  * @param associated_column_name The name of the associated column if there is one.
  * @param associated_column_version The version of the associated column if there is one.
  * @param comments Optional comments associated with the column.
+ * @param elt_names_formatted Whether the separator for the elements names is ';' (false), or '\0' (true, as formatted by format_elements_names()).
  *
  * @returns A pointer on the newly created column structure.
  * @retval NULL if an error occurred.
@@ -206,7 +217,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 								  const char*  indexer_name,
 								  const char*  associated_column_name,
 								  obiversion_t associated_column_version,
-								  const char*  comments
+								  const char*  comments,
+								  bool		   elt_names_formatted
 								 );
 
 
@@ -353,7 +365,7 @@ int obi_close_header(OBIDMS_column_header_p header);
  * @param element_name The name of the element.
  *
  * @returns The index of the element in a line of the column.
- * @retval OBIIdx_NA if an error occurred.						// TODO not sure if this is "clean".
+ * @retval OBIIdx_NA if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -361,6 +373,22 @@ int obi_close_header(OBIDMS_column_header_p header);
 index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
 
 
+/**
+ * @brief Recovers the elements names of the lines of a column, with ';' as separator (i.e. "0;1;2;...;n\0").
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param column A pointer on an OBIDMS column.
+ *
+ * @returns A pointer on a character array where the elements names are stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since January 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_get_elements_names(OBIDMS_column_p column);
+
+
 /**
  * @brief Prepares a column to set a value.
  *

src/obiview.c

@@ -47,7 +47,7 @@
 
 
 /**
- * Internal function building the file name where the informations about an obiview are stored.
+ * Internal function building the file name where the informations about a finished, read-only obiview are stored.
  *
  * @warning The returned pointer has to be freed by the caller.
  *
@@ -63,7 +63,23 @@ static char* build_obiview_file_name(const char* view_name);
 
 
 /**
- * Internal function checking if a view with a given name already exists in a DMS.
+ * Internal function building the file name where the informations about an unfinished, writable obiview are stored.
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param view_name The name of the view.
+ *
+ * @returns A pointer to the file name.
+ * @retval NULL if an error occurred.
+ *
+ * @since February 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static char* build_unfinished_obiview_file_name(const char* view_name);
+
+
+/**
+ * Internal function checking if a view (either finished or unfinished) with a given name already exists in a DMS.
  *
  * @param dms The DMS.
  * @param view_name The name of the view.
@@ -73,7 +89,7 @@ static char* build_obiview_file_name(const char* view_name);
  * @since September 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-bool view_exists(OBIDMS_p dms, const char* view_name);
+static bool view_exists(OBIDMS_p dms, const char* view_name);
 
 
 /**
@@ -84,7 +100,7 @@ bool view_exists(OBIDMS_p dms, const char* view_name);
  * @since June 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-size_t get_platform_view_file_size();
+static size_t get_platform_view_file_size();
 
 
 /**
@@ -99,7 +115,7 @@ size_t get_platform_view_file_size();
  * @since August 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int enlarge_view_file(Obiview_p view, size_t new_size);
+static int enlarge_view_file(Obiview_p view, size_t new_size);
 
 
 /**
@@ -117,7 +133,7 @@ int enlarge_view_file(Obiview_p view, size_t new_size);
  * @since August 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int write_comments_to_view_file(Obiview_p view, const char* comments);
+static int write_comments_to_view_file(Obiview_p view, const char* comments);
 
 
 /**
@@ -134,7 +150,7 @@ int write_comments_to_view_file(Obiview_p view, const char* comments);
  * @since June 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int create_obiview_file(OBIDMS_p dms, const char* view_name);
+static int create_obiview_file(OBIDMS_p dms, const char* view_name);
 
 
 /**
@@ -156,7 +172,7 @@ int create_obiview_file(OBIDMS_p dms, const char* view_name);
  * @since June 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-void update_column_refs(Obiview_p view);
+static void update_column_refs(Obiview_p view);
 
 
 /**
@@ -175,7 +191,7 @@ void update_column_refs(Obiview_p view);
  * @since July 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int create_column_dict(Obiview_p view);
+static int create_column_dict(Obiview_p view);
 
 
 /**
@@ -194,7 +210,7 @@ int create_column_dict(Obiview_p view);
  * @since July 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int update_column_dict(Obiview_p view);
+static int update_column_dict(Obiview_p view);
 
 
 /**
@@ -219,7 +235,7 @@ int update_column_dict(Obiview_p view);
  * @since July 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int update_column_refs_and_dict(Obiview_p view);
+static int update_column_refs_and_dict(Obiview_p view);
 
 
 /**
@@ -239,7 +255,7 @@ int update_column_refs_and_dict(Obiview_p view);
  * @since February 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int update_lines(Obiview_p view, index_t line_count);
+static int update_lines(Obiview_p view, index_t line_count);
 
 
 /**
@@ -257,7 +273,71 @@ int update_lines(Obiview_p view, index_t line_count);
  * @since February 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name);
+static OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name);
+
+
+/**
+ * @brief Saves a view, updating its informations in the view file.
+ *
+ * @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)
+ */
+static int save_view(Obiview_p view);
+
+
+/**
+ * @brief Rename a view file once the view is finished, replacing the '*.obiview_unfinished' extension with '*.obiview'.
+ *
+ * @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 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static int rename_finished_view(Obiview_p view);
+
+
+/**
+ * @brief Finishes a view: check the predicates, save all the informations, rename 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 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static int finish_view(Obiview_p view);
+
+/**
+ * @brief Closes an opened view.
+ *
+ * @warning Doesn't save 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.
+ *
+ * @see obi_save_and_close_view()
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static int close_view(Obiview_p view);
 
 
 /**
@@ -276,7 +356,7 @@ OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name);
  * @since April 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, index_t* line_nb_p);
+static int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, index_t* line_nb_p);
 
 
 /**
@@ -294,7 +374,7 @@ int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, i
  * @since April 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p);
+static int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p);
 
 
 /****** PREDICATE FUNCTIONS *******/
@@ -313,7 +393,7 @@ int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p);
  * @since July 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* view_has_nuc_sequence_column(Obiview_p view);
+static char* view_has_nuc_sequence_column(Obiview_p view);
 
 
 /**
@@ -330,7 +410,7 @@ char* view_has_nuc_sequence_column(Obiview_p view);
  * @since July 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* view_has_quality_column(Obiview_p view);
+static char* view_has_quality_column(Obiview_p view);
 
 
 /**
@@ -347,7 +427,7 @@ char* view_has_quality_column(Obiview_p view);
  * @since July 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* view_has_id_column(Obiview_p view);
+static char* view_has_id_column(Obiview_p view);
 
 
 /**
@@ -364,7 +444,7 @@ char* view_has_id_column(Obiview_p view);
  * @since July 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* view_has_definition_column(Obiview_p view);
+static char* view_has_definition_column(Obiview_p view);
 
 
 /**
@@ -381,7 +461,7 @@ char* view_has_definition_column(Obiview_p view);
  * @since July 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* view_check_qual_match_seqs(Obiview_p view);
+static char* view_check_qual_match_seqs(Obiview_p view);
 
 
 /**
@@ -396,7 +476,7 @@ char* view_check_qual_match_seqs(Obiview_p view);
  * @since July 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* view_check_one_predicate(Obiview_p view, char* (*predicate_function)(Obiview_p view));
+static char* view_check_one_predicate(Obiview_p view, char* (*predicate_function)(Obiview_p view));
 
 
 /**
@@ -410,7 +490,7 @@ char* view_check_one_predicate(Obiview_p view, char* (*predicate_function)(Obivi
  * @since July 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* view_check_all_predicates(Obiview_p view);
+static char* view_check_all_predicates(Obiview_p view);
 
 
 /************************************************************************
@@ -443,11 +523,35 @@ static char* build_obiview_file_name(const char* view_name)
 }
 
 
-bool view_exists(OBIDMS_p dms, const char* view_name)
+static char* build_unfinished_obiview_file_name(const char* view_name)
+{
+	char* file_name;
+
+	// Build file name
+	file_name = (char*) malloc((strlen(view_name) + 19 + 1)*sizeof(char));
+	if (file_name == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for a view file name");
+		return NULL;
+	}
+	if (sprintf(file_name, "%s.obiview_unfinished", view_name) < 0)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nProblem building an unfinished obiview file name");
+		return NULL;
+	}
+
+	return file_name;
+}
+
+
+static bool view_exists(OBIDMS_p dms, const char* view_name)
 {
 	struct dirent* dp;
 	char*		   file_name;
 
+	// Check finished views
 	// Create file name
 	file_name = build_obiview_file_name(view_name);
 	if (file_name == NULL)
@@ -458,13 +562,38 @@ bool view_exists(OBIDMS_p dms, const char* view_name)
 		if ((dp->d_name)[0] == '.')
 			continue;
 		if (strcmp(dp->d_name, file_name) == 0)
+		{
+			free(file_name);
 			return true;
 		}
+	}
+
+	free(file_name);
+
+	// Check unfinished views
+	// Create file name
+	file_name = build_unfinished_obiview_file_name(view_name);
+	if (file_name == NULL)
+		return -1;
+
+	while ((dp = readdir(dms->view_directory)) != NULL)
+	{
+		if ((dp->d_name)[0] == '.')
+			continue;
+		if (strcmp(dp->d_name, file_name) == 0)
+		{
+			free(file_name);
+			return true;
+		}
+	}
+
+	free(file_name);
+
 	return false;
 }
 
 
-size_t get_platform_view_file_size()
+static size_t get_platform_view_file_size()
 {
 	size_t obiview_size;
 	size_t rounded_obiview_size;
@@ -480,7 +609,7 @@ size_t get_platform_view_file_size()
 }
 
 
-int enlarge_view_file(Obiview_p view, size_t new_size)
+static int enlarge_view_file(Obiview_p view, size_t new_size)
 {
 	int    obiview_file_descriptor;
 	double multiple;
@@ -488,7 +617,7 @@ int enlarge_view_file(Obiview_p view, size_t new_size)
 	char*  file_name;
 
 	// Create file name
-	file_name = build_obiview_file_name((view->infos)->name);
+	file_name = build_unfinished_obiview_file_name((view->infos)->name);
 	if (file_name == NULL)
 		return -1;
 
@@ -556,7 +685,7 @@ int enlarge_view_file(Obiview_p view, size_t new_size)
 }
 
 
-int write_comments_to_view_file(Obiview_p view, const char* comments)
+static int write_comments_to_view_file(Obiview_p view, const char* comments)
 {
 	size_t new_size;
 
@@ -580,14 +709,14 @@ int write_comments_to_view_file(Obiview_p view, const char* comments)
 }
 
 
-int create_obiview_file(OBIDMS_p dms, const char* view_name)
+static int create_obiview_file(OBIDMS_p dms, const char* view_name)
 {
 	char* 				file_name;
 	int 				obiview_file_descriptor;
 	size_t  			file_size;
 
 	// Create file name
-	file_name = build_obiview_file_name(view_name);
+	file_name = build_unfinished_obiview_file_name(view_name);
 	if (file_name == NULL)
 		return -1;
 
@@ -634,7 +763,7 @@ int create_obiview_file(OBIDMS_p dms, const char* view_name)
 }
 
 
-void update_column_refs(Obiview_p view)
+static void update_column_refs(Obiview_p view)
 {
 	int i;
 
@@ -646,7 +775,7 @@ void update_column_refs(Obiview_p view)
 }
 
 
-int create_column_dict(Obiview_p view)
+static int create_column_dict(Obiview_p view)
 {
 	int i;
 
@@ -681,7 +810,7 @@ int create_column_dict(Obiview_p view)
 }
 
 
-int update_column_dict(Obiview_p view)
+static int update_column_dict(Obiview_p view)
 {
 	// Re-initialize the dictionary to rebuild it from scratch
 	ht_free(view->column_dict);
@@ -693,14 +822,14 @@ int update_column_dict(Obiview_p view)
 }
 
 
-int update_column_refs_and_dict(Obiview_p view)
+static int update_column_refs_and_dict(Obiview_p view)
 {
 	update_column_refs(view);
 	return update_column_dict(view);
 }
 
 
-int update_lines(Obiview_p view, index_t line_count)
+static int update_lines(Obiview_p view, index_t line_count)
 {
 	int 			i;
 
@@ -739,7 +868,7 @@ int update_lines(Obiview_p view, index_t line_count)
 }
 
 
-OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name)
+static OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name)
 {
 	int i;
 	OBIDMS_column_p column = NULL;
@@ -799,7 +928,161 @@ OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name)
 }
 
 
-int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, index_t* line_nb_p)
+static int save_view(Obiview_p view)
+{
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to save a read-only view");
+		return -1;
+	}
+
+	// Store reference for the line selection associated with that view if there is one
+	if (view->line_selection != NULL)		// Unnecessary in theory, the line selection references are already saved
+	{
+		strcpy(((view->infos)->line_selection).column_name, ((view->line_selection)->header)->name);
+		((view->infos)->line_selection).version = ((view->line_selection)->header)->version;
+		(view->infos)->all_lines = false;
+	}
+	else	// Necessary because line selection could have been deleted if a column was cloned
+	{
+		(((view->infos)->line_selection).column_name)[0] = '\0';
+		((view->infos)->line_selection).version = -1;
+		(view->infos)->all_lines = true;
+	}
+
+	update_column_refs(view);
+
+	return 0;
+}
+
+
+static int rename_finished_view(Obiview_p view)
+{
+	char* old_name;
+	char* new_name;
+	char* path_old_name;
+	char* path_new_name;
+	char* full_path_old_name;
+	char* full_path_new_name;
+
+	old_name = build_unfinished_obiview_file_name((view->infos)->name);
+	new_name = build_obiview_file_name((view->infos)->name);
+
+	path_old_name = malloc(MAX_PATH_LEN);
+	path_new_name = malloc(MAX_PATH_LEN);
+
+	strcpy(path_old_name, "VIEWS/");
+	strcat(path_old_name, old_name);
+
+	strcpy(path_new_name, "VIEWS/");
+	strcat(path_new_name, new_name);
+
+	full_path_old_name = obi_dms_get_full_path(view->dms, path_old_name);
+	full_path_new_name = obi_dms_get_full_path(view->dms, path_new_name);
+
+	if (rename(full_path_old_name, full_path_new_name) < 0)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError renaming the file of a finished view: %s", full_path_new_name);
+		free(old_name);
+		free(new_name);
+		return -1;
+	}
+
+	free(old_name);
+	free(new_name);
+	free(path_new_name);
+	free(path_old_name);
+	free(full_path_old_name);
+	free(full_path_new_name);
+
+	return 0;
+}
+
+
+static int finish_view(Obiview_p view)
+{
+	char* predicates;
+
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to save a read-only view");
+		return -1;
+	}
+
+	// Check predicates
+	predicates = view_check_all_predicates(view);
+	if (predicates == NULL)
+	{
+		obidebug(1, "\nView predicates not respected");
+		return -1;	// TODO reverse view (delete files)
+	}
+	else
+	{
+		write_comments_to_view_file(view, predicates);
+		free(predicates);
+	}
+
+	if (save_view(view) < 0)
+		return -1;
+
+	if (rename_finished_view(view) < 0)
+		return -1;
+
+	// Flag the view as finished
+	(view->infos)->finished = true;
+
+	return 0;
+}
+
+
+static int close_view(Obiview_p view)
+{
+	int i;
+	int ret_value;
+
+	ret_value = 0;
+
+	for (i=0; i < ((view->infos)->column_count); i++)
+	{
+		if (obi_close_column((view->columns)[i]) < 0)
+		{
+			obidebug(1, "\nError closing a column while closing a view");
+			ret_value = -1;
+		}
+	}
+
+	// Close line selection if there is one
+	if (view->line_selection != NULL)
+	{
+		if (obi_close_column(view->line_selection) < 0)
+		{
+			obidebug(1, "\nError closing a line selection while closing a view");
+			ret_value = -1;
+		}
+	}
+
+	// Free the column dictionary
+	ht_free(view->column_dict);
+
+	// Unmap view file
+	if (obi_view_unmap_file(view->dms, view->infos) < 0)
+	{
+		obidebug(1, "\nError unmaping a view file while closing a view");
+		ret_value = -1;
+	}
+
+	free(view);
+
+	return ret_value;
+}
+
+
+static int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, index_t* line_nb_p)
 {
 	int   i;
 	char* column_name = NULL;
@@ -846,7 +1129,7 @@ int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, i
 }
 
 
-int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p)
+static int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p)
 {
 	if (((*line_nb_p)+1) > ((view->infos)->line_count))
 	{
@@ -865,7 +1148,7 @@ int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p)
 
 /****** PREDICATE FUNCTIONS *******/
 
-char* view_has_nuc_sequence_column(Obiview_p view)
+static char* view_has_nuc_sequence_column(Obiview_p view)
 {
 	char* predicate;
 
@@ -889,7 +1172,7 @@ char* view_has_nuc_sequence_column(Obiview_p view)
 }
 
 
-char* view_has_quality_column(Obiview_p view)
+static char* view_has_quality_column(Obiview_p view)
 {
 	char* predicate;
 
@@ -913,7 +1196,7 @@ char* view_has_quality_column(Obiview_p view)
 }
 
 
-char* view_has_id_column(Obiview_p view)
+static char* view_has_id_column(Obiview_p view)
 {
 	char* predicate;
 
@@ -936,7 +1219,8 @@ char* view_has_id_column(Obiview_p view)
 	}
 }
 
-char* view_has_definition_column(Obiview_p view)
+
+static char* view_has_definition_column(Obiview_p view)
 {
 	char* predicate;
 
@@ -960,7 +1244,7 @@ char* view_has_definition_column(Obiview_p view)
 }
 
 
-char* view_check_qual_match_seqs(Obiview_p view)
+static char* view_check_qual_match_seqs(Obiview_p view)
 {
 	index_t 		i, j, k;
 	index_t			nb_elements_per_line;
@@ -1053,13 +1337,13 @@ char* view_check_qual_match_seqs(Obiview_p view)
 }
 
 
-char* view_check_one_predicate(Obiview_p view, char* (*predicate_function)(Obiview_p view))
+static char* view_check_one_predicate(Obiview_p view, char* (*predicate_function)(Obiview_p view))
 {
 	return predicate_function(view);
 }
 
 
-char* view_check_all_predicates(Obiview_p view)
+static char* view_check_all_predicates(Obiview_p view)
 {
 	int    i, j;
 	size_t size_to_allocate;
@@ -1195,7 +1479,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 	}
 
 	// Map view file
-	view->infos = obi_view_map_file(dms, view_name);
+	view->infos = obi_view_map_file(dms, view_name, false);
 	if (view->infos == NULL)
 	{
 		obidebug(1, "\nError mapping the informations of a new view");
@@ -1236,7 +1520,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 		// If there is a new line selection, build it by combining it with the one from the view to clone if there is one
 		else if (line_selection != NULL)
 		{
-			view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, NULL, NULL, NULL, -1, NULL);
+			view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, NULL, NULL, NULL, -1, NULL, false);
 			if ((view->line_selection) == NULL)
 			{
 				obidebug(1, "\nError creating a column corresponding to a line selection");
@@ -1305,7 +1589,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 		if (write_comments_to_view_file(view, clone_comment) < 0)
 		{
 			obidebug(1, "\nError writing comments when creating a view");
-			obi_close_view(view);
+			close_view(view);
 			return NULL;
 		}
 	}
@@ -1341,7 +1625,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 	if (write_comments_to_view_file(view, comments) < 0)
 	{
 		obidebug(1, "\nError writing comments when creating a view");
-		obi_close_view(view);
+		close_view(view);
 		return NULL;
 	}
 
@@ -1360,7 +1644,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 	// Create the column dictionary (hash table) associating column names (or aliases) to column pointers
 	if (create_column_dict(view) < 0)
 	{
-		obi_close_view(view);
+		close_view(view);
 		return NULL;
 	}
 
@@ -1409,7 +1693,7 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
 		return NULL;
 	view = obi_new_view(dms, view_name, view_to_clone, line_selection, comments);
 
-	obi_close_view(view_to_clone);
+	close_view(view_to_clone);
 
 	return view;
 }
@@ -1511,26 +1795,43 @@ Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_
 		return NULL;
 	view = obi_new_view_nuc_seqs(dms, view_name, view_to_clone, line_selection, comments, quality_column);
 
-	obi_close_view(view_to_clone);
+	close_view(view_to_clone);
 
 	return view;
 }
 
 
-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)
 {
 	char*				file_name;
 	Obiview_infos_p		view_infos;
 	int 				obiview_file_descriptor;
 	size_t  			file_size;
+	int 				open_flag;
+	int					mmap_flag;
 
 	// Create file name
+	if (finished)
 		file_name = build_obiview_file_name(view_name);
+	else
+		file_name = build_unfinished_obiview_file_name(view_name);
 	if (file_name == NULL)
 		return NULL;
 
+	// Set flags (read-only or not)
+	if (finished)
+	{
+		open_flag = O_RDONLY;
+		mmap_flag = PROT_READ;
+	}
+	else
+	{
+		open_flag = O_RDWR;
+		mmap_flag = PROT_READ | PROT_WRITE;
+	}
+
     // Open view file
-	obiview_file_descriptor = openat(dms->view_dir_fd, file_name, O_RDWR, 0777);
+	obiview_file_descriptor = openat(dms->view_dir_fd, file_name, open_flag, 0777);
 	if (obiview_file_descriptor < 0)
 	{
 		if (errno == ENOENT)
@@ -1560,7 +1861,7 @@ Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name)
 	// Map the view infos structure
 	view_infos = mmap(NULL,
 				 	  file_size,
-					  PROT_READ | PROT_WRITE,
+					  mmap_flag,
 					  MAP_SHARED,
 					  obiview_file_descriptor,
 					  0
@@ -1590,12 +1891,15 @@ int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos)
 	size_t  file_size;
 
 	// Get file name
+	if (view_infos->finished)
 		file_name = build_obiview_file_name(view_infos->name);
+	else
+		file_name = build_unfinished_obiview_file_name(view_infos->name);
 	if (file_name == NULL)
 		return -1;
 
 	// Open view file
-	obiview_file_descriptor = openat(dms->view_dir_fd, file_name, O_RDWR, 0777);
+	obiview_file_descriptor = openat(dms->view_dir_fd, file_name, O_RDONLY, 0777);
 	if (obiview_file_descriptor < 0)
 	{
 		obi_set_errno(OBIVIEW_ERROR);
@@ -1661,13 +1965,9 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
 	}
 
 	// Map view file
-	view->infos = obi_view_map_file(dms, view_name);
+	view->infos = obi_view_map_file(dms, view_name, true);
-
+	if ((view->infos) == NULL)
-	// Check that the view is finished and can be opened
-	if ((view->infos)->finished == false)
 	{
-		obidebug(1, "\nError opening a view: the view is not finished");
-		obi_view_unmap_file(view->dms, view->infos);
 		free(view);
 		return NULL;
 	}
@@ -1697,7 +1997,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
 		if (column_pointer == NULL)
 		{
 			obidebug(1, "\nError opening a column for a view: column %d: %s, version %d", i, column_name, column_version);
-			obi_close_view(view);
+			close_view(view);
 			return NULL;
 		}
 		(view->columns)[i] = column_pointer;
@@ -1713,7 +2013,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
 	if (create_column_dict(view) < 0)
 	{
 		obidebug(1, "\nError creating the column dictionary when opening a view");
-		obi_close_view(view);
+		close_view(view);
 		return NULL;
 	}
 
@@ -1792,7 +2092,7 @@ int obi_view_add_column(Obiview_p    view,
 	// Open or create the column
 	if (create)
 	{	// Create column
-		column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, indexer_name, associated_column_name, associated_column_version, comments);
+		column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, indexer_name, associated_column_name, associated_column_version, comments, false);
 		if (column == NULL)
 		{
 			obidebug(1, "\nError creating a column to add to a view");
@@ -1963,103 +2263,16 @@ int obi_view_create_column_alias(Obiview_p view, const char* current_name, const
 }
 
 
-int obi_save_view(Obiview_p view)
-{
-	// Check that the view is not read-only
-	if (view->read_only)
-	{
-		obi_set_errno(OBIVIEW_ERROR);
-		obidebug(1, "\nError trying to save a read-only view");
-		return -1;
-	}
-
-	// Store reference for the line selection associated with that view if there is one
-	if (view->line_selection != NULL)		// Unnecessary in theory, the line selection references are already saved
-	{
-		strcpy(((view->infos)->line_selection).column_name, ((view->line_selection)->header)->name);
-		((view->infos)->line_selection).version = ((view->line_selection)->header)->version;
-		(view->infos)->all_lines = false;
-	}
-	else	// Necessary because line selection could have been deleted if a column was cloned
-	{
-		(((view->infos)->line_selection).column_name)[0] = '\0';
-		((view->infos)->line_selection).version = -1;
-		(view->infos)->all_lines = true;
-	}
-
-	update_column_refs(view);
-
-	return 0;
-}
-
-
-int obi_close_view(Obiview_p view)
-{
-	int i;
-	int ret_value;
-
-	ret_value = 0;
-
-	for (i=0; i < ((view->infos)->column_count); i++)
-	{
-		if (obi_close_column((view->columns)[i]) < 0)
-		{
-			obidebug(1, "\nError closing a column while closing a view");
-			ret_value = -1;
-		}
-	}
-
-	// Close line selection if there is one
-	if (view->line_selection != NULL)
-	{
-		if (obi_close_column(view->line_selection) < 0)
-		{
-			obidebug(1, "\nError closing a line selection while closing a view");
-			ret_value = -1;
-		}
-	}
-
-	// Flag the view as finished
-	(view->infos)->finished = true;
-
-	// Free the column dictionary
-	ht_free(view->column_dict);
-
-	// Unmap view file
-	if (obi_view_unmap_file(view->dms, view->infos) < 0)
-	{
-		obidebug(1, "\nError unmaping a view file while closing a view");
-		ret_value = -1;
-	}
-
-	free(view);
-
-	return ret_value;
-}
-
-
 int obi_save_and_close_view(Obiview_p view)
 {
-	char* predicates;
+	// Finish and save the view if it is not read-only
-
 	if ( ! (view->read_only))
-	{
+		if (finish_view(view) < 0)
-		predicates = view_check_all_predicates(view);
-		if (predicates == NULL)
-		{
-			obidebug(1, "\nView predicates not respected");
-			return -1;	// TODO reverse view (delete files)
-		}
-		else
-		{
-			write_comments_to_view_file(view, predicates);
-			free(predicates);
-		}
-		if (obi_save_view(view) < 0)
 			return -1;
-	}
+
-	if (obi_close_view(view) < 0)
+	if (close_view(view) < 0)
 		return -1;
+
 	return 0;
 }
 

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).
  *

src/sse_banded_LCS_alignment.c

@@ -1,16 +1,22 @@
-/*
+/****************************************************************************
- * sse_banded_LCS_alignment.c
+ * LCS alignment of two sequences				                            *
- *
+ ****************************************************************************/
- *  Created on: 7 nov. 2012
+
- *      Author: celine mercier
+/**
+ * @file sse_banded_LCS_alignment.c
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date November 7th 2012
+ * @brief Functions handling the alignment of two sequences to compute their Longest Common Sequence.
  */
 
 
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <math.h>
 #include <stdint.h>
 #include <stdbool.h>
+#include <limits.h>
 
 #include "obierrno.h"
 #include "obidebug.h"
@@ -24,6 +30,231 @@
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
+
+/**************************************************************************
+ *
+ * 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
+ *
+ **************************************************************************/
+
+
+/**
+ * @brief Internal function printing a 128 bits register as 8 16-bits integers.
+ *
+ * @param r The register to print.
+ *
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ */
+static void printreg(__m128i r);
+
+
+/**
+ * @brief Internal function extracting a 16-bits integer from a 128 bits register.
+ *
+ * @param r The register to read.
+ * @param p The position at which the integer should be read (between 0 and 7).
+ *
+ * @returns The extracted integer.
+ *
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ */
+static inline int extract_reg(__m128i r, int p);
+
+
+/**
+ * @brief Internal function aligning two sequences, computing the lengths of their Longest Common Subsequence and of their alignment.
+ *
+ * @warning The first argument (seq1) must correspond to the longest sequence.
+ *
+ * @param seq1 The first sequence, the longest of the two, as prepared by putSeqInSeq() or putBlobInSeq().
+ * @param seq2 The second sequence, the shortest of the two, as prepared by putSeqInSeq() or putBlobInSeq().
+ * @param l1 The length of the first sequence.
+ * @param l2 The length of the second sequence.
+ * @param bandLengthLeft The length of the left band for the banded alignment, as computed by calculateLeftBandLength().
+ * @param bandLengthTotal The length of the complete band for the banded alignment, as computed by calculateSSEBandLength().
+ * @param address A pointer, aligned on a 16 bits boundary, on the int array where the initial values for the alignment length are stored,
+ *                as prepared for the alignment by initializeAddressWithGaps().
+ * @param lcs_length A pointer on the int where the LCS length will be stored.
+ * @param ali_length A pointer on the int where the alignment length will be stored.
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void sse_banded_align_lcs_and_ali_len(int16_t* seq1, int16_t* seq2, int l1, int l2, int bandLengthLeft, int bandLengthTotal, int16_t* address, int* lcs_length, int* ali_length);
+
+
+/**
+ * @brief Internal function aligning two sequences, computing the length of their Longest Common Subsequence (and not the alignment length).
+ *
+ * @warning The first argument (seq1) must correspond to the longest sequence.
+ *
+ * @param seq1 The first sequence, the longest of the two, as prepared by putSeqInSeq() or putBlobInSeq().
+ * @param seq2 The second sequence, the shortest of the two, as prepared by putSeqInSeq() or putBlobInSeq().
+ * @param l1 The length of the first sequence.
+ * @param l2 The length of the second sequence.
+ * @param bandLengthLeft The length of the left band for the banded alignment, as computed by calculateLeftBandLength().
+ * @param bandLengthTotal The length of the complete band for the banded alignment, as computed by calculateSSEBandLength().
+ * @param lcs_length A pointer on the int where the LCS length will be stored.
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void sse_banded_align_just_lcs(int16_t* seq1, int16_t* seq2, int l1, int l2, int bandLengthLeft, int bandLengthTotal, int* lcs_length);
+
+
+/**
+ * @brief Internal function calculating the length of the left band for the banded alignment.
+ *
+ * @param lmax The length of the longest sequence to align.
+ * @param LCSmin The minimum length of the LCS to be above the chosen threshold, as computed by calculateLCSmin().
+ *
+ * @returns The length of the left band.
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int calculateLeftBandLength(int lmax, int LCSmin);
+
+
+/**
+ * @brief Internal function calculating the length of the right band for the banded alignment.
+ *
+ * @param lmin The length of the shortest sequence to align.
+ * @param LCSmin The minimum length of the LCS to be above the chosen threshold, as computed by calculateLCSmin().
+ *
+ * @returns The length of the right band.
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int calculateRightBandLength(int lmin, int LCSmin);
+
+
+/**
+ * @brief Internal function calculating the length of the complete band for the banded alignment.
+ *
+ * @param bandLengthRight The length of the right band for the banded alignment, as computed by calculateRightBandLength().
+ * @param bandLengthLeft The length of the left band for the banded alignment, as computed by calculateLeftBandLength().
+ *
+ * @returns The length of the complete band.
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int calculateSSEBandLength(int bandLengthRight, int bandLengthLeft);
+
+
+/**
+ * @brief Internal function calculating the size to allocate for the int array where the alignment length will be stored in the matrix.
+ *
+ * @param maxLen The length of the longest sequence to align.
+ * @param LCSmin The minimum length of the LCS to be above the chosen threshold, as computed by calculateLCSmin().
+ *
+ * @returns The size to allocate in bytes.
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int calculateSizeToAllocate(int maxLen, int LCSmin);
+
+
+/**
+ * @brief Internal function initializing the int array corresponding to a sequence to align with default values.
+ *
+ * @param seq The int array corresponding to the sequence to align, as prepared by putSeqInSeq() or putBlobInSeq().
+ * @param size The number of positions to initialize.
+ * @param iniValue The value that the positions should be initialized to.
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void iniSeq(int16_t* seq, int size, int16_t iniValue);
+
+
+/**
+ * @brief Internal function building the int array corresponding to a sequence to align.
+ *
+ * Each nucleotide is stored as a short int (int16_t).
+ *
+ * @param seq A pointer on the allocated int array.
+ * @param s A pointer on the character string corresponding to the sequence.
+ * @param l The length of the sequence.
+ * @param reverse A boolean indicating whether the sequence should be written reversed
+ *                (for the second sequence to align).
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void putSeqInSeq(int16_t* seq, char* s, int l, bool reverse);
+
+
+/**
+ * @brief Internal function building the int array corresponding to an obiblob containing a sequence.
+ *
+ * Each nucleotide is stored as a short int (int16_t).
+ *
+ * @param seq A pointer on the allocated int array.
+ * @param b A pointer on the obiblob containing the sequence.
+ * @param l The length of the (decoded) sequence.
+ * @param reverse A boolean indicating whether the sequence should be written reversed
+ *                (for the second sequence to align).
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void putBlobInSeq(int16_t* seq, Obi_blob_p b, int l, bool reverse);
+
+
+/**
+ * @brief Internal function preparing an int array with the initial values for the alignment lengths before the alignment.
+ *
+ * The int array containing the initial alignment lengths (corresponding to the first line of the diagonalized band of the alignment matrix)
+ * needs to be initialized with external gap lengths before the alignment.
+ *
+ * @param address A pointer, aligned on a 16 bits boundary, on the int array where the initial values for the alignment length are to be stored.
+ * @param bandLengthTotal The length of the complete band for the banded alignment, as computed by calculateSSEBandLength().
+ * @param bandLengthLeft The length of the left band for the banded alignment, as computed by calculateLeftBandLength().
+ * @param lmax The length of the longest sequence to align.
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void initializeAddressWithGaps(int16_t* address, int bandLengthTotal, int bandLengthLeft, int lmax);
+
+
+/**
+ * @brief Internal function aligning two sequences, computing the lengths of their Longest Common Subsequence and of their alignment.
+ *
+ * @warning The first argument (seq1) must correspond to the longest sequence.
+ *
+ * @param seq1 The first sequence, the longest of the two, as prepared by putSeqInSeq() or putBlobInSeq().
+ * @param seq2 The second sequence, the shortest of the two, as prepared by putSeqInSeq() or putBlobInSeq().
+ * @param l1 The length of the first sequence.
+ * @param l2 The length of the second sequence.
+ * @param normalize Whether the score should be normalized with the reference sequence length.
+ * @param reference The reference length. 0: The alignment length; 1: The longest sequence's length; 2: The shortest sequence's length.
+ * @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false).
+ * @param address A pointer, aligned on a 16 bits boundary, on an allocated int array where the initial values for the alignment length will be stored.
+ * @param LCSmin The minimum length of the LCS to be above the chosen threshold, as computed by calculateLCSmin().
+ * @param lcs_length A pointer on the int where the LCS length will be stored.
+ * @param ali_length A pointer on the int where the alignment length will be stored.
+ *
+ * @returns The alignment score (normalized according to the parameters).
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+double sse_banded_lcs_align(int16_t* seq1, int16_t* seq2, int l1, int l2, bool normalize, int reference, bool similarity_mode, int16_t* address, int LCSmin, int* lcs_length, int* ali_length);
+
+
+
+/************************************************************************
+ *
+ * D E F I N I 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
+ *
+ ************************************************************************/
+
+
 static void  printreg(__m128i r)
 {
 	int16_t a0,a1,a2,a3,a4,a5,a6,a7;
@@ -61,7 +292,6 @@ static inline int extract_reg(__m128i r, int p)
 }
 
 
-// TODO warning on length order
 void sse_banded_align_lcs_and_ali_len(int16_t* seq1, int16_t* seq2, int l1, int l2, int bandLengthLeft, int bandLengthTotal, int16_t* address, int* lcs_length, int* ali_length)
 {
 	register int j;
@@ -287,7 +517,6 @@ void sse_banded_align_lcs_and_ali_len(int16_t* seq1, int16_t* seq2, int l1, int
 }
 
 
-// TODO warning on length order
 void sse_banded_align_just_lcs(int16_t* seq1, int16_t* seq2, int l1, int l2, int bandLengthLeft, int bandLengthTotal, int* lcs_length)
 {
 	register int j;
@@ -446,8 +675,7 @@ int calculateSSEBandLength(int bandLengthRight, int bandLengthLeft)
 }
 
 
-// TODO that's gonna be fun to doc
+int calculateSizeToAllocate(int maxLen, int LCSmin)
-int calculateSizeToAllocate(int maxLen, int minLen, int LCSmin)
 {
 	int size;
 
@@ -522,13 +750,13 @@ void putBlobInSeq(int16_t* seq, Obi_blob_p b, int l, bool reverse)
 }
 
 
-void initializeAddressWithGaps(int16_t* address, int bandLengthTotal, int bandLengthLeft, int l1)
+void initializeAddressWithGaps(int16_t* address, int bandLengthTotal, int bandLengthLeft, int lmax)
 {
 	int i;
 	int address_00, x_address_10, address_01, address_01_shifted;
 	int numberOfRegistersPerLine;
 	int bm;
-	int value=INT16_MAX-l1;
+	int value=INT16_MAX-lmax;
 
 	numberOfRegistersPerLine = bandLengthTotal / 8;
 	bm = bandLengthLeft%2;
@@ -556,7 +784,6 @@ void initializeAddressWithGaps(int16_t* address, int bandLengthTotal, int bandLe
 }
 
 
-// TODO warning on length order
 double sse_banded_lcs_align(int16_t* seq1, int16_t* seq2, int l1, int l2, bool normalize, int reference, bool similarity_mode, int16_t* address, int LCSmin, int* lcs_length, int* ali_length)
 {
 	double id;
@@ -610,10 +837,14 @@ double sse_banded_lcs_align(int16_t* seq1, int16_t* seq2, int l1, int l2, bool n
 
 
 
-// PUBLIC FUNCTIONS
+/**********************************************************************
+ *
+ * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
+ *
+ **********************************************************************/
 
 
-int calculateLCSmin(int l1, int l2, double threshold, bool normalize, int reference, bool similarity_mode)
+int calculateLCSmin(int lmax, int lmin, double threshold, bool normalize, int reference, bool similarity_mode)
 {
 	int LCSmin;
 
@@ -622,16 +853,16 @@ int calculateLCSmin(int l1, int l2, double threshold, bool normalize, int refere
 		if (normalize)
 		{
 			if (reference == MINLEN)
-				LCSmin = threshold*l2;
+				LCSmin = threshold*lmin;
 			else 		// ref = maxlen or alilen
-				LCSmin = threshold*l1;
+				LCSmin = threshold*lmax;
 		}
 		else if (similarity_mode)
 			LCSmin = threshold;
 		else if (reference == MINLEN) // not similarity_mode
-			LCSmin = l2 - threshold;
+			LCSmin = lmin - threshold;
 		else	// not similarity_mode and ref = maxlen or alilen
-			LCSmin = l1 - threshold;
+			LCSmin = lmax - threshold;
 	}
 	else
 		LCSmin = 0;
@@ -669,6 +900,14 @@ double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, bo
 		lmin = l1;
 	}
 
+	// Check that the sequences are not greater than what can be aligned using the 16 bits registers (as the LCS and alignment lengths are kept on 16 bits)
+	if (lmax > SHRT_MAX)
+	{
+		obi_set_errno(OBI_ALIGN_ERROR);
+		obidebug(1, "\nError: can not align sequences longer than %d (as the LCS and alignment lengths are kept on 16 bits)", SHRT_MAX);
+		return 0; 		// TODO DOUBLE_MIN to flag error
+	}
+
 	// If the score is expressed as a normalized distance, get the corresponding identity
 	if (!similarity_mode && normalize)
 		threshold = 1.0 - threshold;
@@ -679,7 +918,7 @@ double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, bo
 	// Allocate space for matrix band if the alignment length must be computed
 	if ((reference == ALILEN) && (normalize || !similarity_mode)) // cases in which alignment length must be computed
 	{
-		sizeToAllocateForBand = calculateSizeToAllocate(lmax, lmin, LCSmin);
+		sizeToAllocateForBand = calculateSizeToAllocate(lmax, LCSmin);
 		address = obi_get_memory_aligned_on_16(sizeToAllocateForBand, &shift);
 		if (address == NULL)
 		{
@@ -764,6 +1003,14 @@ double obiblob_sse_banded_lcs_align(Obi_blob_p seq1, Obi_blob_p seq2, double thr
 		lmin = l1;
 	}
 
+	// Check that the sequences are not greater than what can be aligned using the 16 bits registers (as the LCS and alignment lengths are kept on 16 bits)
+	if (lmax > SHRT_MAX)
+	{
+		obi_set_errno(OBI_ALIGN_ERROR);
+		obidebug(1, "\nError: can not align sequences longer than %d (as the LCS and alignment lengths are kept on 16 bits)", SHRT_MAX);
+		return 0; 		// TODO DOUBLE_MIN to flag error
+	}
+
 	// If the score is expressed as a normalized distance, get the corresponding identity
 	if (!similarity_mode && normalize)
 		threshold = 1.0 - threshold;
@@ -774,13 +1021,13 @@ double obiblob_sse_banded_lcs_align(Obi_blob_p seq1, Obi_blob_p seq2, double thr
 	// Allocate space for matrix band if the alignment length must be computed
 	if ((reference == ALILEN) && (normalize || !similarity_mode)) // cases in which alignment length must be computed
 	{
-		sizeToAllocateForBand = calculateSizeToAllocate(lmax, lmin, LCSmin);
+		sizeToAllocateForBand = calculateSizeToAllocate(lmax, LCSmin);
 		address = obi_get_memory_aligned_on_16(sizeToAllocateForBand, &shift);
 		if (address == NULL)
 		{
 			obi_set_errno(OBI_MALLOC_ERROR);
-			obidebug(1, "\nError getting a memory address aligned on 16 bytes boundary");
+			obidebug(1, "\nError getting a memory address aligned on a 16 bits boundary");
-			return 0;	// TODO DOUBLE_MIN
+			return 0;	// TODO DOUBLE_MIN to flag error
 		}
 	}
 

src/sse_banded_LCS_alignment.h

@@ -1,10 +1,15 @@
-/*
+/****************************************************************************
- * sse_banded_LCS_alignment.h
+ * LCS alignment of two sequences header file                               *
- *
+ ****************************************************************************/
- *  Created on: november 29, 2012
+
- *      Author: mercier
+/**
+ * @file sse_banded_LCS_alignment.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date November 7th 2012
+ * @brief header file for the functions handling the alignment of two sequences to compute their Longest Common Sequence.
  */
 
+
 #ifndef SSE_BANDED_LCS_ALIGNMENT_H_
 #define SSE_BANDED_LCS_ALIGNMENT_H_
 
@@ -15,13 +20,97 @@
 #include "obiblob.h"
 
 
-#define ALILEN (0)	// TODO enum
+/**
+ * @brief Macros for reference lengths to use when aligning.
+ *
+ * @since 2012
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ */
+#define ALILEN (0)
 #define MAXLEN (1)
 #define MINLEN (2)
 
-// TODO doc
+
-int calculateLCSmin(int l1, int l2, double threshold, bool normalize, int reference, bool lcsmode);
+/**
+ * @brief Function calculating the minimum length of the Longest Common Subsequence between two sequences to be above a chosen score threshold.
+ *
+ * @warning The first argument (lmax) must correspond to length of the longest sequence.
+ *
+ * @param lmax The length of the longest sequence to align.
+ * @param lmin The length of the shortest sequence to align.
+ * @param threshold Score threshold. If the score is normalized and expressed in similarity, it is an identity, e.g. 0.95
+ * 					for an identity of 95%. If the score is normalized and expressed in distance, it is (1.0 - identity),
+ * 					e.g. 0.05 for an identity of 95%. If the score is not normalized and expressed in similarity, it is
+ * 					the length of the Longest Common Subsequence. If the score is not normalized and expressed in distance,
+ *                  it is (reference length - LCS length). Only sequence pairs with a similarity above the threshold are printed.
+ * @param normalize Whether the score should be normalized with the reference sequence length.
+ * @param reference The reference length. 0: The alignment length; 1: The longest sequence's length; 2: The shortest sequence's length.	// TODO
+ * @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false).
+ *
+ * @returns The minimum length of the Longest Common Subsequence between two sequences to be above the chosen score threshold.
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int calculateLCSmin(int lmax, int lmin, double threshold, bool normalize, int reference, bool similarity_mode);
+
+
+/**
+ * @brief Function aligning two sequences.
+ *
+ * The alignment algorithm is a banded global alignment algorithm, a modified version of the classical Needleman and Wunsch algorithm,
+ * and uses indices based on the length of the Longest Common Subsequence between the two sequences.
+ *
+ * Note: the sequences do not need to be ordered (e.g. with the longest sequence as first argument).
+ *
+ * @param seq1 A pointer on the character string corresponding to the first sequence.
+ * @param seq2 A pointer on the character string corresponding to the second sequence.
+ * @param threshold Score threshold. If the score is normalized and expressed in similarity, it is an identity, e.g. 0.95
+ * 					for an identity of 95%. If the score is normalized and expressed in distance, it is (1.0 - identity),
+ * 					e.g. 0.05 for an identity of 95%. If the score is not normalized and expressed in similarity, it is
+ * 					the length of the Longest Common Subsequence. If the score is not normalized and expressed in distance,
+ *                  it is (reference length - LCS length). Only sequence pairs with a similarity above the threshold are printed.
+ * @param normalize Whether the score should be normalized with the reference sequence length.
+ * @param reference The reference length. 0: The alignment length; 1: The longest sequence's length; 2: The shortest sequence's length.	// TODO
+ * @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false).
+ * @param lcs_length A pointer on the int where the LCS length will be stored.
+ * @param ali_length A pointer on the int where the alignment length will be stored.
+ *
+ * @returns The alignment score (normalized according to the parameters).
+ *
+ * @since 2012
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
 double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, bool normalize, int reference, bool similarity_mode, int* lcs_length, int* ali_length);
+
+
+/**
+ * @brief Function aligning two sequences encoded in obiblobs.
+ *
+ * The alignment algorithm is a banded global alignment algorithm, a modified version of the classical Needleman and Wunsch algorithm,
+ * and uses indices based on the length of the Longest Common Subsequence between the two sequences.
+ *
+ * Note: the obiblobs do not need to be ordered (e.g. with the obiblob containing the longest sequence as first argument).
+ *
+ * @param seq1 A pointer on the blob containing the first sequence.
+ * @param seq2 A pointer on the blob containing the second sequence.
+ * @param threshold Score threshold. If the score is normalized and expressed in similarity, it is an identity, e.g. 0.95
+ * 					for an identity of 95%. If the score is normalized and expressed in distance, it is (1.0 - identity),
+ * 					e.g. 0.05 for an identity of 95%. If the score is not normalized and expressed in similarity, it is
+ * 					the length of the Longest Common Subsequence. If the score is not normalized and expressed in distance,
+ *                  it is (reference length - LCS length). Only sequence pairs with a similarity above the threshold are printed.
+ * @param normalize Whether the score should be normalized with the reference sequence length.
+ * @param reference The reference length. 0: The alignment length; 1: The longest sequence's length; 2: The shortest sequence's length.	// TODO
+ * @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false).
+ * @param lcs_length A pointer on the int where the LCS length will be stored.
+ * @param ali_length A pointer on the int where the alignment length will be stored.
+ *
+ * @returns The alignment score (normalized according to the parameters).
+ *
+ * @since December 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
 double obiblob_sse_banded_lcs_align(Obi_blob_p seq1, Obi_blob_p seq2, double threshold, bool normalize, int reference, bool similarity_mode, int* lcs_length, int* ali_length);
 
+
 #endif

src/upperband.c

@@ -8,8 +8,6 @@
 #include "obidmscolumn.h"
 #include "obiview.h"
 
-//#include "../libutils/utilities.h"
-//#include "../libfasta/sequence.h"
 
 
 inline static uchar_v hash4m128(uchar_v frag)
@@ -242,7 +240,7 @@ Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col, index_t se
 
 	fprintf(stderr,"Building kmer tables...");
 
-	seq_count = (seq_col->header)->lines_used;
+	seq_count = (view->infos)->line_count;
 
 	// Allocate memory for the table structure
 	ktable = (Kmer_table_p) malloc(sizeof(Kmer_table_t) * seq_count);
@@ -267,6 +265,44 @@ Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col, index_t se
 }
 
 
+Kmer_table_p hash_two_seq_columns(Obiview_p view1, OBIDMS_column_p seq1_col, index_t seq1_idx,
+								  Obiview_p view2, OBIDMS_column_p seq2_col, index_t seq2_idx)
+{
+	size_t       seq1_count;
+	size_t       seq2_count;
+	Kmer_table_p ktable1;
+	Kmer_table_p ktable2;
+	Kmer_table_p ktable;
+
+	seq1_count = (view1->infos)->line_count;
+	seq2_count = (view2->infos)->line_count;
+
+	// Build the two tables then concatenate them
+	ktable1 = hash_seq_column(view1, seq1_col, seq1_idx);
+	if (ktable1 == NULL)
+		return NULL;
+	ktable2 = hash_seq_column(view2, seq2_col, seq2_idx);
+	if (ktable2 == NULL)
+		return NULL;
+
+	// Realloc to hold the 2 tables
+	ktable = realloc(ktable1, sizeof(Kmer_table_t) * (seq1_count + seq2_count));
+	if (ktable == NULL)
+	{
+		free_kmer_tables(ktable2, seq2_count);
+		return NULL;
+	}
+
+	// Concatenate
+	memcpy(ktable+seq1_count, ktable2, sizeof(Kmer_table_t) * seq2_count);
+
+	// Free copied table
+	free(ktable2);
+
+	return ktable;
+}
+
+
 void free_kmer_tables(Kmer_table_p ktable, size_t count)
 {
 	size_t      i;

src/upperband.h

@@ -18,7 +18,11 @@ typedef struct {
 } Kmer_table_t, *Kmer_table_p;
 
 
+// TODO doc
+
 Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col, index_t seq_idx);
+Kmer_table_p hash_two_seq_columns(Obiview_p view1, OBIDMS_column_p seq1_col, index_t seq1_idx,
+								  Obiview_p view2, OBIDMS_column_p seq2_col, index_t seq2_idx);
 void align_filters(Kmer_table_p ktable, Obi_blob_p seq1, Obi_blob_p seq2, index_t idx1, index_t idx2, double threshold, bool normalize, int reference, bool similarity_mode, double* score, int* LCSmin, bool can_be_identical);
 void free_kmer_tables(Kmer_table_p ktable, size_t count);
 

src/utils.c

@@ -116,3 +116,193 @@ void* obi_get_memory_aligned_on_16(int size, int* shift)
 	return (memory);
 }
 
+
+/*
+ * A generic implementation of binary search for the Linux kernel
+ *
+ * Copyright (C) 2008-2009 Ksplice, Inc.
+ * Author: Tim Abbott <tabbott@ksplice.com>
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; version 2.
+ */
+void* bsearch_user_data(const void* key, const void* base, size_t num, size_t size, const void* user_data,
+              	  	  	int (*cmp)(const void *key, const void *elt, const void* user_data))
+{
+	size_t start = 0;
+	size_t end   = num;
+	size_t mid;
+    int result;
+
+    while (start < end)
+    {
+    	mid = start + (end - start) / 2;
+    	result = cmp(key, base + mid * size, user_data);
+		if (result < 0)
+			end = mid;
+		else if (result > 0)
+			start = mid + 1;
+		else
+			return (void*)base + mid * size;
+    }
+
+    return NULL;
+}
+
+
+/*
+ * Copyright (c) 1992, 1993
+ *      The Regents of the University of California.  All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the University nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ */
+/*
+ * Qsort routine from Bentley & McIlroy's "Engineering a Sort Function".
+ */
+
+#define MIN(a,b) ((a) < (b) ? a : b)
+
+#define swapcode(TYPE, parmi, parmj, n) {               \
+        long i = (n) / sizeof (TYPE);                   \
+        register TYPE *pi = (TYPE *) (parmi);           \
+        register TYPE *pj = (TYPE *) (parmj);           \
+        do {                                            \
+                register TYPE   t = *pi;                \
+                *pi++ = *pj;                            \
+                *pj++ = t;                              \
+        } while (--i > 0);                              \
+}
+
+#define SWAPINIT(a, es) swaptype = ((char *)a - (char *)0) % sizeof(long) || \
+        es % sizeof(long) ? 2 : es == sizeof(long)? 0 : 1;
+
+static __inline void
+swapfunc(char *a, char *b, int n, int swaptype)
+{
+        if (swaptype <= 1)
+                swapcode(long, a, b, n)
+        else
+                swapcode(char, a, b, n)
+}
+
+#define swap(a, b)                                      \
+        if (swaptype == 0) {                            \
+                long t = *(long *)(a);                  \
+                *(long *)(a) = *(long *)(b);            \
+                *(long *)(b) = t;                       \
+        } else                                          \
+                swapfunc(a, b, es, swaptype)
+
+#define vecswap(a, b, n)        if ((n) > 0) swapfunc(a, b, n, swaptype)
+
+static __inline char *
+med3(char *a, char *b, char *c, const void *user_data, int (*cmp)(const void *, const void *, const void *))
+{
+        return cmp(a, b, user_data) < 0 ?
+               (cmp(b, c, user_data) < 0 ? b : (cmp(a, c, user_data) < 0 ? c : a ))
+              :(cmp(b, c, user_data) > 0 ? b : (cmp(a, c, user_data) < 0 ? a : c ));
+}
+
+void
+qsort_user_data(void *aa, size_t n, size_t es, const void *user_data, int (*cmp)(const void *, const void *, const void *))
+{
+        char *pa, *pb, *pc, *pd, *pl, *pm, *pn;
+        int d, r, swaptype, swap_cnt;
+        register char *a = aa;
+
+loop:   SWAPINIT(a, es);
+        swap_cnt = 0;
+        if (n < 7) {
+                for (pm = (char *)a + es; pm < (char *) a + n * es; pm += es)
+                        for (pl = pm; pl > (char *) a && cmp(pl - es, pl, user_data) > 0;
+                             pl -= es)
+                                swap(pl, pl - es);
+                return;
+        }
+        pm = (char *)a + (n / 2) * es;
+        if (n > 7) {
+                pl = (char *)a;
+                pn = (char *)a + (n - 1) * es;
+                if (n > 40) {
+                        d = (n / 8) * es;
+                        pl = med3(pl, pl + d, pl + 2 * d, user_data, cmp);
+                        pm = med3(pm - d, pm, pm + d, user_data, cmp);
+                        pn = med3(pn - 2 * d, pn - d, pn, user_data, cmp);
+                }
+                pm = med3(pl, pm, pn, user_data, cmp);
+        }
+        swap(a, pm);
+        pa = pb = (char *)a + es;
+
+        pc = pd = (char *)a + (n - 1) * es;
+        for (;;) {
+                while (pb <= pc && (r = cmp(pb, a, user_data)) <= 0) {
+                        if (r == 0) {
+                                swap_cnt = 1;
+                                swap(pa, pb);
+                                pa += es;
+                        }
+                        pb += es;
+                }
+                while (pb <= pc && (r = cmp(pc, a, user_data)) >= 0) {
+                        if (r == 0) {
+                                swap_cnt = 1;
+                                swap(pc, pd);
+                                pd -= es;
+                        }
+                        pc -= es;
+                }
+                if (pb > pc)
+                        break;
+                swap(pb, pc);
+                swap_cnt = 1;
+                pb += es;
+                pc -= es;
+        }
+        if (swap_cnt == 0) {  /* Switch to insertion sort */
+                for (pm = (char *) a + es; pm < (char *) a + n * es; pm += es)
+                        for (pl = pm; pl > (char *) a && cmp(pl - es, pl, user_data) > 0;
+                             pl -= es)
+                                swap(pl, pl - es);
+                return;
+        }
+
+        pn = (char *)a + n * es;
+        r = MIN(pa - (char *)a, pb - pa);
+        vecswap(a, pb - r, r);
+        r = MIN((long)(pd - pc), (long)(pn - pd - es));
+        vecswap(pb, pn - r, r);
+        if ((r = pb - pa) > (int)es)
+                qsort_user_data(a, r / es, es, user_data, cmp);
+        if ((r = pd - pc) > (int)es) {
+                /* Iterate rather than recurse to save stack space */
+                a = pn - r;
+                n = r / es;
+                goto loop;
+        }
+/*              qsort(pn - r, r / es, es, cmp);*/
+}
+

src/utils.h

@@ -74,4 +74,41 @@ char* obi_format_date(time_t date);
 void* obi_get_memory_aligned_on_16(int size, int* shift);
 
 
+/**
+ * @brief Version of quick sort modified to allow the user to provide an
+ *        additional pointer sent to the comparison function.
+ *
+ * @param key This is the pointer to the object that serves as key for the search, type-casted as a void*.
+ * @param base This is the pointer to the first object of the array where the search is performed, type-casted as a void*.
+ * @param num This is the number of elements in the array pointed by base.
+ * @param size This is the size in bytes of each element in the array.
+ * @param user_data This is an additional pointer passed to the comparison function.
+ * @param cmp This is the function that compares two elements, eventually with an additional pointer.
+ *
+ * @returns A pointer to an entry in the array that matches the search key.
+ * @retval NULL if key is not found.
+ *
+ * @since January 2017
+ * @author original code modified by Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void* bsearch_user_data(const void* key, const void* base, size_t num, size_t size, const void* user_data,
+              	  	  	int (*cmp)(const void *key, const void *elt, const void* user_data));
+
+
+/**
+ * @brief Version of quick sort modified to allow the user to provide an
+ *        additional pointer sent to the comparison function.
+ *
+ * @param aa This is the pointer to the first element of the array to be sorted.
+ * @param n This is the number of elements in the array pointed by base.
+ * @param es This is the size in bytes of each element in the array.
+ * @param user_data This is an additional pointer passed to the comparison function.
+ * @param cmp This is the function that compares two elements, eventually with an additional pointer.
+ *
+ * @since January 2017
+ * @author original code modified by Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void qsort_user_data(void *aa, size_t n, size_t es, const void *user_data, int (*cmp)(const void *, const void *, const void *));
+
+
 #endif /* UTILS_H_ */