Major update : views

python/obitools3/obidms/_obidms.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidms.h
 ../../../src/obidms.c
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
@@ -15,4 +17,6 @@
 ../../../src/obiavl.h
 ../../../src/obiavl.c
 ../../../src/encode.h
-../../../src/encode.c
+../../../src/encode.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c

python/obitools3/obidms/_obidms.pxd

@@ -2,52 +2,80 @@
 
 from .capi.obidms       cimport OBIDMS_p
 from .capi.obidmscolumn cimport OBIDMS_column_p
+from .capi.obiview      cimport Obiview_p
 from .capi.obitypes     cimport obiversion_t, OBIType_t, index_t
 
 
-cdef class OBIDMS_column
-
-            
-cdef class OBIDMS:
-
-    cdef OBIDMS_p pointer
-    cdef str dms_name
-    
-    cpdef dict list(self)
-    cpdef close(self)
-    cpdef OBIDMS_column open_column(self,
-                                    str column_name,
-                                    bint create=*, 
-                                    bint clone=*, bint clone_data=*,
-                                    bint referring=*,
-                                    obiversion_t version_number=*, 
-                                    str type=*,
-                                    index_t nb_lines=*, 
-                                    index_t nb_elements_per_line=*, 
-                                    list elements_names=*,
-                                    str avl_name=*,
-                                    str comments=*)
-
-
 cdef class OBIDMS_column:
 
-    cdef  OBIDMS_column_p    pointer
+    cdef  OBIDMS_column_p*   pointer
     cdef  OBIDMS             dms
+    cdef  Obiview_p          view
     cdef  str                data_type
     cdef  str                dms_name
     cdef  str                column_name
     cdef  index_t            nb_elements_per_line
     cdef  list               elements_names
-    
+        
-    cpdef OBIDMS_column_p    referred_column_pointer
+    cpdef         update_pointer(self)
-    
-#    cpdef object get_item(self, index_t line_nb, str element_name)                  TODO can't declare because not the same in all subclasses
-#    cpdef        set_item(self, index_t line_nb, str element_name, object value)    TODO can't declare because object value
-    cpdef         grep_line(self, index_t line_nb)
     cpdef list    get_elements_names(self)
     cpdef str     get_data_type(self)
     cpdef index_t get_nb_lines_used(self)
     cpdef str     get_creation_date(self)
     cpdef str     get_comments(self)
     cpdef         close(self)
+    @staticmethod
+    cdef  object  get_subclass_type(OBIDMS_column_p column_p)
+
+
+cdef class OBIDMS_column_multi_elts(OBIDMS_column):
+    
+    cpdef set_line(self, index_t line_nb, dict values)
+
+
+cdef class OBIDMS_column_line:
+
+    cdef OBIDMS_column column
+    cdef index_t index
+
+
+cdef class OBIView:
+    
+    cdef Obiview_p pointer
+    cdef str       name
+    cdef dict      columns
+    cdef dict      columns_pp    # TODO this dict might be unnecessary
+    cdef OBIDMS    dms
+    
+    cpdef delete_column(self, str column_name)
+    cpdef add_column(self, 
+                     str column_name, 
+                     obiversion_t version_number=*, 
+                     str type=*,
+                     index_t nb_lines=*, 
+                     index_t nb_elements_per_line=*,
+                     list elements_names=*,
+                     str avl_name=*,
+                     str comments=*,
+                     bint create=*
+                    )
+    cpdef select_line(self, index_t line_nb)
+    cpdef select_lines(self, list line_selection)
+    cpdef save_and_close(self)
+
+
+cdef class OBIView_line :
+
+    cdef index_t index
+    cdef OBIView view
+
+
+cdef class OBIDMS:
+
+    cdef OBIDMS_p pointer
+    cdef str dms_name
+    
+    cpdef close(self)
+    cpdef OBIView open_view(self, str view_name)
+    cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*)
 

python/obitools3/obidms/_obidms.pyx

@@ -6,16 +6,12 @@ from obitools3.utils cimport bytes2str, str2bytes
 
 from .capi.obidms cimport obi_dms, \
                           obi_close_dms
-from .capi.obidmscolumn cimport obi_column_get_header_from_name, \
+                          
-                                obi_unmap_header, \
+from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
-                                obi_column_get_latest_version_from_name, \
-                                obi_create_column, \
-                                obi_clone_column, \
-                                obi_open_column, \
-                                obi_close_column, \
                                 obi_column_format_date, \
-                                obi_grep_line, \
+                                OBIDMS_column_p, \
                                 OBIDMS_column_header_p
+                                
 from .capi.obitypes cimport const_char_p, \
                             OBIType_t, \
                             OBI_INT, \
@@ -24,42 +20,486 @@ from .capi.obitypes cimport const_char_p, \
                             OBI_CHAR, \
                             OBI_STR, \
                             OBI_SEQ, \
-                            name_data_type
+                            name_data_type, \
+                            only_ATGC    # discuss
                             
-
 from ._obidms cimport OBIDMS
 from ._obidms cimport OBIDMS_column
+from ._obidms cimport OBIView_line
 
 from ._obidmscolumn_int cimport OBIDMS_column_int, \
-                                OBIDMS_column_int_writable, \
+                                OBIDMS_column_multi_elts_int
-                                OBIDMS_column_int_multi_elts, \
-                                OBIDMS_column_int_multi_elts_writable
                                 
 from ._obidmscolumn_float cimport OBIDMS_column_float, \
-                                  OBIDMS_column_float_writable, \
+                                  OBIDMS_column_multi_elts_float
-                                  OBIDMS_column_float_multi_elts, \
-                                  OBIDMS_column_float_multi_elts_writable
 
 from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
-                                 OBIDMS_column_bool_writable, \
+                                 OBIDMS_column_multi_elts_bool
-                                 OBIDMS_column_bool_multi_elts, \
-                                 OBIDMS_column_bool_multi_elts_writable
 
 from ._obidmscolumn_char cimport OBIDMS_column_char, \
-                                 OBIDMS_column_char_writable, \
+                                 OBIDMS_column_multi_elts_char
-                                 OBIDMS_column_char_multi_elts, \
-                                 OBIDMS_column_char_multi_elts_writable
 
 from ._obidmscolumn_str cimport OBIDMS_column_str, \
-                                OBIDMS_column_str_writable, \
+                                OBIDMS_column_multi_elts_str
-                                OBIDMS_column_str_multi_elts, \
-                                OBIDMS_column_str_multi_elts_writable
 
 from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
-                                OBIDMS_column_seq_writable, \
+                                OBIDMS_column_multi_elts_seq
-                                OBIDMS_column_seq_multi_elts, \
-                                OBIDMS_column_seq_multi_elts_writable
 
+from ._obidms cimport OBIView, OBIView_line
+
+from .capi.obiview cimport Obiview_p, \
+                           obi_new_view, \
+                           obi_new_view_cloned_from_name, \
+                           obi_open_view,  \
+                           obi_view_delete_column, \
+                           obi_view_add_column, \
+                           obi_view_get_column, \
+                           obi_view_get_pointer_on_column_in_view, \
+                           obi_select_line, \
+                           obi_select_lines, \
+                           obi_save_and_close_view
+                           
+from libc.stdlib cimport malloc
+from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
+
+
+cdef class OBIDMS_column :
+
+    # Should only be initialized through a subclass
+    def __init__(self, OBIView view, str column_name):
+        
+        cdef OBIDMS_column_p  column_p
+        cdef OBIDMS_column_p* column_pp
+        
+        column_pp = <OBIDMS_column_p*> PyCapsule_GetPointer(((view.columns_pp)[column_name]), NULL) # or use C function
+        column_p = column_pp[0]     # TODO ugly cython dereferencing but can't find better
+        
+        # Fill structure
+        self.pointer = column_pp
+        self.dms = view.dms
+        self.view = view.pointer    # TODO pointer or instance?
+        self.data_type = bytes2str(name_data_type((column_p.header).returned_data_type))
+        self.column_name = bytes2str((column_p.header).name)
+        self.nb_elements_per_line = (column_p.header).nb_elements_per_line
+        self.elements_names = (bytes2str((column_p.header).elements_names)).split(';')
+
+    def __setitem__(self, index_t line_nb, object value):
+        self.set_line(line_nb, value)
+
+    def __getitem__(self, index_t line_nb):
+        return self.get_line(line_nb)
+
+    def __len__(self):
+        return (self.pointer)[0].header.lines_used
+    
+    def __sizeof__(self):
+        return ((self.pointer)[0].header.header_size + (self.pointer)[0].header.data_size)
+    
+    def __iter__(self):
+    
+        # Declarations
+        cdef index_t lines_used
+        cdef index_t line_nb
+        
+        # Yield each line
+        lines_used = (self.pointer)[0].header.lines_used
+        for line_nb in range(lines_used):
+            yield self.get_line(line_nb)
+    
+    cpdef update_pointer(self):
+        self.pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self.view, str2bytes(self.column_name))
+
+    cpdef list get_elements_names(self):
+        return self.elements_names
+         
+    cpdef str get_data_type(self):
+        return self.data_type
+    
+    cpdef index_t get_nb_lines_used(self):
+        return (self.pointer)[0].header.lines_used
+        
+    cpdef str get_creation_date(self):
+        return bytes2str(obi_column_format_date((self.pointer)[0].header.creation_date))
+    
+    cpdef str get_comments(self):
+        return bytes2str((self.pointer)[0].header.comments)
+    
+    def __repr__(self) :
+        cdef str to_print
+        to_print = ''
+        for line in self :
+            to_print = to_print + str(line) + "\n"
+        return to_print
+        
+    cpdef close(self):
+        if obi_truncate_and_close_column((self.pointer)[0]) < 0 :
+            raise Exception("Problem closing a column")
+
+
+    @staticmethod
+    cdef object get_subclass_type(OBIDMS_column_p column_p) :
+        
+        cdef object subclass
+        cdef OBIDMS_column_header_p header
+        cdef OBIType_t col_type
+        cdef bint col_writable
+        cdef bint col_one_element_per_line
+
+        header = column_p.header        
+        col_type = header.returned_data_type
+        col_writable = column_p.writable
+        col_one_element_per_line = ((header.nb_elements_per_line) == 1)
+        
+        if col_type == OBI_INT :
+            if col_one_element_per_line :
+                subclass = OBIDMS_column_int
+            else :
+                subclass = OBIDMS_column_multi_elts_int
+        elif col_type == OBI_FLOAT :
+            if col_one_element_per_line :
+                subclass = OBIDMS_column_float
+            else :
+                subclass = OBIDMS_column_multi_elts_float
+        elif col_type == OBI_BOOL :
+            if col_one_element_per_line :
+                subclass = OBIDMS_column_bool
+            else :
+                subclass = OBIDMS_column_multi_elts_bool
+        elif col_type == OBI_CHAR :
+            if col_one_element_per_line :
+                subclass = OBIDMS_column_char
+            else :
+                subclass = OBIDMS_column_multi_elts_char
+        elif col_type == OBI_STR :
+            if col_one_element_per_line :
+                subclass = OBIDMS_column_str
+            else :
+                subclass = OBIDMS_column_multi_elts_str
+        elif col_type == OBI_SEQ :
+            if col_one_element_per_line :
+                subclass = OBIDMS_column_seq
+            else :
+                subclass = OBIDMS_column_multi_elts_seq
+        else :
+            raise Exception("Problem with the data type")
+
+        return subclass
+
+    
+######################################################################################################
+
+cdef class OBIDMS_column_multi_elts(OBIDMS_column) :
+    
+    def __getitem__(self, index_t line_nb):
+        return OBIDMS_column_line(self, line_nb)
+
+    cpdef set_line(self, index_t line_nb, dict values):
+        for element_name in values :
+            self.set_item(line_nb, element_name, values[element_name])
+
+######################################################################################################
+
+cdef class OBIDMS_column_line :
+
+    def __init__(self, OBIDMS_column column, index_t line_nb) :
+        self.index = line_nb
+        self.column = column
+        
+    def __getitem__(self, str element_name) :
+        return self.column.get_item(self.index, element_name)
+     
+    def __setitem__(self, str element_name, object value):
+        self.column.set_item(self.index, element_name, value)
+
+    def __contains__(self, str element_name):
+        return (element_name in self.column.elements_names)
+
+    def __repr__(self) :
+        return str(self.column.get_line(self.index))
+
+##########################################
+
+
+cdef class OBIView :
+    
+    def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None): 
+        
+        cdef Obiview_p view = NULL
+        cdef int i
+        cdef list col_list
+        cdef str col_name
+        cdef OBIDMS_column column
+        cdef OBIDMS_column_p column_p
+        cdef OBIDMS_column_p* column_pp
+        cdef OBIDMS_column_header_p header
+        cdef index_t* line_selection_p
+                
+        self.dms = dms
+        
+        if line_selection is not None :
+            line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
+            for i in range(len(line_selection)) :
+                line_selection_p[i] = line_selection[i]     # TODO type problem?
+                print(line_selection_p[i], line_selection[i])
+            line_selection_p[len(line_selection)] = -1
+        else :
+            line_selection_p = NULL
+       
+        if new :
+            if view_to_clone is not None :
+                if type(view_to_clone) == str :
+                    view = obi_new_view_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p)
+                else :
+                    view = obi_new_view(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p)
+            elif view_to_clone is None :
+                view = obi_new_view(dms.pointer, str2bytes(view_name), NULL, line_selection_p)
+        elif not new :
+            if view_name is not None :
+                view = obi_open_view(dms.pointer, str2bytes(view_name))
+            elif view_name is None :
+                view = obi_open_view(dms.pointer, NULL)
+        
+        if view == NULL :
+            raise Exception("Error creating/opening view")
+
+        self.pointer = view
+        self.name = bytes2str(view.name)
+        
+        # go through columns to build list and open python object (TODO make separate function?)
+        self.columns = {}
+        self.columns_pp = {}
+                
+        i = 0
+        while i < view.column_count :
+            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
+            column_p = <OBIDMS_column_p> (view.columns)[i]
+            header = (column_p).header
+            
+            col_name = bytes2str(header.name)
+            col_capsule = PyCapsule_New(column_pp, NULL, NULL)   # TODO discuss
+            (self.columns_pp)[col_name] = col_capsule
+            
+            subclass = OBIDMS_column.get_subclass_type(column_p)
+            self.columns[col_name] = subclass(self, col_name)
+            
+            i+=1
+
+
+    def __repr__(self) :
+        
+        cdef str s
+        cdef OBIDMS_column column
+        cdef OBIDMS_column_p column_p
+        
+        s = self.name
+        s = s + ", " + str(self.pointer.line_count) + " lines" 
+        for column_name in self.columns :   # TODO make function in OBIDMS_column class
+            column = self.columns[column_name]
+            column_p = (column.pointer)[0]
+            s = s + "\n" + column_name + ", version " + str(column_p.header.version) + ", data type: " + column.data_type
+        return s
+        
+    
+    cpdef delete_column(self, str column_name) :
+        
+        cdef int i
+        cdef Obiview_p view
+        cdef OBIDMS_column column
+        cdef OBIDMS_column_p column_p
+        cdef OBIDMS_column_p* column_pp
+        cdef OBIDMS_column_header_p header
+        cdef str column_n
+ 
+        view = self.pointer
+ 
+        if obi_view_delete_column(view, str2bytes(column_name)) < 0 :
+            raise Exception("Problem deleting a column from a view")
+        
+        # Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
+        (self.columns).pop(column_name)
+        (self.columns_pp).pop(column_name)
+        
+        i = 0
+        while i < view.column_count :
+            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
+            column_p = <OBIDMS_column_p> (view.columns)[i]
+            header = (column_p).header
+            col_name = bytes2str(header.name)
+            col_capsule = PyCapsule_New(column_pp, NULL, NULL)
+            (self.columns_pp)[col_name] = col_capsule
+            i+=1
+
+        for column_n in self.columns :
+            (self.columns[column_n]).update_pointer()
+
+    
+    cpdef add_column(self, 
+                     str column_name, 
+                     obiversion_t version_number=-1, 
+                     str type='',
+                     index_t nb_lines=0, 
+                     index_t nb_elements_per_line=1,    # TODO 1?
+                     list elements_names=None,
+                     str avl_name="default_AVL_tree",
+                     str comments="",
+                     bint create=True   # TODO
+                     ) :
+        
+        cdef bytes column_name_b
+        cdef bytes elements_names_b
+        cdef object subclass
+        cdef OBIDMS_column_p* column_pp
+        cdef OBIDMS_column_p column_p
+        
+        column_name_b = str2bytes(column_name)
+        
+        if nb_elements_per_line > 1 :
+            elements_names_b = str2bytes(';'.join(elements_names))
+        elif nb_elements_per_line == 1 :
+            elements_names_b = column_name_b
+    
+        if type :    
+            if type == 'OBI_INT' :
+                data_type = OBI_INT
+            elif type == 'OBI_FLOAT' :
+                data_type = OBI_FLOAT
+            elif type == 'OBI_BOOL' :
+                data_type = OBI_BOOL
+            elif type == 'OBI_CHAR' :
+                data_type = OBI_CHAR
+            elif type == 'OBI_STR' :
+                data_type = OBI_STR
+            elif type == 'OBI_SEQ' :
+                data_type = OBI_SEQ
+            else :
+                raise Exception("Invalid provided data type")
+        
+        if (obi_view_add_column(self.pointer, column_name_b, version_number,     # should return pointer on column?
+                                data_type, nb_lines, nb_elements_per_line, 
+                                elements_names_b, str2bytes(avl_name), 
+                                str2bytes(comments), create) < 0) :
+            raise Exception("Problem adding a column in a view")
+        
+        # Store the column pointer
+        
+        column_pp = obi_view_get_pointer_on_column_in_view(self.pointer, column_name_b)
+        if column_pp == NULL :
+            raise Exception("Problem getting a column in a view")
+        
+        col_capsule = PyCapsule_New(column_pp, NULL, NULL)   # TODO
+        (self.columns_pp)[column_name] = col_capsule
+        
+        # Open and store the subclass
+        column_p = column_pp[0]     # TODO ugly cython dereferencing
+        subclass = OBIDMS_column.get_subclass_type(column_p)
+        (self.columns)[column_name] = subclass(self, column_name)
+                
+    
+    cpdef save_and_close(self) :
+        if (obi_save_and_close_view(self.pointer) < 0) :
+            raise Exception("Problem closing a view")
+    
+
+    def __iter__(self):
+        # iter on each line of all columns
+        
+        # Declarations
+        cdef index_t lines_used
+        cdef index_t line_nb
+        cdef OBIView_line line
+        
+        # Yield each line TODO line class
+        lines_used = (self.pointer).line_count
+        
+        for line_nb in range(lines_used) :
+            line = self[line_nb]
+            yield line
+
+
+    def __getitem__(self, object item) :
+        if type(item) == str :
+            return (self.columns)[item]
+        elif type(item) == int :     # TODO int?
+            return OBIView_line(self, item)
+
+
+    cpdef select_line(self, index_t line_nb) :
+        if obi_select_line(self.pointer, line_nb) < 0 :
+            raise Exception("Problem selecting a line")
+
+    
+    cpdef select_lines(self, list line_selection) :
+        cdef index_t* line_selection_p
+        line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
+        for i in range(len(line_selection)) :
+            line_selection_p[i] = line_selection[i]     # TODO type problem?
+        line_selection_p[len(line_selection)] = -1
+        if obi_select_lines(self.pointer, line_selection_p) < 0 :
+            raise Exception("Problem selecting a list of lines")
+    
+    
+    def __contains__(self, str column_name):
+        return (column_name in self.columns)
+    
+    
+    def __str__(self) :
+        cdef OBIView_line line
+        cdef str to_print
+        to_print = ""
+        for line in self.__iter__() :
+            to_print = to_print + str(line) + "\n"
+        return to_print
+
+#############################################
+
+cdef class OBIView_line :
+
+    def __init__(self, OBIView view, index_t line_nb) :
+        self.index = line_nb
+        self.view = view
+    
+    def __getitem__(self, str column_name) :
+        return ((self.view).columns)[column_name][self.index]
+    
+    def __setitem__(self, str column_name, object value):
+        # TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
+        cdef type value_type
+        cdef str value_obitype
+        if column_name not in self.view :
+            if value == None :
+                raise Exception("Trying to create a column from a None value (can't guess type)")
+            value_type = type(value)
+            if value_type == int :
+                value_obitype = 'OBI_INT'
+            elif value_type == float :
+                value_obitype = 'OBI_FLOAT'
+            elif value_type == bool :
+                value_obitype = 'OBI_BOOL'            
+            elif value_type == str :
+                if only_ATGC(str2bytes(value)) :    # TODO
+                    value_obitype = 'OBI_SEQ'
+                elif len(value) == 1 :
+                    value_obitype = 'OBI_CHAR'
+                elif (len(value) > 1) :
+                    value_obitype = 'OBI_STR'
+            else :
+                raise Exception("Could not guess the type of a value to create a new column")
+            self.view.add_column(column_name, type=value_obitype)
+
+        (((self.view).columns)[column_name]).set_line(self.index, value)
+
+    def __contains__(self, str column_name):
+        return (column_name in self.view)
+        
+    def __repr__(self):
+        cdef dict line
+        cdef str column_name
+        line = {}
+        for column_name in self.view.columns :
+            line[column_name] = self[column_name]
+        return str(line)
+
+##########################################
 
 cdef class OBIDMS :
     
@@ -81,310 +521,12 @@ cdef class OBIDMS :
     cpdef close(self) :
         if (obi_close_dms(self.pointer)) < 0 :
             raise Exception("Problem closing an OBIDMS")
-
-
-    cpdef dict list(self):  # TDODO This is a temporary function that will be rewritten
-    
-        # Declarations
-        cdef object p
-        cdef dict dms = {}
-        cdef str column_name
-        cdef bytes column_name_b
-        cdef str data_type
-        cdef str creation_date
-        cdef obiversion_t latest_version
-        cdef index_t line_count
-        cdef OBIDMS_column_header_p header
-        
-        p = Path(self.dms_name+'.obidms')
-
-        print("{:<30} {:<12} {:<25} {:<30} {:<40}".format('-Column name-', 
-                                                   '-Data type-', 
-                                                   '-Latest version number-', 
-                                                   '-Line count of latest version-',
-                                                   '-Creation date of latest version-'))
-        for entry in p.iterdir():
-            if entry.suffix == ".obicol":
-                column_name = entry.stem
-                column_name_b = str2bytes(column_name)
-                dms[column_name] = {}
-                header = obi_column_get_header_from_name(self.pointer, column_name_b, -1)
-                data_type = bytes2str(name_data_type(header.returned_data_type))
-                line_count = header.line_count
-                creation_date = bytes2str(obi_column_format_date(header.creation_date))
-                obi_unmap_header(header)
-                latest_version = obi_column_get_latest_version_from_name(self.pointer, column_name_b)
-                dms[column_name]['data_type'] = data_type
-                dms[column_name]['latest_version'] = latest_version
-                dms[column_name]['line_count'] = line_count
-                dms[column_name]['creation_date'] = creation_date
-                print("{:<30} {:<12} {:<25} {:<30} {:<40}".format(column_name, data_type, latest_version, line_count, creation_date))
-
-        return dms
      
-     
-    cpdef OBIDMS_column open_column(self,
-                                    str column_name,
-                                    bint create=False, 
-                                    bint clone=False, bint clone_data=True,
-                                    bint referring=False,
-                                    obiversion_t version_number=-1, 
-                                    str type='',
-                                    index_t nb_lines=0, 
-                                    index_t nb_elements_per_line=0, 
-                                    list elements_names=None,
-                                    str avl_name="default_AVL_tree",
-                                    str comments=""):
-        
-        # Declarations
-        cdef OBIDMS_column column
-        cdef object subclass        # TODO object?
-        cdef bytes column_name_b
-        cdef OBIDMS_column_header_p header
-        cdef OBIType_t data_type
-                
-        header = NULL
-        
-        # Format the character string to send to C function
-        column_name_b = str2bytes(column_name)
-        
-        # Get the header of the latest version of the column if 
-        # some needed informations are not provided
-        if ((not type or not nb_elements_per_line) and not create) :
-            header = obi_column_get_header_from_name(self.pointer, column_name_b, version_number)
-            
-        # Get the data type if not provided
-        if not type :
-            if create :
-                raise Exception("A data type must be specified")
-            else :
-                data_type = header.returned_data_type
-        else :
-            if type == 'OBI_INT' :
-                data_type = OBI_INT
-            elif type == 'OBI_FLOAT' :
-                data_type = OBI_FLOAT
-            elif type == 'OBI_BOOL' :
-                data_type = OBI_BOOL
-            elif type == 'OBI_CHAR' :
-                data_type = OBI_CHAR
-            elif type == 'OBI_STR' :
-                data_type = OBI_STR
-            elif type == 'OBI_SEQ' :
-                data_type = OBI_SEQ
-            else :
-                raise Exception("Invalid provided data type")
-
-        # Get the number of elements per line if not provided and needed
-        if not nb_elements_per_line :
-            if create : # Set to one if not provided (default value)
-                nb_elements_per_line = 1
-            else :
-                nb_elements_per_line = header.returned_nb_elements_per_line
-                if nb_elements_per_line > 1 :
-                    elements_names = bytes2str(header.elements_names).split(';')
-
-        if header != NULL :
-            obi_unmap_header(header)        # TODO check if error? but C will already warn and there's nothing to do
-        
-        # Open the column with the right subclass depending on the data type, the mode 
-        # (read-only or writable) and whether there are multiple elements per line or not  
-        if data_type == OBI_INT :
-            if (create or clone) :
-                if nb_elements_per_line == 1 :
-                    subclass = OBIDMS_column_int_writable
-                else :
-                    subclass = OBIDMS_column_int_multi_elts_writable
-            else :
-                if nb_elements_per_line == 1 :
-                    subclass = OBIDMS_column_int
-                else :
-                    subclass = OBIDMS_column_int_multi_elts
-        elif data_type == OBI_FLOAT :
-            if (create or clone) :
-                if nb_elements_per_line == 1 :
-                    subclass = OBIDMS_column_float_writable
-                else :
-                    subclass = OBIDMS_column_float_multi_elts_writable
-            else :
-                if nb_elements_per_line == 1 :
-                    subclass = OBIDMS_column_float
-                else :
-                    subclass = OBIDMS_column_float_multi_elts
-        elif data_type == OBI_BOOL :
-            if (create or clone) :
-                if nb_elements_per_line == 1 :
-                    subclass = OBIDMS_column_bool_writable
-                else :
-                    subclass = OBIDMS_column_bool_multi_elts_writable
-            else :
-                if nb_elements_per_line == 1 :
-                    subclass = OBIDMS_column_bool
-                else :
-                    subclass = OBIDMS_column_bool_multi_elts
-        elif data_type == OBI_CHAR :
-            if (create or clone) :
-                if nb_elements_per_line == 1 :
-                    subclass = OBIDMS_column_char_writable
-                else :
-                    subclass = OBIDMS_column_char_multi_elts_writable
-            else :
-                if nb_elements_per_line == 1 :
-                    subclass = OBIDMS_column_char
-                else :
-                    subclass = OBIDMS_column_char_multi_elts
-        elif data_type == OBI_STR :
-            if (create or clone) :
-                if nb_elements_per_line == 1 :
-                    subclass = OBIDMS_column_str_writable
-                else :
-                    subclass = OBIDMS_column_str_multi_elts_writable
-            else :
-                if nb_elements_per_line == 1 :
-                    subclass = OBIDMS_column_str
-                else :
-                    subclass = OBIDMS_column_str_multi_elts
-        elif data_type == OBI_SEQ :
-            if (create or clone) :
-                if nb_elements_per_line == 1 :
-                    subclass = OBIDMS_column_seq_writable
-                else :
-                    subclass = OBIDMS_column_seq_multi_elts_writable
-            else :
-                if nb_elements_per_line == 1 :
-                    subclass = OBIDMS_column_seq
-                else :
-                    subclass = OBIDMS_column_seq_multi_elts
-        else :
-            raise Exception("Problem with the data type")
-            
-        column = subclass(self, column_name, 
-                          create, clone, clone_data,
-                          referring, 
-                          version_number, data_type, 
-                          nb_lines, nb_elements_per_line, 
-                          elements_names, avl_name, 
-                          comments)
-
-        return column
-
-
-
-cdef class OBIDMS_column :
-
-    # Should only be initialized through a subclass
-    def __init__(self, 
-                 OBIDMS dms, 
-                 str column_name,
-                 bint create, 
-                 bint clone, bint clone_data,
-                 bint referring,
-                 obiversion_t version_number, 
-                 OBIType_t type,
-                 index_t nb_lines, 
-                 index_t nb_elements_per_line, 
-                 list elements_names,
-                 str avl_name,
-                 str comments):
-        
-        # Declarations
-        cdef bytes column_name_b
-        cdef bytes dms_name_b
-        cdef bytes avl_name_b
-        cdef bytes elements_names_b
-        cdef bytes comments_b
-       
-        # Fill structure
-        self.dms = dms
-        self.data_type = bytes2str(name_data_type(type))
-        self.column_name = column_name
-        self.nb_elements_per_line = nb_elements_per_line
-        self.elements_names = elements_names
-        
-        # Format the character strings to send them to C functions
-        column_name_b = str2bytes(column_name)
-        dms_name_b = str2bytes(self.dms.dms_name)
-        avl_name_b = str2bytes(avl_name)
-        comments_b = str2bytes(comments)
-        
-        # Create, clone or open column
-        if create :
-            if elements_names == None :  
-                elements_names_b = column_name_b
-            else :
-                elements_names_b = str2bytes(";".join(elements_names))
-            self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, 
-                                             nb_lines, nb_elements_per_line, 
-                                             elements_names_b, avl_name_b, comments_b,
-                                             referring)
-        else :
-            if clone :
-                self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, referring, clone_data)
-            elif referring :
-                self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, referring, False)
-                referred_column_pointer = self.pointer.referred_column
-            else :
-                self.pointer = obi_open_column(self.dms.pointer, column_name_b, version_number)
-
-
-    def __len__(self):
-        return self.pointer.header.lines_used
     
-    
+    cpdef OBIView open_view(self, str view_name) :
-    def __sizeof__(self):
+        return OBIView(self, view_name)
-        return (self.pointer.header.header_size + self.pointer.header.data_size)
+  
-    
+  
-    
+    cpdef OBIView new_view(self, str view_name, object view_to_clone=None, list line_selection=None) :
-    def __iter__(self):
+        return OBIView(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection)
-    
-        # Declarations
-        cdef index_t lines_used
-        cdef index_t line_nb
-        
-        # Yield each line
-        lines_used = self.pointer.header.lines_used
-        for line_nb in range(lines_used):
-            yield self.get_line(line_nb)
 
-
-    def __setitem__(self, index_t line_nb, object value):
-        self.set_line(line_nb, value)
-
-
-    def __getitem__(self, index_t line_nb):
-        return self.get_line(line_nb)
-
-
-#    cpdef object get_item(self, index_t line_nb, str element_name):           TODO
-#        raise NotImplementedError
-
-
-#    cpdef set_item(self, index_t line_nb, str element_name, object value):    TODO
-#        raise NotImplementedError
-
-    cpdef grep_line(self, index_t line_nb):
-         if obi_grep_line(self.pointer, line_nb) < 0 :
-             raise Exception("Error grepping line")
-    
-    cpdef list get_elements_names(self):
-        return self.elements_names
-
-             
-    cpdef str get_data_type(self):
-        return self.data_type
-    
-    
-    cpdef index_t get_nb_lines_used(self):
-        return self.pointer.header.lines_used
-    
-    
-    cpdef str get_creation_date(self):
-        return bytes2str(obi_column_format_date(self.pointer.header.creation_date))
-    
-    cpdef str get_comments(self):
-        return bytes2str(self.pointer.header.comments)
-    
-    cpdef close(self):
-        raise NotImplementedError
-   
-   

python/obitools3/obidms/_obidmscolumn_bool.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidmscolumn_bool.c
 ../../../src/obidmscolumn_bool.h
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h

python/obitools3/obidms/_obidmscolumn_bool.pxd

@@ -1,25 +1,14 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obibool_t, index_t
+from .capi.obitypes cimport index_t
-from ._obidms       cimport OBIDMS_column
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_bool(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
 
-cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):     
+cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
-    cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
     cpdef object get_item(self, index_t line_nb, str element_name)
     cpdef object get_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, obibool_t value)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)
-    cpdef set_line(self, index_t line_nb, object values)
-
-cdef class OBIDMS_column_bool_multi_elts_writable(OBIDMS_column_bool_multi_elts):
-    cpdef set_item(self, index_t line_nb, str element_name, obibool_t value)
-    cpdef set_line(self, index_t line_nb, object values)
-    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_bool.pyx

@@ -1,13 +1,12 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_close_column,\
+from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
-                                obi_truncate_and_close_column, \
+                                obi_column_get_obibool_with_elt_name_in_view, \
-                                obi_column_get_obibool_with_elt_name, \
+                                obi_column_get_obibool_with_elt_idx_in_view, \
-                                obi_column_get_obibool_with_elt_idx, \
+                                obi_column_set_obibool_with_elt_name_in_view, \
-                                obi_column_set_obibool_with_elt_name, \
+                                obi_column_set_obibool_with_elt_idx_in_view
-                                obi_column_set_obibool_with_elt_idx
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIBool_NA
+from .capi.obitypes     cimport OBIBool_NA, obibool_t
 
 from obitools3.utils cimport str2bytes
 
@@ -19,7 +18,7 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb):
         cdef obibool_t value
         cdef object result
-        value = obi_column_get_obibool_with_elt_idx(self.pointer, line_nb, 0)
+        value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
         if obi_errno > 0 :
             raise IndexError(line_nb)
         if value == OBIBool_NA :
@@ -27,32 +26,20 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
         else :
             result = PyBool_FromLong(value)
         return result
-
-    cpdef set_line(self, index_t line_nb, object value):
-        raise Exception("Column is read-only")
     
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
-
-cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):     
-
     cpdef set_line(self, index_t line_nb, object value):
-        if obi_column_set_obibool_with_elt_idx(self.pointer, line_nb, 0, <obibool_t> value) < 0:
+        if value is None :
+            value = OBIBool_NA
+        if obi_column_set_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obibool_t> value) < 0:
             raise Exception("Problem setting a value in a column")
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 
-
+cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
-cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
 
     cpdef object get_item(self, index_t line_nb, str element_name):
         cdef obibool_t value
         cdef object result
-        value = obi_column_get_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = obi_column_get_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
         if value == OBIBool_NA :
@@ -63,42 +50,29 @@ cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
     
     cpdef object get_line(self, index_t line_nb) :
         cdef obibool_t value
-        cdef object result
+        cdef object value_in_result
+        cdef dict result
         cdef index_t i
         cdef bint all_NA
         result = {}
         all_NA = True
         for i in range(self.nb_elements_per_line) :
-            value = obi_column_get_obibool_with_elt_idx(self.pointer, line_nb, i)
+            value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
             if obi_errno > 0 :
-                raise IndexError(line_nb)           
+                raise IndexError(line_nb)
-            result[self.elements_names[i]] = PyBool_FromLong(value)
+            if value == OBIBool_NA :
-            if all_NA and (value != OBIBool_NA) :
+                value_in_result = None
+            else :
+                value_in_result = PyBool_FromLong(value)   
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
                 all_NA = False
         if all_NA :
             result = None
         return result
 
-    cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
-        raise Exception("Column is read-only")
+        if value is None :
-
+            value = OBIBool_NA
-    cpdef set_line(self, index_t line_nb, object values):
+        if obi_column_set_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
-        raise Exception("Column is read-only")
-
-
-cdef class OBIDMS_column_bool_multi_elts_writable(OBIDMS_column_bool_multi_elts):     
-
-    cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
-        if obi_column_set_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
             raise Exception("Problem setting a value in a column")
-    
-    cpdef set_line(self, index_t line_nb, object values):
-        cdef obibool_t value
-        for element_name in values :
-            value = <obibool_t> values[element_name]
-            self.set_item(line_nb, element_name, value)
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-

python/obitools3/obidms/_obidmscolumn_char.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidmscolumn_char.c
 ../../../src/obidmscolumn_char.h
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h

python/obitools3/obidms/_obidmscolumn_char.pxd

@@ -1,25 +1,14 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obichar_t, index_t
+from .capi.obitypes cimport index_t
-from ._obidms       cimport OBIDMS_column
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_char(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
 
-cdef class OBIDMS_column_char_writable(OBIDMS_column_char):     
+cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
-    cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
     cpdef object get_item(self, index_t line_nb, str element_name)
     cpdef object get_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, str value)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)
-    cpdef set_line(self, index_t line_nb, object values)
-
-cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts):
-    cpdef set_item(self, index_t line_nb, str element_name, str value)
-    cpdef set_line(self, index_t line_nb, object values)
-    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_char.pyx

@@ -1,13 +1,12 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_close_column,\
+from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
-                                obi_truncate_and_close_column, \
+                                obi_column_get_obichar_with_elt_name_in_view, \
-                                obi_column_get_obichar_with_elt_name, \
+                                obi_column_get_obichar_with_elt_idx_in_view, \
-                                obi_column_get_obichar_with_elt_idx, \
+                                obi_column_set_obichar_with_elt_name_in_view, \
-                                obi_column_set_obichar_with_elt_name, \
+                                obi_column_set_obichar_with_elt_idx_in_view
-                                obi_column_set_obichar_with_elt_idx
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIChar_NA
+from .capi.obitypes     cimport OBIChar_NA, obichar_t
 
 from obitools3.utils cimport str2bytes, bytes2str
 
@@ -17,7 +16,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb):
         cdef obichar_t value
         cdef object result
-        value = obi_column_get_obichar_with_elt_idx(self.pointer, line_nb, 0)
+        value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
         if obi_errno > 0 :
             raise IndexError(line_nb)
         if value == OBIChar_NA :
@@ -27,30 +26,18 @@ cdef class OBIDMS_column_char(OBIDMS_column):
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
-        raise Exception("Column is read-only")
+        if value is None :
-    
+            value = OBIChar_NA
-    cpdef close(self):
+        if obi_column_set_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, str2bytes(value)[0]) < 0:
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
-
-cdef class OBIDMS_column_char_writable(OBIDMS_column_char):     
-
-    cpdef set_line(self, index_t line_nb, object value):
-        if obi_column_set_obichar_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)[0]) < 0:
             raise Exception("Problem setting a value in a column")
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 
-
+cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
-cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
 
     cpdef object get_item(self, index_t line_nb, str element_name):
         cdef obichar_t value
         cdef object result
-        value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = obi_column_get_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
         if value == OBIChar_NA :
@@ -58,45 +45,33 @@ cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
         else :
             result = bytes2str(value)
         return result
-    
+
     cpdef object get_line(self, index_t line_nb) :
         cdef obichar_t value
-        cdef object result
+        cdef object value_in_result
+        cdef dict result
         cdef index_t i
         cdef bint all_NA
         result = {}
         all_NA = True
         for i in range(self.nb_elements_per_line) :
-            value = obi_column_get_obichar_with_elt_idx(self.pointer, line_nb, i)
+            value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
             if obi_errno > 0 :
-                raise IndexError(line_nb)           
+                raise IndexError(line_nb)
-            result[self.elements_names[i]] = bytes2str(value)
+            if value == OBIChar_NA :
-            if all_NA and (value != OBIChar_NA) :
+                value_in_result = None
+            else :
+                value_in_result = bytes2str(value)   
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
                 all_NA = False
         if all_NA :
             result = None
         return result
 
-    cpdef set_item(self, index_t line_nb, str element_name, str value):
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
-        raise Exception("Column is read-only")
+        if value is None :
-
+            value = OBIChar_NA
-    cpdef set_line(self, index_t line_nb, object values):
+        if obi_column_set_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
-        raise Exception("Column is read-only")
-
-
-cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts):     
-
-    cpdef set_item(self, index_t line_nb, str element_name, str value):
-        if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
             raise Exception("Problem setting a value in a column")
-    
-    cpdef set_line(self, index_t line_nb, object values):
-        cdef str value
-        for element_name in values :
-            value = values[element_name]
-            self.set_item(line_nb, element_name, value)
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 

python/obitools3/obidms/_obidmscolumn_float.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidmscolumn_float.c
 ../../../src/obidmscolumn_float.h
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h

python/obitools3/obidms/_obidmscolumn_float.pxd

@@ -1,25 +1,14 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obifloat_t, index_t
+from .capi.obitypes cimport index_t
-from ._obidms       cimport OBIDMS_column
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_float(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
 
-cdef class OBIDMS_column_float_writable(OBIDMS_column_float):     
+cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
-    cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
     cpdef object get_item(self, index_t line_nb, str element_name)
     cpdef object get_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)
-    cpdef set_line(self, index_t line_nb, object values)
-
-cdef class OBIDMS_column_float_multi_elts_writable(OBIDMS_column_float_multi_elts):
-    cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value)
-    cpdef set_line(self, index_t line_nb, object values)
-    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_float.pyx

@@ -1,13 +1,12 @@
 #cython: language_level=3
 
-from .capi.obidmscolumn cimport obi_close_column,\
+from .capi.obidmscolumn cimport obi_truncate_and_close_column,\
-                                obi_truncate_and_close_column, \
+                                obi_column_get_obifloat_with_elt_name_in_view, \
-                                obi_column_get_obifloat_with_elt_name, \
+                                obi_column_get_obifloat_with_elt_idx_in_view, \
-                                obi_column_get_obifloat_with_elt_idx, \
+                                obi_column_set_obifloat_with_elt_name_in_view, \
-                                obi_column_set_obifloat_with_elt_name, \
+                                obi_column_set_obifloat_with_elt_idx_in_view
-                                obi_column_set_obifloat_with_elt_idx
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIFloat_NA
+from .capi.obitypes     cimport OBIFloat_NA, obifloat_t
 
 from obitools3.utils cimport str2bytes
 
@@ -17,7 +16,7 @@ cdef class OBIDMS_column_float(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb):
         cdef obifloat_t value
         cdef object result
-        value = obi_column_get_obifloat_with_elt_idx(self.pointer, line_nb, 0)
+        value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
         if obi_errno > 0 :
             raise IndexError(line_nb)
         if value == OBIFloat_NA :
@@ -27,30 +26,18 @@ cdef class OBIDMS_column_float(OBIDMS_column):
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
-        raise Exception("Column is read-only")
+        if value is None :
-    
+            value = OBIFloat_NA
-    cpdef close(self):
+        if obi_column_set_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obifloat_t> value) < 0:
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
-
-cdef class OBIDMS_column_float_writable(OBIDMS_column_float):     
-
-    cpdef set_line(self, index_t line_nb, object value):
-        if obi_column_set_obifloat_with_elt_idx(self.pointer, line_nb, 0, <obifloat_t> value) < 0:
             raise Exception("Problem setting a value in a column")
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 
-
+cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
-cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
 
     cpdef object get_item(self, index_t line_nb, str element_name):
         cdef obifloat_t value
         cdef object result
-        value = obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = obi_column_get_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
         if value == OBIFloat_NA :
@@ -58,46 +45,33 @@ cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
         else :
             result = <double> value
         return result
-    
+
     cpdef object get_line(self, index_t line_nb) :
         cdef obifloat_t value
-        cdef object result
+        cdef object value_in_result
+        cdef dict result
         cdef index_t i
         cdef bint all_NA
         result = {}
         all_NA = True
         for i in range(self.nb_elements_per_line) :
-            value = obi_column_get_obifloat_with_elt_idx(self.pointer, line_nb, i)
+            value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
             if obi_errno > 0 :
-                raise IndexError(line_nb)           
+                raise IndexError(line_nb)
-            result[self.elements_names[i]] = <double> value
+            if value == OBIFloat_NA :
-            if all_NA and (value != OBIFloat_NA) :
+                value_in_result = None
+            else :
+                value_in_result = <double> value
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
                 all_NA = False
         if all_NA :
             result = None
         return result
-
+   
-    cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value):
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
-        raise Exception("Column is read-only")
+        if value is None :
-
+            value = OBIFloat_NA
-    cpdef set_line(self, index_t line_nb, object values):
+        if obi_column_set_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obifloat_t> value) < 0:
-        raise Exception("Column is read-only")
-
-
-cdef class OBIDMS_column_float_multi_elts_writable(OBIDMS_column_float_multi_elts):     
-
-    cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value):
-        if obi_column_set_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
             raise Exception("Problem setting a value in a column")
-    
-    cpdef set_line(self, index_t line_nb, object values):
-        cdef obifloat_t value
-        for element_name in values :
-            value = <obifloat_t> values[element_name]
-            self.set_item(line_nb, element_name, value)
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
  

python/obitools3/obidms/_obidmscolumn_int.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidmscolumn_int.c
 ../../../src/obidmscolumn_int.h
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h

python/obitools3/obidms/_obidmscolumn_int.pxd

@@ -1,25 +1,14 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obiint_t, index_t
+from .capi.obitypes cimport index_t
-from ._obidms       cimport OBIDMS_column
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_int(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
 
-cdef class OBIDMS_column_int_writable(OBIDMS_column_int):     
+cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
-    cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
     cpdef object get_item(self, index_t line_nb, str element_name)
     cpdef object get_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, obiint_t value)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)
-    cpdef set_line(self, index_t line_nb, object values)
-
-cdef class OBIDMS_column_int_multi_elts_writable(OBIDMS_column_int_multi_elts):
-    cpdef set_item(self, index_t line_nb, str element_name, obiint_t value)
-    cpdef set_line(self, index_t line_nb, object values)
-    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_int.pyx

@@ -1,13 +1,12 @@
 #cython: language_level=3
 
-from .capi.obidmscolumn cimport obi_close_column,\
+from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
-                                obi_truncate_and_close_column, \
+                                obi_column_get_obiint_with_elt_name_in_view, \
-                                obi_column_get_obiint_with_elt_name, \
+                                obi_column_get_obiint_with_elt_idx_in_view, \
-                                obi_column_get_obiint_with_elt_idx, \
+                                obi_column_set_obiint_with_elt_name_in_view, \
-                                obi_column_set_obiint_with_elt_name, \
+                                obi_column_set_obiint_with_elt_idx_in_view
-                                obi_column_set_obiint_with_elt_idx
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIInt_NA
+from .capi.obitypes     cimport OBIInt_NA, obiint_t
 
 from obitools3.utils cimport str2bytes
 
@@ -19,7 +18,7 @@ cdef class OBIDMS_column_int(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb):
         cdef obiint_t value
         cdef object result
-        value = obi_column_get_obiint_with_elt_idx(self.pointer, line_nb, 0)
+        value = obi_column_get_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
         if obi_errno > 0 :
             raise IndexError(line_nb)
         if value == OBIInt_NA :
@@ -27,32 +26,20 @@ cdef class OBIDMS_column_int(OBIDMS_column):
         else :
             result = PyInt_FromLong(value)
         return result
-
+            
     cpdef set_line(self, index_t line_nb, object value):
-        raise Exception("Column is read-only")
+        if value is None :
-    
+            value = OBIInt_NA
-    cpdef close(self):
+        if obi_column_set_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obiint_t> value) < 0:
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
-
-cdef class OBIDMS_column_int_writable(OBIDMS_column_int):     
-
-    cpdef set_line(self, index_t line_nb, object value):
-        if obi_column_set_obiint_with_elt_idx(self.pointer, line_nb, 0, <obiint_t> value) < 0:
             raise Exception("Problem setting a value in a column")
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 
-
+cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
-cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
 
     cpdef object get_item(self, index_t line_nb, str element_name):
         cdef obiint_t value
         cdef object result
-        value = obi_column_get_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = obi_column_get_obiint_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
         if value == OBIInt_NA :
@@ -63,42 +50,30 @@ cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
     
     cpdef object get_line(self, index_t line_nb) :
         cdef obiint_t value
-        cdef object result
+        cdef object value_in_result
+        cdef dict result
         cdef index_t i
         cdef bint all_NA
         result = {}
         all_NA = True
         for i in range(self.nb_elements_per_line) :
-            value = obi_column_get_obiint_with_elt_idx(self.pointer, line_nb, i)
+            value = obi_column_get_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
             if obi_errno > 0 :
-                raise IndexError(line_nb)           
+                raise IndexError(line_nb)
-            result[self.elements_names[i]] = PyInt_FromLong(value)
+            if value == OBIInt_NA :
-            if all_NA and (value != OBIInt_NA) :
+                value_in_result = None
+            else :
+                value_in_result = PyInt_FromLong(value)
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
                 all_NA = False
         if all_NA :
-            result = None
+            result = None   # TODO discuss
         return result
 
-    cpdef set_item(self, index_t line_nb, str element_name, obiint_t value):
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
-        raise Exception("Column is read-only")
+        if value is None :
-
+            value = OBIInt_NA
-    cpdef set_line(self, index_t line_nb, object values):
+        if obi_column_set_obiint_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obiint_t> value) < 0:
-        raise Exception("Column is read-only")
-
-
-cdef class OBIDMS_column_int_multi_elts_writable(OBIDMS_column_int_multi_elts):     
-
-    cpdef set_item(self, index_t line_nb, str element_name, obiint_t value):
-        if obi_column_set_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
             raise Exception("Problem setting a value in a column")
-    
-    cpdef set_line(self, index_t line_nb, object values):
-        cdef obiint_t value
-        for element_name in values :
-            value = <obiint_t> values[element_name]
-            self.set_item(line_nb, element_name, value)
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 

python/obitools3/obidms/_obidmscolumn_seq.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidmscolumn_seq.c
 ../../../src/obidmscolumn_seq.h
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h

python/obitools3/obidms/_obidmscolumn_seq.pxd

@@ -1,25 +1,14 @@
 #cython: language_level=3
 
 from .capi.obitypes cimport index_t
-from ._obidms       cimport OBIDMS_column
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_seq(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
 
-cdef class OBIDMS_column_seq_writable(OBIDMS_column_seq):     
+cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
-    cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_seq_multi_elts(OBIDMS_column_seq):
     cpdef object get_item(self, index_t line_nb, str element_name)
     cpdef object get_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, str value)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)
-    cpdef set_line(self, index_t line_nb, object values)
-
-cdef class OBIDMS_column_seq_multi_elts_writable(OBIDMS_column_seq_multi_elts):
-    cpdef set_item(self, index_t line_nb, str element_name, str value)
-    cpdef set_line(self, index_t line_nb, object values)
-    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_seq.pyx

@@ -1,13 +1,12 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_close_column,\
+from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
-                                obi_truncate_and_close_column, \
+                                obi_column_get_obiseq_with_elt_name_in_view, \
-                                obi_column_get_obiseq_with_elt_name, \
+                                obi_column_get_obiseq_with_elt_idx_in_view, \
-                                obi_column_get_obiseq_with_elt_idx, \
+                                obi_column_set_obiseq_with_elt_name_in_view, \
-                                obi_column_set_obiseq_with_elt_name, \
+                                obi_column_set_obiseq_with_elt_idx_in_view
-                                obi_column_set_obiseq_with_elt_idx
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIIdx_NA, const_char_p
+from .capi.obitypes     cimport OBISeq_NA, const_char_p
 
 from obitools3.utils cimport str2bytes, bytes2str
 
@@ -17,87 +16,68 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb):
         cdef bytes value
         cdef object result
-        value = <bytes> obi_column_get_obiseq_with_elt_idx(self.pointer, line_nb, 0)
+        value = <bytes> obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
         if obi_errno > 0 :
             raise IndexError(line_nb)
-        if value == OBIIdx_NA :
+        if value == OBISeq_NA :     # TODO
             result = None
         else :
             result = bytes2str(value)
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
-        raise Exception("Column is read-only")
+        cdef bytes value_b
-    
+        if value is None :
-    cpdef close(self):
+            value_b = OBISeq_NA
-        if obi_close_column(self.pointer) < 0 :
+        else :
-            raise Exception("Problem closing a column")
+            value_b = str2bytes(value)
-
+        if obi_column_set_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, value_b) < 0:
-
-cdef class OBIDMS_column_seq_writable(OBIDMS_column_seq):     
-
-    cpdef set_line(self, index_t line_nb, object value):
-        if obi_column_set_obiseq_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)) < 0:
             raise Exception("Problem setting a value in a column")
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 
-
+cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
-cdef class OBIDMS_column_seq_multi_elts(OBIDMS_column_seq):
 
     cpdef object get_item(self, index_t line_nb, str element_name):
         cdef bytes value
         cdef object result
-        value = <bytes> obi_column_get_obiseq_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = <bytes> obi_column_get_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
-        if value == OBIIdx_NA :
+        if value == OBISeq_NA :
             result = None
         else :
             result = bytes2str(value)
         return result
-    
+
     cpdef object get_line(self, index_t line_nb) :
         cdef bytes value
-        cdef object result
+        cdef object value_in_result
+        cdef dict result
         cdef index_t i
         cdef bint all_NA
         result = {}
         all_NA = True
         for i in range(self.nb_elements_per_line) :
-            value = <bytes> obi_column_get_obiseq_with_elt_idx(self.pointer, line_nb, i)
+            value = <bytes> obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
             if obi_errno > 0 :
-                raise IndexError(line_nb)           
+                raise IndexError(line_nb)
-            result[self.elements_names[i]] = bytes2str(value)
+            if value == OBISeq_NA :
-            if all_NA and (value != OBIIdx_NA) :
+                value_in_result = None
+            else :
+                value_in_result = bytes2str(value)    
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
                 all_NA = False
         if all_NA :
             result = None
         return result
 
-    cpdef set_item(self, index_t line_nb, str element_name, str value):
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
-        raise Exception("Column is read-only")
+        cdef bytes value_b
-
+        if value is None :
-    cpdef set_line(self, index_t line_nb, object values):
+            value_b = OBISeq_NA
-        raise Exception("Column is read-only")
+        else :
-
+            value_b = str2bytes(value)
-
+        if obi_column_set_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
-cdef class OBIDMS_column_seq_multi_elts_writable(OBIDMS_column_seq_multi_elts):     
-
-    cpdef set_item(self, index_t line_nb, str element_name, str value):
-        if obi_column_set_obiseq_with_elt_name(self.pointer, line_nb, str2bytes(element_name), str2bytes(value)) < 0:
             raise Exception("Problem setting a value in a column")
     
-    cpdef set_line(self, index_t line_nb, object values):
-        cdef str value
-        for element_name in values :
-            value = values[element_name]
-            self.set_item(line_nb, element_name, value)
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
- 

python/obitools3/obidms/_obidmscolumn_str.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidmscolumn_str.c
 ../../../src/obidmscolumn_str.h
+../../../src/obiview.h
+../../../src/obiview.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h

python/obitools3/obidms/_obidmscolumn_str.pxd

@@ -1,25 +1,14 @@
 #cython: language_level=3
 
 from .capi.obitypes cimport index_t
-from ._obidms       cimport OBIDMS_column
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_str(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
 
-cdef class OBIDMS_column_str_writable(OBIDMS_column_str):     
+cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
-    cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
     cpdef object get_item(self, index_t line_nb, str element_name)
     cpdef object get_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, str value)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)
-    cpdef set_line(self, index_t line_nb, object values)
-
-cdef class OBIDMS_column_str_multi_elts_writable(OBIDMS_column_str_multi_elts):
-    cpdef set_item(self, index_t line_nb, str element_name, str value)
-    cpdef set_line(self, index_t line_nb, object values)
-    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_str.pyx

@@ -1,13 +1,12 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_close_column,\
+from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
-                                obi_truncate_and_close_column, \
+                                obi_column_get_obistr_with_elt_name_in_view, \
-                                obi_column_get_obistr_with_elt_name, \
+                                obi_column_get_obistr_with_elt_idx_in_view, \
-                                obi_column_get_obistr_with_elt_idx, \
+                                obi_column_set_obistr_with_elt_name_in_view, \
-                                obi_column_set_obistr_with_elt_name, \
+                                obi_column_set_obistr_with_elt_idx_in_view
-                                obi_column_set_obistr_with_elt_idx
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIIdx_NA, const_char_p
+from .capi.obitypes     cimport OBIStr_NA, const_char_p
 
 from obitools3.utils cimport str2bytes, bytes2str
 
@@ -17,87 +16,68 @@ cdef class OBIDMS_column_str(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb):
         cdef bytes value
         cdef object result
-        value = <bytes> obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, 0)
+        value = <bytes> obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
         if obi_errno > 0 :
             raise IndexError(line_nb)
-        if value == OBIIdx_NA :
+        if value == OBIStr_NA :     # TODO
             result = None
         else :
             result = bytes2str(value)
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
-        raise Exception("Column is read-only")
+        cdef bytes value_b
-    
+        if value is None :
-    cpdef close(self):
+            value_b = OBIStr_NA
-        if obi_close_column(self.pointer) < 0 :
+        else :
-            raise Exception("Problem closing a column")
+            value_b = str2bytes(value)
-
+        if obi_column_set_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, value_b) < 0:
-
-cdef class OBIDMS_column_str_writable(OBIDMS_column_str):     
-
-    cpdef set_line(self, index_t line_nb, object value):
-        if obi_column_set_obistr_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)) < 0:
             raise Exception("Problem setting a value in a column")
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 
-
+cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
-cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
 
     cpdef object get_item(self, index_t line_nb, str element_name):
         cdef bytes value
         cdef object result
-        value = <bytes> obi_column_get_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = <bytes> obi_column_get_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
-        if value == OBIIdx_NA :
+        if value == OBIStr_NA :
             result = None
         else :
             result = bytes2str(value)
         return result
-    
+
     cpdef object get_line(self, index_t line_nb) :
         cdef bytes value
-        cdef object result
+        cdef object value_in_result
+        cdef dict result
         cdef index_t i
         cdef bint all_NA
         result = {}
         all_NA = True
         for i in range(self.nb_elements_per_line) :
-            value = <bytes> obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, i)
+            value = <bytes> obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
             if obi_errno > 0 :
-                raise IndexError(line_nb)           
+                raise IndexError(line_nb)
-            result[self.elements_names[i]] = bytes2str(value)
+            if value == OBIStr_NA :
-            if all_NA and (value != OBIIdx_NA) :
+                value_in_result = None
+            else :
+                value_in_result = bytes2str(value)    
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
                 all_NA = False
         if all_NA :
             result = None
         return result
 
-    cpdef set_item(self, index_t line_nb, str element_name, str value):
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
-        raise Exception("Column is read-only")
+        cdef bytes value_b
-
+        if value is None :
-    cpdef set_line(self, index_t line_nb, object values):
+            value_b = OBIStr_NA
-        raise Exception("Column is read-only")
+        else :
-
+            value_b = str2bytes(value)
-
+        if obi_column_set_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
-cdef class OBIDMS_column_str_multi_elts_writable(OBIDMS_column_str_multi_elts):     
-
-    cpdef set_item(self, index_t line_nb, str element_name, str value):
-        if obi_column_set_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name), str2bytes(value)) < 0:
             raise Exception("Problem setting a value in a column")
     
-    cpdef set_line(self, index_t line_nb, object values):
-        cdef str value
-        for element_name in values :
-            value = values[element_name]
-            self.set_item(line_nb, element_name, value)
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
- 

python/obitools3/obidms/capi/obidmscolumn.pxd

@@ -19,16 +19,13 @@ cdef extern from "obidmscolumn.h" nogil:
         size_t          data_size
         index_t         line_count
         index_t         lines_used
-        index_t         returned_nb_elements_per_line
+        index_t         nb_elements_per_line
-        index_t         stored_nb_elements_per_line
         const_char_p    elements_names
         OBIType_t       returned_data_type
         OBIType_t       stored_data_type
         time_t          creation_date
         obiversion_t    version
         obiversion_t    cloned_from
-        bint            referring
-        obiversion_t    referred_column_version
         const_char_p    name
         const_char_p    avl_name
         const_char_p    comments
@@ -36,9 +33,10 @@ cdef extern from "obidmscolumn.h" nogil:
     ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
 
     struct OBIDMS_column_t:
+        OBIDMS_p               dms
         OBIDMS_column_header_p header
-        OBIDMS_column_t*       referred_column 
+        bint                   writable
-
+        
     ctypedef OBIDMS_column_t* OBIDMS_column_p
 
     OBIDMS_column_p obi_create_column(OBIDMS_p dms, 
@@ -48,8 +46,7 @@ cdef extern from "obidmscolumn.h" nogil:
                                       index_t nb_elements_per_line, 
                                       const_char_p elements_names,
                                       const_char_p avl_name,
-                                      const_char_p comments,
+                                      const_char_p comments)
-                                      bint referring)
                 
     OBIDMS_column_p obi_open_column(OBIDMS_p dms, 
                                     const_char_p column_name, 
@@ -58,9 +55,9 @@ cdef extern from "obidmscolumn.h" nogil:
     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 referring,
                                      bint clone_data)
     
     int obi_truncate_and_close_column(OBIDMS_column_p column)
@@ -76,10 +73,34 @@ cdef extern from "obidmscolumn.h" nogil:
         
     char* obi_column_format_date(time_t date)
 
-    int obi_grep_line(OBIDMS_column_p referring_column, index_t line_to_grep)
+    int obi_select(OBIDMS_column_p line_selection_column, index_t line_to_grep)
+
+
+from ..capi.obiview  cimport Obiview_p  # TODO
 
-    
 cdef extern from "obidmscolumn_int.h" nogil:
+    int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    const_char_p element_name, 
+                                                    obiint_t value)
+
+    int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view,
+                                                   OBIDMS_column_p column, 
+                                                   index_t line_nb, 
+                                                   index_t element_idx, 
+                                                   obiint_t value)
+    
+    obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view,
+                                                         OBIDMS_column_p column, 
+                                                         index_t line_nb, 
+                                                         const_char_p element_name)
+    
+    obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view,
+                                                        OBIDMS_column_p column, 
+                                                        index_t line_nb, 
+                                                        index_t element_idx)
+
     int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, 
                                             index_t line_nb, 
                                             const_char_p element_name, 
@@ -88,7 +109,7 @@ cdef extern from "obidmscolumn_int.h" nogil:
     int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, 
                                            index_t line_nb, 
                                            index_t element_idx, 
-                                        obiint_t value)
+                                           obiint_t value)
     
     obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, 
                                                  index_t line_nb, 
@@ -98,14 +119,35 @@ cdef extern from "obidmscolumn_int.h" nogil:
                                                 index_t line_nb, 
                                                 index_t element_idx)
 
-
 cdef extern from "obidmscolumn_bool.h" nogil:
 
+    int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view,
+                                                     OBIDMS_column_p column, 
+                                                     index_t line_nb, 
+                                                     const_char_p element_name, 
+                                                     obibool_t value)
+
+    int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    index_t element_idx, 
+                                                    obibool_t value)
+    
+    obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view,
+                                                          OBIDMS_column_p column, 
+                                                          index_t line_nb, 
+                                                          const_char_p element_name)
+    
+    obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view,
+                                                         OBIDMS_column_p column, 
+                                                         index_t line_nb, 
+                                                         index_t element_idx)
+
     int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, 
                                              index_t line_nb, 
                                              const_char_p element_name, 
                                              obibool_t value)
-    
+
     int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, 
                                             index_t line_nb, 
                                             index_t element_idx, 
@@ -121,11 +163,33 @@ cdef extern from "obidmscolumn_bool.h" nogil:
 
 cdef extern from "obidmscolumn_char.h" nogil:
 
+    int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view,
+                                                     OBIDMS_column_p column, 
+                                                     index_t line_nb, 
+                                                     const_char_p element_name, 
+                                                     obichar_t value)
+
+    int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    index_t element_idx, 
+                                                    obichar_t value)
+    
+    obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view,
+                                                          OBIDMS_column_p column, 
+                                                          index_t line_nb, 
+                                                          const_char_p element_name)
+    
+    obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view,
+                                                         OBIDMS_column_p column, 
+                                                         index_t line_nb, 
+                                                         index_t element_idx)
+
     int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, 
                                              index_t line_nb, 
                                              const_char_p element_name, 
                                              obichar_t value)
-    
+
     int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, 
                                             index_t line_nb, 
                                             index_t element_idx, 
@@ -141,39 +205,83 @@ cdef extern from "obidmscolumn_char.h" nogil:
 
 cdef extern from "obidmscolumn_float.h" nogil:
 
-    int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, 
+    int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view,
-                                              index_t line_nb, 
+                                                     OBIDMS_column_p column, 
-                                              const_char_p element_name, 
+                                                     index_t line_nb, 
-                                              obifloat_t value)
+                                                     const_char_p element_name, 
+                                                     obifloat_t value)
+
+    int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    index_t element_idx, 
+                                                    obifloat_t value)
     
-    int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, 
+    obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view,
+                                                          OBIDMS_column_p column, 
+                                                          index_t line_nb, 
+                                                          const_char_p element_name)
+    
+    obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view,
+                                                         OBIDMS_column_p column, 
+                                                         index_t line_nb, 
+                                                         index_t element_idx)
+
+    int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, 
                                              index_t line_nb, 
-                                             index_t element_idx, 
+                                             const_char_p element_name, 
                                              obifloat_t value)
+
+    int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, 
+                                            index_t line_nb, 
+                                            index_t element_idx, 
+                                            obifloat_t value)
     
     obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, 
-                                                     index_t line_nb, 
+                                                   index_t line_nb, 
-                                                     const_char_p element_name)
+                                                   const_char_p element_name)
     
     obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, 
-                                                    index_t line_nb, 
+                                                  index_t line_nb, 
-                                                    index_t element_idx)
+                                                  index_t element_idx)
 
 cdef extern from "obidmscolumn_str.h" nogil:
 
+    int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    const_char_p element_name, 
+                                                    char* value)
+
+    int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view,
+                                                   OBIDMS_column_p column, 
+                                                   index_t line_nb, 
+                                                   index_t element_idx, 
+                                                   char* value)
+    
+    const_char_p obi_column_get_obistr_with_elt_name_in_view(Obiview_p view,
+                                                           OBIDMS_column_p column, 
+                                                           index_t line_nb, 
+                                                           const_char_p element_name)
+    
+    const_char_p obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view,
+                                                            OBIDMS_column_p column, 
+                                                            index_t line_nb, 
+                                                            index_t element_idx)
+
     int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, 
                                             index_t line_nb, 
                                             const_char_p element_name, 
                                             char* value)
-    
+
     int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, 
                                            index_t line_nb, 
                                            index_t element_idx, 
                                            char* value)
     
     const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, 
-                                                     index_t line_nb, 
+                                                    index_t line_nb, 
-                                                     const_char_p element_name)
+                                                    char* element_name)
     
     const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, 
                                                     index_t line_nb, 
@@ -181,19 +289,41 @@ cdef extern from "obidmscolumn_str.h" nogil:
 
 cdef extern from "obidmscolumn_seq.h" nogil:
 
+    int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    const_char_p element_name, 
+                                                    char* value)
+
+    int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view,
+                                                   OBIDMS_column_p column, 
+                                                   index_t line_nb, 
+                                                   index_t element_idx, 
+                                                   char* value)
+    
+    const_char_p obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view,
+                                                           OBIDMS_column_p column, 
+                                                           index_t line_nb, 
+                                                           const_char_p element_name)
+    
+    const_char_p obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view,
+                                                            OBIDMS_column_p column, 
+                                                            index_t line_nb, 
+                                                            index_t element_idx)
+
     int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, 
                                             index_t line_nb, 
                                             const_char_p element_name, 
                                             char* value)
-    
+
     int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, 
                                            index_t line_nb, 
                                            index_t element_idx, 
                                            char* value)
     
     const_char_p obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, 
-                                                     index_t line_nb, 
+                                                    index_t line_nb, 
-                                                     const_char_p element_name)
+                                                    char* element_name)
     
     const_char_p obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, 
                                                     index_t line_nb, 

python/obitools3/obidms/capi/obitypes.pxd

@@ -8,6 +8,9 @@ from posix.types cimport time_t
 cdef extern from *:
     ctypedef char* const_char_p "const char*"
 
+cdef extern from "encode.h" nogil:
+    bint only_ATGC(const_char_p seq)
+
 
 cdef extern from "obidmscolumn.h" nogil:
 
@@ -38,10 +41,12 @@ cdef extern from "obitypes.h" nogil:
     ctypedef char obichar_t  
     ctypedef int64_t index_t
 
-    extern obiint_t   OBIInt_NA
+    extern obiint_t      OBIInt_NA
-    extern index_t    OBIIdx_NA
+    extern index_t       OBIIdx_NA
-    extern obifloat_t OBIFloat_NA
+    extern obifloat_t    OBIFloat_NA
-    extern obichar_t  OBIChar_NA
+    extern obichar_t     OBIChar_NA
-    extern obibool_t  OBIBool_NA
+    extern obibool_t     OBIBool_NA
+    extern const_char_p  OBISeq_NA
+    extern const_char_p  OBIStr_NA
 
-    char* name_data_type(int data_type)
+    const_char_p name_data_type(int data_type)

python/obitools3/obidms/capi/obiview.pxd

@@ -0,0 +1,68 @@
+#cython: language_level=3
+
+from .obitypes           cimport const_char_p, \
+                                 OBIType_t, \
+                                 obiversion_t, \
+                                 index_t
+from ..capi.obidms       cimport OBIDMS_p
+from ..capi.obidmscolumn cimport OBIDMS_column_p
+
+
+cdef extern from "obiview.h" nogil:
+
+    struct Column_reference_t :
+        char          column_name
+        obiversion_t  version
+    
+    ctypedef Column_reference_t* Column_reference_p
+
+
+    struct Obiview_t :
+        OBIDMS_p            dms
+        const_char_p        name
+        OBIDMS_column_p     line_selection
+        OBIDMS_column_p     new_line_selection
+        OBIDMS_column_p     columns
+        bint                read_only
+        Column_reference_t  line_selection_reference
+        index_t             line_count
+        int                 column_count
+
+    ctypedef Obiview_t* Obiview_p
+
+
+    Obiview_p obi_new_view(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection)
+    
+    Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection)
+
+    Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
+    
+    int obi_view_add_column(Obiview_p view,
+                            const_char_p column_name,
+                            obiversion_t version_number,
+                            OBIType_t data_type,
+                            index_t nb_lines,
+                            index_t nb_elements_per_line,
+                            const_char_p elements_names,
+                            const_char_p avl_name,
+                            const_char_p comments,
+                            bint create)
+
+    int obi_view_delete_column(Obiview_p view, const_char_p column_name)
+    
+    int obi_select_line(Obiview_p view, index_t line_nb)
+
+    int obi_select_lines(Obiview_p view, index_t* line_nbs)
+
+    OBIDMS_column_p obi_view_clone_column(Obiview_p view, const_char_p column_name)
+        
+    OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name)
+
+    OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const_char_p column_name)
+
+    int obi_save_view(Obiview_p view)
+    
+    int obi_close_view(Obiview_p view)
+    
+    int obi_save_and_close_view(Obiview_p view)
+

src/obidms.c

@@ -202,8 +202,8 @@ int create_dms_infos_file(int dms_file_descriptor, const char* dms_name)
 int obi_dms_exists(const char* dms_name)
 {
     struct stat buffer;
-	char *directory_name;
+	char*       directory_name;
-    int check_dir;
+    int 		check_dir;
 
 	// Build and check the directory name
     directory_name = build_directory_name(dms_name);

src/obidms.h

@@ -39,7 +39,7 @@ struct OBIDMS_column;		// TODO
 
 typedef struct Opened_columns_list {
 	size_t	 		 		nb_opened_columns;
-	struct OBIDMS_column** 	columns;
+	struct OBIDMS_column** 	columns;				// TODO allocate array size here
 } Opened_columns_list_t, *Opened_columns_list_p;
 
 

src/obidmscolumn.c

@@ -515,8 +515,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 								  index_t     nb_elements_per_line,
 								  const char* elements_names,
 								  const char* avl_name,
-								  const char* comments,
+								  const char* comments
-								  bool        referring)
+								 )
 {
 	OBIDMS_column_p 			new_column;
 	OBIDMS_column_directory_p	column_directory;
@@ -531,8 +531,6 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 	index_t						minimum_line_count;
 	OBIType_t  					returned_data_type;
 	OBIType_t  					stored_data_type;
-    index_t                     returned_nb_elements_per_line;
-    index_t                     stored_nb_elements_per_line;
 
 	new_column = NULL;
 
@@ -547,7 +545,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 		obidebug(1, "\nCan't create column because of empty column name");
 		return NULL;
 	}
-	if ((data_type < 1) || (data_type > 6))
+	if ((data_type < 1) || (data_type > 7))
 	{
 		obidebug(1, "\nCan't create column because of invalid data type");
 		return NULL;
@@ -559,21 +557,14 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 	}
 
 	returned_data_type = data_type;
-	if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || referring)
+	if ((data_type == OBI_STR) || (data_type == OBI_SEQ))
 	// stored data is indices referring to data stored elsewhere
 		stored_data_type = OBI_IDX;
 	else
 		stored_data_type = returned_data_type;
 
-	returned_nb_elements_per_line = nb_elements_per_line;
-	if (referring)
-	// stored data is indices referring to lines in another column
-		stored_nb_elements_per_line = 1;
-	else
-		stored_nb_elements_per_line = returned_nb_elements_per_line;
-
 	// The initial line count should be between the minimum (corresponding to the page size) and the maximum allowed
-	minimum_line_count = get_line_count_per_page(stored_data_type, stored_nb_elements_per_line);
+	minimum_line_count = get_line_count_per_page(stored_data_type, nb_elements_per_line);
 	if (nb_lines > MAXIMUM_LINE_COUNT)
 	{
 		obidebug(1, "\nCan't create column because of line count greater than the maximum allowed (%d)", MAXIMUM_LINE_COUNT);
@@ -583,12 +574,12 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 		nb_lines = minimum_line_count;
 
 	// The number of elements names should be equal to the number of elements per line
-	if ((elements_names == NULL) && (returned_nb_elements_per_line > 1))
+	if ((elements_names == NULL) && (nb_elements_per_line > 1))
 	{
 		obidebug(1, "\nCan't create column because no elements names were given for a number of elements per line greater than 1");
 		return NULL;
 	}
-	else if ((elements_names != NULL) && (returned_nb_elements_per_line > 1))
+	else if ((elements_names != NULL) && (nb_elements_per_line > 1))
 	{
 		char* token;
 		index_t n = 0;
@@ -605,7 +596,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 			return NULL;
 		}
 	}
-	else if ((returned_nb_elements_per_line == 1) && (strcmp(elements_names, column_name) != 0))
+	else if ((nb_elements_per_line == 1) && (strcmp(elements_names, column_name) != 0))
 	{
 		obidebug(1, "\nCan't create column because the element name does not match the column name");
 		return NULL;
@@ -622,7 +613,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 
 	// Calculate the size needed
 	header_size = obi_get_platform_header_size();
-	data_size = obi_array_sizeof(stored_data_type, nb_lines, stored_nb_elements_per_line);
+	data_size = obi_array_sizeof(stored_data_type, nb_lines, nb_elements_per_line);
 	file_size = header_size + data_size;
 
 	// Get the latest version number
@@ -708,22 +699,19 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 		return NULL;
 	}
 
-	new_column->writable  = true;
+	new_column->writable = true;
 
 	header 				  		 		  = new_column->header;
 	header->header_size   		   		  = header_size;
 	header->data_size			 		  = data_size;
 	header->line_count   	 	 		  = nb_lines;
 	header->lines_used    		          = 0;
-	header->stored_nb_elements_per_line   = stored_nb_elements_per_line;
+	header->nb_elements_per_line          = nb_elements_per_line;
-	header->returned_nb_elements_per_line = returned_nb_elements_per_line;
 	header->stored_data_type     		  = stored_data_type;
 	header->returned_data_type   		  = returned_data_type;
 	header->creation_date 		 		  = time(NULL);
 	header->version       		          = version_number;
 	header->cloned_from    		          = -1;
-	header->referring      				  = referring;
-	header->referred_column_version       = -1;
 
 	obi_column_set_elements_names(new_column, elements_names);
 
@@ -780,7 +768,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 	column_directory = obi_open_column_directory(dms, column_name);
 	if (column_directory == NULL)
 	{
-		obidebug(1, "\nError opening a column directory structure");
+		//obidebug(1, "\nError opening a column directory structure");
 		return NULL;
 	}
 
@@ -818,7 +806,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 	if (column_file_descriptor < 0)
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError opening column file");
+		//obidebug(1, "\nError opening column file");
 		free(column_file_name);
 		return NULL;
 	}
@@ -854,7 +842,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 			                  	  	MAP_PRIVATE,
 			                  	  	column_file_descriptor,
 			                  	  	0
-			                 	 	);
+			                 	   );
 
 	if (column->header == MAP_FAILED)
 	{
@@ -872,7 +860,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 									MAP_PRIVATE,
 			                 	 	column_file_descriptor,
 			                 	 	header_size
-			                	    );
+			                	   );
 
 	if (column->data == MAP_FAILED)
 	{
@@ -884,7 +872,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 		return NULL;
 	}
 
-	column->writable  = false;
+	column->writable = false;
 
 	// If the data type is OBI_STR or OBI_SEQ, the associated AVL tree is opened
 	if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
@@ -901,18 +889,6 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 		column->avl = avl;
 	}
 
-	if ((column->header)->referring)
-	{
-		column->referred_column = obi_open_column(dms, column_name, (column->header)->referred_column_version);
-		if (column->referred_column == NULL)
-		{
-			obidebug(1, "\nError opening a referred column");
-			obi_close_column(column);
-			close(column_file_descriptor);
-			return NULL;
-		}
-	}
-
 	close(column_file_descriptor);
 
 	// Add in the list of opened columns and set column counter to 1
@@ -925,9 +901,9 @@ 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,
 								 obiversion_t     version_number,
-								 bool		      referring,
 								 bool 		      clone_data)
 {
 	OBIDMS_column_p   column_to_clone;
@@ -935,6 +911,10 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 	index_t 		  nb_lines;
 	index_t			  nb_elements_per_line;
 	OBIType_t		  data_type;
+	size_t 			  line_size;
+	index_t			  i, index;
+
+	obidebug(1, "\nline_selection == NULL = %d\n", (line_selection == NULL));
 
 	column_to_clone = obi_open_column(dms, column_name, version_number);
 	if (column_to_clone == NULL)
@@ -944,25 +924,11 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 		return NULL;
 	}
 
-	// A referring column can't be cloned
-	if ((column_to_clone->header)->referring)
-	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError: can't clone a referring column");
-		return NULL;
-	}
-
 	data_type = (column_to_clone->header)->returned_data_type;
 
-	nb_elements_per_line = (column_to_clone->header)->returned_nb_elements_per_line;
+	nb_elements_per_line = (column_to_clone->header)->nb_elements_per_line;
 
-	if (clone_data && referring)
+	if (clone_data)
-	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError: can't clone the data when creating a referring column");
-		return NULL;
-	}
-	else if (clone_data)
 		nb_lines = (column_to_clone->header)->line_count;
 	else
 		nb_lines = get_line_count_per_page(data_type, nb_elements_per_line);	// minimum line count corresponding to one memory page
@@ -974,8 +940,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 								   nb_elements_per_line,
 								   (column_to_clone->header)->elements_names,
 								   (column_to_clone->header)->avl_name,
-								   (column_to_clone->header)->comments,
+								   (column_to_clone->header)->comments
-								   referring);
+								  );
 
 	if (new_column == NULL)
 	{
@@ -989,24 +955,29 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 
 	(new_column->header)->cloned_from = (column_to_clone->header)->version;
 
-	if (referring)
+	if (clone_data && (line_selection == NULL))
-	{
-		if ((column_to_clone->header)->referring)
-			(new_column->header)->referred_column_version = (column_to_clone->header)->referred_column_version;
-		else
-			(new_column->header)->referred_column_version = (column_to_clone->header)->version;
-	}
-
-	if (clone_data)
 	{
 		memcpy(new_column->data, column_to_clone->data, (column_to_clone->header)->data_size);
 		(new_column->header)->lines_used = (column_to_clone->header)->lines_used;
 	}
+	else if (clone_data && (line_selection != NULL))
+	{
+		obidebug(1, "\nCloning data from line selection\n");
+		line_size = obi_sizeof((new_column->header)->stored_data_type) * (new_column->header)->nb_elements_per_line;
+		fprintf(stderr, "\nline size = %ld\n", line_size);
+		for (i=0; i<((line_selection->header)->lines_used); i++)
+		{
+			index = *(((index_t*) (line_selection->data)) + i);
+			fprintf(stderr, "\nindex = %lld, i = %lld\n", index, i);
+			memcpy((new_column->data)+(i*line_size), (column_to_clone->data)+(index*line_size), line_size);
+			fprintf(stderr, "\nmemcpied\n");
+		}
+		(new_column->header)->lines_used = (line_selection->header)->lines_used;
+		obidebug(1, "\nCloned data from line selection\n");
+	}
 
-	// close column_to_clone or store the pointer if it's referred
+	// Close column_to_clone
-	if (referring)
+	if (obi_close_column(column_to_clone) < 0)
-		new_column->referred_column = column_to_clone;
-	else if (obi_close_column(column_to_clone) < 0)
 	{
 		obidebug(1, "\nError closing a column that has been cloned");
 		// TODO return NULL or not?
@@ -1049,9 +1020,6 @@ int obi_close_column(OBIDMS_column_p column)
 			}
 		}
 
-		if ((column->header)->referring)
-			obi_close_column(column->referred_column);
-
 		// If the data type is OBI_STR or OBI_SEQ, the associated AVL tree is closed
 		if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
 		{
@@ -1095,8 +1063,8 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column)	// TODO is it nece
 	char* 	column_file_name;
 
 	// Compute the new line count = the number of lines used rounded to the nearest greater multiple of page size greater than 0
-	multiple = ceil((double) (ONE_IF_ZERO((column->header)->lines_used) * (column->header)->stored_nb_elements_per_line * obi_sizeof((column->header)->stored_data_type)) / (double) getpagesize());
+	multiple = ceil((double) (ONE_IF_ZERO((column->header)->lines_used) * (column->header)->nb_elements_per_line * obi_sizeof((column->header)->stored_data_type)) / (double) getpagesize());
-	new_line_count = floor((((int) multiple) * getpagesize()) / ((column->header)->stored_nb_elements_per_line * obi_sizeof((column->header)->stored_data_type)));
+	new_line_count = floor((((int) multiple) * getpagesize()) / ((column->header)->nb_elements_per_line * obi_sizeof((column->header)->stored_data_type)));
 
 	// Check that it is actually greater than the current number of lines allocated in the file, otherwise no need to truncate
 	if ((column->header)->line_count == new_line_count)
@@ -1131,7 +1099,7 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column)	// TODO is it nece
 	}
 
 	// Truncate the column file
-	data_size = obi_array_sizeof((column->header)->stored_data_type, new_line_count, (column->header)->stored_nb_elements_per_line);
+	data_size = obi_array_sizeof((column->header)->stored_data_type, new_line_count, (column->header)->nb_elements_per_line);
 	file_size = (column->header)->header_size + data_size;
 	if (ftruncate(column_file_descriptor, file_size) < 0)
 	{
@@ -1262,8 +1230,11 @@ int obi_enlarge_column(OBIDMS_column_p column)
 
 int obi_truncate_and_close_column(OBIDMS_column_p column)
 {
-	if (obi_truncate_column_to_lines_used(column) < 0)
+	if (column->writable)	// TODO discuss
-		return -1;
+	{
+		if (obi_truncate_column_to_lines_used(column) < 0)
+			return -1;
+	}
 	if (obi_close_column(column) < 0)
 		return -1;
 
@@ -1277,8 +1248,8 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
 {
 	index_t i, start, end, nb_elements;
 
-	nb_elements = nb_lines*((column->header)->stored_nb_elements_per_line);
+	nb_elements = nb_lines*((column->header)->nb_elements_per_line);
-	start = first_line_nb*((column->header)->stored_nb_elements_per_line);
+	start = first_line_nb*((column->header)->nb_elements_per_line);
 	end = start + nb_elements;
 
 	switch ((column->header)->stored_data_type) {
@@ -1476,35 +1447,3 @@ char* obi_column_format_date(time_t date)
 	return formatted_time;
 }
 
-
-// TODO put in separate file ?
-// warning for the dependency and for the fact that it's always added at the next line (or not cuz might not be a good idea?)
-int obi_grep_line(OBIDMS_column_p referring_column, index_t line_to_grep)
-{
-	// Check that the column is referring another
-	if (!((referring_column->header)->referring))
-	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError: Grepping a line can only be done with a referring column");
-	  	return -1;
-	}
-
-	// Check if the file needs to be enlarged
-	if ((referring_column->header)->lines_used == (referring_column->header)->line_count)
-	{
-		// Enlarge the file
-		if (obi_enlarge_column(referring_column) < 0)
-	    	return -1;
-	}
-
-	// Set the value
-	*(((index_t*) (referring_column->data)) + (referring_column->header)->lines_used) = line_to_grep;
-
-	// Update lines used
-	((referring_column->header)->lines_used)++;
-
-	return 0;
-}
-
-
-

src/obidmscolumn.h

@@ -57,11 +57,7 @@ typedef struct OBIDMS_column_header {
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	index_t			lines_used;							    /**< Number of lines of data used.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t			returned_nb_elements_per_line;      	/**< Number of elements per line returned when getting a
+	index_t			nb_elements_per_line;   			   	/**< Number of elements per line.
-															 *   line from the column.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t			stored_nb_elements_per_line;       		/**< Number of elements per line that is actually stored
-															 *   in the data part of the column.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	char			elements_names[ELEMENTS_NAMES_MAX+1];	/**< Names of the line elements with ';' as separator
 															 *	 (should be the column name if one element per line).
@@ -80,10 +76,6 @@ typedef struct OBIDMS_column_header {
 															 *   was cloned from (-1 if it was not created by cloning
 															 *   another column).
 															 */
-	bool            referring;			    				/**< Whether the column contains indices referring to another column.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	obiversion_t    referred_column_version;                /**< Version of the column to which this column is referring.
-															 */
 	char            name[OBIDMS_COLUMN_MAX_NAME+1]; 	    /**< The column name as a NULL terminated string.
 	                                             	 	 	 */
 	char            avl_name[AVL_MAX_NAME+1]; 	    		/**< If there is one, the AVL tree name as a NULL terminated string.
@@ -108,14 +100,12 @@ typedef struct OBIDMS_column {
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	OBIDMS_avl_p 				avl;				/**< A pointer to the AVL tree associated with the column if there is one.
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	struct OBIDMS_column*       referred_column;    /**< A pointer to the referred column if the column is referring.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	void*                   	data;   		 	/**< A `void` pointer to the beginning of the data.
 	                                 	 	         *
 													 *   @warning Never use this member directly outside of the code of the
 													 *            low level functions of the OBIDMS.
 													 */
-	bool						writable;	     	/**< Indicates if the column is writable or not.	TODO delete?
+	bool						writable;	     	/**< Indicates if the column is writable or not.
 													 *       - `true` the column is writable
 													 *       - `false` the column is read-only
 													 *
@@ -186,7 +176,6 @@ size_t obi_get_platform_header_size();
  * @param elements_names The names of the elements with ';' as separator.
  * @param avl_name The name of the AVL tree if there is one associated with the column.
  * @param comments Optional comments associated with the column.
- * @param referring
  *
  * @returns A pointer on the newly created column structure.
  * @retval NULL if an error occurred.
@@ -201,8 +190,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 								  index_t nb_elements_per_line,
 								  const char* elements_names,
 								  const char* avl_name,
-								  const char* comments,
+								  const char* comments
-								  bool referring);
+								 );
 
 
 /**
@@ -235,7 +224,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversio
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number, bool referring, bool clone_data);
+OBIDMS_column_p obi_clone_column(OBIDMS_p dms, OBIDMS_column_p line_selection, const char* column_name, obiversion_t version_number, bool clone_data);
 
 
 /**
@@ -372,7 +361,7 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
 char* obi_column_format_date(time_t date);
 
 
-int obi_grep_line(OBIDMS_column_p referring_column, index_t line_to_grep);
+int obi_select(OBIDMS_column_p lines_column, index_t line_to_grep);
 
 
 

src/obidmscolumn_bool.c

@@ -14,6 +14,7 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
+#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
@@ -28,16 +29,9 @@
  *
  **********************************************************************/
 
+
 int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
 {
-	// Check that the column is not referring another
-	if ((column->header)->referring)
-	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError: Setting a value from a referring column is not allowed. The referred column must be cloned to be modified");
-	  	return -1;
-	}
-
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
 	{
@@ -59,7 +53,44 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 		(column->header)->lines_used = line_nb+1;
 
 	// Set the value
-	*(((obibool_t*) (column->data)) + (line_nb * ((column->header)->stored_nb_elements_per_line)) + element_idx) = value;
+	*(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
+
+	return 0;
+}
+
+
+int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
+{
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to set a value in a column in a read-only view");
+		return -1;
+	}
+
+	if ((view->line_selection != NULL) || (!(column->writable)))
+	{
+		// Get the right line number
+		if (column->writable)
+			line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+		column = obi_view_clone_column(view, (column->header)->name);
+		if (column == NULL)
+		{
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
+		}
+	}
+
+	if ((line_nb+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, (line_nb+1)) < 0)
+			return -1;
+	}
+
+	if (obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
 
 	return 0;
 }
@@ -67,22 +98,30 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 
 obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
-	index_t referring_idx;
+	if ((line_nb+1) > ((column->header)->line_count))
-
-	if ((line_nb+1) > (column->header)->lines_used)
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
 		return OBIBool_NA;
 	}
 
-	if ((column->header)->referring)
+	return *(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+}
+
+
+obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	if ((line_nb+1) > (view->line_count))
 	{
-		referring_idx = *(((index_t*) (column->data)) + line_nb);
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		return *(((obibool_t*) ((column->referred_column)->data)) + (referring_idx * ((column->header)->returned_nb_elements_per_line)) + element_idx);
+		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
+		return OBIBool_NA;
 	}
-	else
+
-		return *(((obibool_t*) (column->data)) + (line_nb * ((column->header)->stored_nb_elements_per_line)) + element_idx);
+	if (view->line_selection)
+		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+	return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
 }
 
 
@@ -97,6 +136,17 @@ int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb
 }
 
 
+int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+	return 0;
+}
+
+
 obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
 {
 	index_t element_idx;
@@ -107,3 +157,13 @@ obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t l
 	return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
 }
 
+
+obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIBool_NA;
+	return obi_column_get_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx);
+}

src/obidmscolumn_bool.h

@@ -19,6 +19,7 @@
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
+#include "obiview.h"
 
 
 /**
@@ -38,7 +39,7 @@
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, size_t element_idx, obibool_t value);
+int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value);
 
 
 /**
@@ -54,7 +55,7 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, size_t element_idx);
+obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
 
 
 /**
@@ -95,5 +96,79 @@ int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb
 obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
 
 
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL,
+ *        using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL,
+ *        using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
 #endif /* OBIDMSCOLUMN_BOOL_H_ */
 

src/obidmscolumn_char.c

@@ -14,6 +14,7 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
+#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
@@ -28,16 +29,9 @@
  *
  **********************************************************************/
 
+
 int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value)
 {
-	// Check that the column is not referring another
-	if ((column->header)->referring)
-	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError: Setting a value from a referring column is not allowed. The referred column must be cloned to be modified");
-	  	return -1;
-	}
-
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
 	{
@@ -59,7 +53,44 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 		(column->header)->lines_used = line_nb+1;
 
 	// Set the value
-	*(((obichar_t*) (column->data)) + (line_nb * ((column->header)->stored_nb_elements_per_line)) + element_idx) = value;
+	*(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
+
+	return 0;
+}
+
+
+int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value)
+{
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to set a value in a column in a read-only view");
+		return -1;
+	}
+
+	if ((view->line_selection != NULL) || (!(column->writable)))
+	{
+		// Get the right line number
+		if (column->writable)
+			line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+		column = obi_view_clone_column(view, (column->header)->name);
+		if (column == NULL)
+		{
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
+		}
+	}
+
+	if ((line_nb+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, (line_nb+1)) < 0)
+			return -1;
+	}
+
+	if (obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
 
 	return 0;
 }
@@ -67,22 +98,30 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 
 obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
-	index_t referring_idx;
+	if ((line_nb+1) > ((column->header)->line_count))
-
-	if ((line_nb+1) > (column->header)->lines_used)
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
 		return OBIChar_NA;
 	}
 
-	if ((column->header)->referring)
+	return *(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+}
+
+
+obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	if ((line_nb+1) > (view->line_count))
 	{
-		referring_idx = *(((index_t*) (column->data)) + line_nb);
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		return *(((obichar_t*) ((column->referred_column)->data)) + (referring_idx * ((column->header)->returned_nb_elements_per_line)) + element_idx);
+		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
+		return OBIChar_NA;
 	}
-	else
+
-		return *(((obichar_t*) (column->data)) + (line_nb * ((column->header)->stored_nb_elements_per_line)) + element_idx);
+	if (view->line_selection)
+		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+	return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
 }
 
 
@@ -97,6 +136,17 @@ int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb
 }
 
 
+int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+	return 0;
+}
+
+
 obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
 {
 	index_t element_idx;
@@ -107,3 +157,13 @@ obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t l
 	return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
 }
 
+
+obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIChar_NA;
+	return obi_column_get_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx);
+}

src/obidmscolumn_char.h

@@ -19,6 +19,7 @@
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
+#include "obiview.h"
 
 
 /**
@@ -49,7 +50,7 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
  * @param element_idx The index of the element that should be recovered in the line.
  *
  * @returns The recovered value.
- * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
+ * @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -87,7 +88,7 @@ int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb
  * @param element_name The name of the element that should be recovered in the line.
  *
  * @returns The recovered value.
- * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
+ * @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -95,5 +96,79 @@ int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb
 obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
 
 
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR,
+ *        using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR,
+ *        using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
 #endif /* OBIDMSCOLUMN_CHAR_H_ */
 

src/obidmscolumn_float.c

@@ -14,6 +14,7 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
+#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
@@ -30,14 +31,6 @@
 
 int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value)
 {
-	// Check that the column is not referring another
-	if ((column->header)->referring)
-	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError: Setting a value from a referring column is not allowed. The referred column must be cloned to be modified");
-	  	return -1;
-	}
-
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
 	{
@@ -59,7 +52,44 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb
 		(column->header)->lines_used = line_nb+1;
 
 	// Set the value
-	*(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->stored_nb_elements_per_line)) + element_idx) = value;
+	*(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
+
+	return 0;
+}
+
+
+int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value)
+{
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to set a value in a column in a read-only view");
+		return -1;
+	}
+
+	if ((view->line_selection != NULL) || (!(column->writable)))
+	{
+		// Get the right line number
+		if (column->writable)
+			line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+		column = obi_view_clone_column(view, (column->header)->name);
+		if (column == NULL)
+		{
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
+		}
+	}
+
+	if ((line_nb+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, (line_nb+1)) < 0)
+			return -1;
+	}
+
+	if (obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
 
 	return 0;
 }
@@ -67,22 +97,30 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb
 
 obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
-	index_t referring_idx;
+	if ((line_nb+1) > ((column->header)->line_count))
-
-	if ((line_nb+1) > (column->header)->lines_used)
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
 		return OBIFloat_NA;
 	}
 
-	if ((column->header)->referring)
+	return *(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+}
+
+
+obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	if ((line_nb+1) > (view->line_count))
 	{
-		referring_idx = *(((index_t*) (column->data)) + line_nb);
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		return *(((obifloat_t*) ((column->referred_column)->data)) + (referring_idx * ((column->header)->returned_nb_elements_per_line)) + element_idx);
+		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
+		return OBIFloat_NA;
 	}
-	else
+
-		return *(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->stored_nb_elements_per_line)) + element_idx);
+	if (view->line_selection)
+		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+	return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
 }
 
 
@@ -97,6 +135,17 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_n
 }
 
 
+int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+	return 0;
+}
+
+
 obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
 {
 	index_t element_idx;
@@ -107,3 +156,13 @@ obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t
 	return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
 }
 
+
+obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIFloat_NA;
+	return obi_column_get_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx);
+}

src/obidmscolumn_float.h

@@ -19,6 +19,7 @@
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
+#include "obiview.h"
 
 
 /**
@@ -49,7 +50,7 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb
  * @param element_idx The index of the element that should be recovered in the line.
  *
  * @returns The recovered value.
- * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
+ * @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -87,7 +88,7 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_n
  * @param element_name The name of the element that should be recovered in the line.
  *
  * @returns The recovered value.
- * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
+ * @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -95,5 +96,79 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_n
 obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
 
 
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT,
+ *        using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT,
+ *        using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
 #endif /* OBIDMSCOLUMN_FLOAT_H_ */
 

src/obidmscolumn_idx.c

@@ -0,0 +1,72 @@
+/****************************************************************************
+ * OBIDMS_column_idx functions                                              *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_idx.c
+ * @author Celine Mercier
+ * @date February 14th 2016
+ * @brief Functions handling OBIColumns containing data with the index_t type.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidmscolumn.h"
+#include "obitypes.h"
+#include "obierrno.h"
+#include "obidebug.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+/**********************************************************************
+ *
+ * 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 obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value)
+{
+	// Check that the line number is not greater than the maximum allowed
+	if (line_nb >= MAXIMUM_LINE_COUNT)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
+    	return -1;
+	}
+
+	// Check if the file needs to be enlarged
+	while ((line_nb+1) > (column->header)->line_count)
+	{
+		// Enlarge the file
+		if (obi_enlarge_column(column) < 0)
+	    	return -1;
+	}
+
+	// Update lines used
+	if ((line_nb+1) > (column->header)->lines_used)
+		(column->header)->lines_used = line_nb+1;
+
+	// Set the value
+	*(((index_t*) (column->data)) + line_nb) = value;
+
+	return 0;
+}
+
+
+index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb)
+{
+	if ((line_nb+1) > ((column->header)->line_count))
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
+		return OBIIdx_NA;
+	}
+
+	return *(((index_t*) (column->data)) + line_nb);
+}
+

src/obidmscolumn_idx.h

@@ -0,0 +1,30 @@
+/****************************************************************************
+ * OBIDMS_column_idx header file                                            *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_idx.h
+ * @author Celine Mercier
+ * @date February 14th 2016
+ * @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_IDX.
+ */
+
+
+#ifndef OBIDMSCOLUMN_IDX_H_
+#define OBIDMSCOLUMN_IDX_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidmscolumn.h"
+#include "obitypes.h"
+
+
+int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value);
+
+index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb);
+
+
+#endif /* OBIDMSCOLUMN_IDX_H_ */
+

src/obidmscolumn_int.c

@@ -14,6 +14,7 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
+#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
@@ -28,16 +29,9 @@
  *
  **********************************************************************/
 
+
 int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value)
 {
-	// Check that the column is not referring another
-	if ((column->header)->referring)
-	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError: Setting a value from a referring column is not allowed. The referred column must be cloned to be modified");
-	  	return -1;
-	}
-
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
 	{
@@ -59,7 +53,44 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 		(column->header)->lines_used = line_nb+1;
 
 	// Set the value
-	*(((obiint_t*) (column->data)) + (line_nb * ((column->header)->stored_nb_elements_per_line)) + element_idx) = value;
+	*(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
+
+	return 0;
+}
+
+
+int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value)
+{
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to set a value in a column in a read-only view");
+		return -1;
+	}
+
+	if ((view->line_selection != NULL) || (!(column->writable)))
+	{
+		// Get the right line number
+		if (column->writable)
+			line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+		column = obi_view_clone_column(view, (column->header)->name);
+		if (column == NULL)
+		{
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
+		}
+	}
+
+	if ((line_nb+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, (line_nb+1)) < 0)
+			return -1;
+	}
+
+	if (obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
 
 	return 0;
 }
@@ -67,22 +98,30 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 
 obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
-	index_t referring_idx;
+	if ((line_nb+1) > ((column->header)->line_count))
-
-	if ((line_nb+1) > (column->header)->lines_used)
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
 		return OBIInt_NA;
 	}
 
-	if ((column->header)->referring)
+	return *(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+}
+
+
+obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	if ((line_nb+1) > (view->line_count))
 	{
-		referring_idx = *(((index_t*) (column->data)) + line_nb);
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		return *(((obiint_t*) ((column->referred_column)->data)) + (referring_idx * ((column->header)->returned_nb_elements_per_line)) + element_idx);
+		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
+		return OBIInt_NA;
 	}
-	else
+
-		return *(((obiint_t*) (column->data)) + (line_nb * ((column->header)->stored_nb_elements_per_line)) + element_idx);
+	if (view->line_selection)
+		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+	return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
 }
 
 
@@ -97,6 +136,17 @@ int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb,
 }
 
 
+int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	obi_column_set_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+	return 0;
+}
+
+
 obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
 {
 	index_t element_idx;
@@ -107,3 +157,14 @@ obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t lin
 	return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
 }
 
+
+obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIInt_NA;
+	return obi_column_get_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx);
+}
+

src/obidmscolumn_int.h

@@ -19,6 +19,7 @@
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
+#include "obiview.h"
 
 
 /**
@@ -95,5 +96,79 @@ int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb,
 obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
 
 
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT,
+ *        using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT,
+ *        using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
 #endif /* OBIDMSCOLUMN_INT_H_ */
 

src/obidmscolumn_seq.c

@@ -14,6 +14,7 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
+#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
@@ -29,19 +30,12 @@
  *
  **********************************************************************/
 
+
 int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
 {
 	byte_t* value_b;
 	index_t idx;
 
-	// Check that the column is not referring another
-	if ((column->header)->referring)
-	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError: Setting a value from a referring column is not allowed. The referred column must be cloned to be modified");
-	  	return -1;
-	}
-
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
 	{
@@ -73,7 +67,7 @@ int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 		return -1;
 
 	// Add the value's index in the column
-	*(((index_t*) (column->data)) + (line_nb * ((column->header)->stored_nb_elements_per_line)) + element_idx) = idx;
+	*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
 
 	free(value_b);
 
@@ -81,44 +75,100 @@ int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 }
 
 
+int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
+{
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to set a value in a column in a read-only view");
+		return -1;
+	}
+
+	if ((view->line_selection != NULL) || (!(column->writable)))
+	{
+		// Get the right line number
+		if (column->writable)
+			line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+		column = obi_view_clone_column(view, (column->header)->name);
+		if (column == NULL)
+		{
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
+		}
+	}
+
+	if ((line_nb+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, (line_nb+1)) < 0)
+			return -1;
+	}
+
+	if (obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
+
+	return 0;
+}
+
+
 const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
 	index_t idx;
 	byte_t* value_b;
-	index_t referring_idx;
 
-	if ((line_nb+1) > (column->header)->lines_used)
+	if ((line_nb+1) > ((column->header)->line_count))
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
-		return "\0";		// TODO
+		return OBISeq_NA;
 	}
 
-	if ((column->header)->referring)
+	idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
-	{
-		referring_idx = *(((index_t*) (column->data)) + line_nb);
-		idx = *(((index_t*) ((column->referred_column)->data)) + (referring_idx * ((column->header)->returned_nb_elements_per_line)) + element_idx);
-	}
-	else
-		idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->stored_nb_elements_per_line)) + element_idx);
 
 	// Check NA
 	if (idx == OBIIdx_NA)
-		return "\0";		// TODO
+		return OBISeq_NA;
 
 	value_b = obi_avl_get(column->avl, idx);
 	return obi_obibytes_to_seq(value_b);
 }
 
 
+const char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	if ((line_nb+1) > (view->line_count))
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
+		return OBISeq_NA;
+	}
+
+	if (view->line_selection)
+		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+	return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
+}
+
+
 int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
 {
 	index_t element_idx;
 	element_idx = obi_column_get_element_index_from_name(column, element_name);
 	if (element_idx == OBIIdx_NA)
 		return -1;
-	if (obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value) < 0)
+	obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
 		return -1;
+	obi_column_set_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
 	return 0;
 }
 
@@ -129,7 +179,18 @@ const char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t
 
 	element_idx = obi_column_get_element_index_from_name(column, element_name);
 	if (element_idx == OBIIdx_NA)
-		return "\0";
+		return OBISeq_NA;
 	return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
 }
 
+
+const char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBISeq_NA;
+	return obi_column_get_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx);
+}
+

src/obidmscolumn_seq.h

@@ -19,6 +19,7 @@
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
+#include "obiview.h"
 
 
 /**
@@ -97,5 +98,81 @@ int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb,
 const char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
 
 
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences in an AVL tree, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences in an AVL tree, using the index of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences in an AVL tree, using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to DNA sequences in an AVL tree, using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
 #endif /* OBIDMSCOLUMN_SEQ_H_ */
 

src/obidmscolumn_str.c

@@ -14,6 +14,7 @@
 #include <stdio.h>
 
 #include "obidmscolumn.h"
+#include "obiview.h"
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
@@ -34,14 +35,6 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 	byte_t* value_b;
 	index_t idx;
 
-	// Check that the column is not referring another
-	if ((column->header)->referring)
-	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError: Setting a value from a referring column is not allowed. The referred column must be cloned to be modified");
-	  	return -1;
-	}
-
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
 	{
@@ -73,7 +66,7 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 		return -1;
 
 	// Add the value's index in the column
-	*(((index_t*) (column->data)) + (line_nb * ((column->header)->stored_nb_elements_per_line)) + element_idx) = idx;
+	*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
 
 	free(value_b);
 
@@ -81,44 +74,100 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 }
 
 
+int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
+{
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to set a value in a column in a read-only view");
+		return -1;
+	}
+
+	if ((view->line_selection != NULL) || (!(column->writable)))
+	{
+		// Get the right line number
+		if (column->writable)
+			line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+		column = obi_view_clone_column(view, (column->header)->name);
+		if (column == NULL)
+		{
+			obidebug(1, "\nError trying to clone a column to modify it");
+			return -1;
+		}
+	}
+
+	if ((line_nb+1) > view->line_count)
+	{
+		if (obi_view_update_lines(view, (line_nb+1)) < 0)
+			return -1;
+	}
+
+	if (obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
+
+	return 0;
+}
+
+
 const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
 	index_t idx;
 	byte_t* value_b;
-	index_t referring_idx;
 
-	if ((line_nb+1) > (column->header)->lines_used)
+	if ((line_nb+1) > ((column->header)->line_count))
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
-		return "\0";		// TODO
+		return OBIStr_NA;
 	}
 
-	if ((column->header)->referring)
+	idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
-	{
-		referring_idx = *(((index_t*) (column->data)) + line_nb);
-		idx = *(((index_t*) ((column->referred_column)->data)) + (referring_idx * ((column->header)->returned_nb_elements_per_line)) + element_idx);
-	}
-	else
-		idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->stored_nb_elements_per_line)) + element_idx);
 
 	// Check NA
 	if (idx == OBIIdx_NA)
-		return "\0";		// TODO
+		return OBIStr_NA;
 
 	value_b = obi_avl_get(column->avl, idx);
 	return obi_obibytes_to_str(value_b);
 }
 
 
+const char* obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	if ((line_nb+1) > (view->line_count))
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
+		return OBIStr_NA;
+	}
+
+	if (view->line_selection)
+		line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
+
+	return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
+}
+
+
 int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
 {
 	index_t element_idx;
 	element_idx = obi_column_get_element_index_from_name(column, element_name);
 	if (element_idx == OBIIdx_NA)
 		return -1;
-	if (obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value) < 0)
+	obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
+	return 0;
+}
+
+
+int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
 		return -1;
+	obi_column_set_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
 	return 0;
 }
 
@@ -129,7 +178,18 @@ const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t
 
 	element_idx = obi_column_get_element_index_from_name(column, element_name);
 	if (element_idx == OBIIdx_NA)
-		return "\0";
+		return OBIStr_NA;
 	return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
 }
 
+
+const char* obi_column_get_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIStr_NA;
+	return obi_column_get_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx);
+}
+

src/obidmscolumn_str.h

@@ -19,6 +19,7 @@
 
 #include "obidmscolumn.h"
 #include "obitypes.h"
+#include "obiview.h"
 
 
 /**
@@ -97,5 +98,81 @@ int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb,
 const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
 
 
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an AVL tree, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an AVL tree, using the index of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an AVL tree, using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an AVL tree, using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since February 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
 #endif /* OBIDMSCOLUMN_STR_H_ */
 

src/obierrno.h

@@ -100,6 +100,8 @@ extern int obi_errno;
                                     		 */
 #define OBI_AVL_ERROR				(20)    /** Error while handling an AVL tree
 											 */
+#define OBIVIEW_ERROR				(21)    /** Error while handling an OBIView
+											 */
 /**@}*/
 
 #endif /* OBIERRNO_H_ */

src/obitypes.h

@@ -23,6 +23,8 @@
 #define OBIFloat_NA (float_NA())	/**< NA value for the type OBI_FLOAT */
 #define OBIChar_NA (0)				/**< NA value for the type OBI_CHAR */
 										 // TODO not sure about this one as it can be impossible to distinguish from uninitialized values
+#define OBISeq_NA ("\0")			// TODO
+#define OBIStr_NA ("\0")			// TODO
 
 
 /**
@@ -32,7 +34,7 @@ typedef enum OBIBool {
     FALSE      = 0,
     TRUE       = 1,
     OBIBool_NA = 2
-} obibool_t, *obibool_p; 		/**< a boolean true/false value */
+} obibool_t, *obibool_p; 		/**< a boolean true/false value */	// TODO check name convention?
 
 
 /**
@@ -46,7 +48,7 @@ typedef enum OBIType {
 	OBI_CHAR,					/**< a character (C type : char) */
 	OBI_STR,				    /**< an index in a data structure (C type : int64_t) referring to a character string */
 	OBI_SEQ,					/**< an index in a data structure (C type : int64_t) referring to a DNA sequence */
-	OBI_IDX					    /**< an index referring to a line in another column (C type : int64_t) */
+	OBI_IDX					    /**< an index referring to a line in another column (C type : int64_t) */	// TODO delete?
 } OBIType_t, *OBIType_p;
 
 

src/obiview.c

@@ -0,0 +1,949 @@
+/********************************************************************
+ * Obiview functions                                                 *
+ ********************************************************************/
+
+/**
+ * @file obiview.c
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date 16 December 2015
+ * @brief Obiview functions.
+ */
+
+
+// TODO
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdbool.h>
+#include <fcntl.h>
+#include <sys/mman.h>
+
+#include "obidms.h"
+#include "obiview.h"
+#include "obierrno.h"
+#include "obidebug.h"
+#include "obidmscolumn.h"
+#include "private_at_functions.h"
+#include "obilittlebigman.h"
+#include "obidmscolumn_idx.h"
+
+
+#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
+ *
+ **************************************************************************/
+
+
+/**
+ * Internal function building the file name where obiviews are stored.
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @returns A pointer to the file name.
+ * @retval NULL if an error occurred.
+ *
+ * @param dms_name The name of the OBIDMS.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static char* build_obiview_file_name();
+
+
+/**	TODO public
+ * Internal function creating the file containing basic informations on the OBIDMS.
+ *
+ * This file contains:
+ * 		- The endianness of the platform
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param dms_file_descriptor The file descriptor for the OBIDMS directory.
+ * @param dms_name The name of the OBIDMS.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int create_obiview_file(int dms_file_descriptor);
+
+
+/************************************************************************
+ *
+ * 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 char* build_obiview_file_name()
+{
+	char* file_name;
+
+	// Build file name
+	if (asprintf(&file_name, OBIVIEW_FILE_NAME) < 0)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nProblem building an obiview file name");
+		return NULL;
+	}
+
+	return file_name;
+}
+
+
+size_t get_platform_header_size()
+{
+	size_t header_size;
+	size_t rounded_header_size;
+	double multiple;
+
+	header_size = sizeof(Obiviews_header_t);
+
+	multiple = 	ceil((double) header_size / (double) getpagesize());
+
+	rounded_header_size = multiple * getpagesize();
+
+	return rounded_header_size;
+}
+
+
+size_t get_platform_views_size(nb_of_views)
+{
+	size_t obiview_size;
+	size_t rounded_obiview_size;
+	double multiple;
+
+	obiview_size = sizeof(Obiview_infos_t);
+
+	multiple = 	ceil((double) (obiview_size*nb_of_views) / (double) getpagesize());
+
+	rounded_obiview_size = multiple * getpagesize();
+
+	return rounded_obiview_size;
+}
+
+
+int create_obiview_file(int dms_file_descriptor)
+{
+	char* 				file_name;
+	int 				obiview_file_descriptor;
+	size_t  			header_size;
+//	size_t  			view_size;
+	size_t  			file_size;
+	Obiviews_header_p 	header;
+
+	// Create file name
+	file_name = build_obiview_file_name();
+	if (file_name == NULL)
+		return -1;
+
+    // Create file
+	obiview_file_descriptor = openat(dms_file_descriptor, file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
+	if (obiview_file_descriptor < 0)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError creating an obiview file");
+		free(file_name);
+		return -1;
+	}
+
+	free(file_name);
+
+	// Truncate file to the right size
+	header_size = get_platform_header_size();
+	//view_size = get_platform_views_size(1);
+	file_size = header_size; // + view_size;
+
+	if (ftruncate(obiview_file_descriptor, file_size) < 0)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError truncating an obiview file to the right size");
+		close(obiview_file_descriptor);
+		return -1;
+	}
+
+	// Map the header
+	header = mmap(NULL,
+  	  	   	      header_size,
+				  PROT_READ | PROT_WRITE,
+				  MAP_SHARED,
+				  obiview_file_descriptor,
+				  0
+ 	 	   	   	 );
+	if (header == MAP_FAILED)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError mmapping an obiview file header");
+		close(obiview_file_descriptor);
+		return -1;
+	}
+
+	// Initialize the header
+	header->header_size = header_size;
+	header->views_size = 0;
+	header->view_count = 0;
+
+	// Unmap the header
+	if (munmap(header, header_size) < 0)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError munmapping an obiview file header");
+		close(obiview_file_descriptor);
+		return -1;
+	}
+
+	close(obiview_file_descriptor);
+
+	return 0;
+}
+
+
+/**********************************************************************
+ *
+ * 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
+ *
+ **********************************************************************/
+
+
+Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection)
+{
+	Obiview_p view;
+	int i;
+	index_t line_nb;
+
+	view = (Obiview_p) malloc(sizeof(Obiview_t));
+	if (view == NULL)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError allocating memory for a view");
+		return NULL;
+	}
+
+	// Clone view to clone if there is one
+	if (view_to_clone != NULL)
+	{
+		if (!(view_to_clone->read_only))
+		{
+			obi_set_errno(OBIVIEW_ERROR);
+			obidebug(1, "\nA view can not be cloned if it is not read-only");
+			free(view);
+			return NULL;
+		}
+
+		view->dms          = dms;
+		view->column_count = view_to_clone->column_count;
+		if ((view_to_clone->line_selection != NULL) && (line_selection == NULL))	// reorder conditions
+		{
+			view->line_selection = obi_open_column(dms, ((view_to_clone->line_selection)->header)->name, ((view_to_clone->line_selection)->header)->version);
+			if (view->line_selection == NULL)
+				return NULL;
+			view->line_count = view_to_clone->line_count;
+		}
+		else if (line_selection != NULL)
+		{
+			view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
+			if ((view->line_selection) == NULL)
+			{
+				obidebug(1, "\nError creating a column corresponding to a line selection");
+				return NULL;
+			}
+			view->line_count = 0;
+			i = 0;
+			for (i=0; line_selection[i] != -1; i++)
+			{
+				line_nb = line_selection[i];
+
+				if (line_nb > view_to_clone->line_count)
+				{
+					obi_set_errno(OBIVIEW_ERROR);
+					obidebug(1, "\nError trying to select a line for a new view that is beyond the line count of the view to clone");
+					obi_close_column(view->line_selection);
+					free(view);
+					return NULL;
+				}
+
+				if (view_to_clone->line_selection != NULL)
+					line_nb = obi_column_get_index(view_to_clone->line_selection, line_nb);
+
+				if (obi_column_set_index(view->line_selection, ((view->line_selection)->header)->lines_used, line_nb) < 0)
+				{
+					obi_close_column(view->line_selection);
+					free(view);
+					return NULL;
+				}
+
+				// Update view line count
+				(view->line_count)++;
+			}
+		}
+		else
+		{
+			view->line_selection = NULL;
+			view->line_count = view_to_clone->line_count;
+		}
+
+		for (i=0; i<(view_to_clone->column_count); i++)
+		{
+			(view->columns)[i] = obi_open_column(dms, (((view_to_clone->columns)[i])->header)->name, (((view_to_clone->columns)[i])->header)->version);
+			if ((view->columns)[i] == NULL)
+			{
+				obi_close_column(view->line_selection);
+				free(view);
+				return NULL;
+			}
+		}
+
+		strcpy(view->created_from, view_to_clone->name);
+		view->new_line_selection = NULL;
+	}
+	// Else, fill empty view structure
+	else
+	{
+		view->dms                = dms;
+		view->column_count       = 0;
+		view->line_count         = 0;
+		view->line_selection     = NULL;
+		view->new_line_selection = NULL;
+		(view->created_from)[0]    = '\0';
+		//view->columns            = NULL; TODO
+	}
+
+	strcpy(view->name, view_name);
+	view->read_only = 0;
+
+	return view;
+}
+
+
+Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection)
+{
+	Obiview_p view;
+	Obiview_p view_to_clone;
+
+	view_to_clone = obi_open_view(dms, view_to_clone_name);
+	if (view_to_clone == NULL)
+		return NULL;
+	view = obi_new_view(dms, view_name, view_to_clone, line_selection);
+	return view;
+}
+
+
+Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
+{
+	Obiview_p			view;
+	bool      			first_view;
+	char*       		view_file_name;
+	int 				obiview_file_descriptor;
+	size_t  			header_size;
+	Obiviews_header_p 	header;
+	Obiview_infos_p 	views;
+	Obiview_infos_p     view_infos;
+	OBIDMS_column_p     column;
+	int					i;
+	int 				view_number;
+
+	// Check if 1st view : view file doesn't exist
+	first_view = 0;
+
+	view_file_name = build_obiview_file_name();
+	if (view_file_name == NULL)
+		return NULL;
+
+	// Open view file, read header size and map header and views
+	obiview_file_descriptor = openat(dms->dir_fd, view_file_name, O_RDWR, 0777);
+	if (obiview_file_descriptor < 0)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError opening an obiview file");
+		free(view_file_name);
+		return NULL;
+	}
+
+	free(view_file_name);
+
+	// Read the header size
+	if (read(obiview_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError reading the header size of an obiview file (trying to open a view when there are none?)");
+		close(obiview_file_descriptor);
+		return NULL;
+	}
+
+	// Map the header
+	header = mmap(NULL,
+				  header_size,
+				  PROT_READ | PROT_WRITE,
+				  MAP_SHARED,
+				  obiview_file_descriptor,
+				  0
+ 	 	   	   	 );
+	if (header == MAP_FAILED)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError mmapping an obiview file header");
+		close(obiview_file_descriptor);
+		return NULL;
+	}
+
+	// Map the views
+	views = mmap(NULL,
+				 header->views_size,
+				 PROT_READ | PROT_WRITE,
+				 MAP_SHARED,
+				 obiview_file_descriptor,
+				 header_size
+ 	 	   	   	);
+	if (views == MAP_FAILED)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError mmapping the views from an obiview file");
+		munmap(header, header_size);
+		close(obiview_file_descriptor);
+		return NULL;
+	}
+
+	// Find and open view that should be read with the line selection associated
+	view_number = -1;
+	if (view_name == NULL)	// If view name is NULL, open the latest view TODO discuss
+		view_number = (header->view_count) - 1;
+	else
+	{
+		for (i=0; i<(header->view_count); i++)
+		{
+			if (!strcmp((views+i)->name, view_name))
+			{	// Found the view to open
+				view_number = i;
+			}
+		}
+	}
+
+	if (view_number == -1)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError: the view '%s' to open was not found", view_name);
+		munmap(views, header->views_size);
+		munmap(header, header_size);
+		close(obiview_file_descriptor);
+		return NULL;
+	}
+
+	view_infos = views + view_number;
+
+	view = (Obiview_p) malloc(sizeof(Obiview_t));
+	if (view == NULL)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError allocating memory for a view");
+		munmap(views, header->views_size);
+		munmap(header, header_size);
+		close(obiview_file_descriptor);
+		return NULL;
+	}
+
+	if (view_infos->all_lines)
+		view->line_selection = NULL;
+	else
+	{
+		view->line_selection = obi_open_column(dms, (view_infos->line_selection).column_name, (view_infos->line_selection).version);
+		if (view->line_selection == NULL)
+		{
+			munmap(views, header->views_size);
+			munmap(header, header_size);
+			close(obiview_file_descriptor);
+			return NULL;
+		}
+	}
+
+	view->dms = dms;
+	view->new_line_selection = NULL;
+	view->read_only = 1;
+	view->column_count = 0;
+	view->line_count = view_infos->line_count;
+	strcpy(view->created_from, view_infos->created_from);
+	strcpy(view->name, view_infos->name);
+
+	// Open the columns to read
+	for (i=0; i<(view_infos->column_count); i++)
+	{
+		column = obi_open_column(dms, ((view_infos->column_references)+i)->column_name, ((view_infos->column_references)+i)->version);
+		if (column == NULL)
+		{
+			obidebug(1, "\nError opening a column for a view: column %d: %s, version %d", i, ((view_infos->column_references)+i)->column_name, ((view_infos->column_references)+i)->version);
+			munmap(views, header->views_size);
+			munmap(header, header_size);
+			close(obiview_file_descriptor);
+			return NULL;
+		}
+		// Store column in the view
+		(view->columns)[view->column_count] = column;
+		view->column_count++;
+	}
+
+	// Munmap and close things TODO
+	munmap(views, header->views_size);
+	munmap(header, header_size);
+	close(obiview_file_descriptor);
+
+	return view;
+}
+
+
+int obi_view_add_column(Obiview_p view,
+						const char* column_name,
+						obiversion_t version_number,
+						OBIType_t data_type,
+						index_t nb_lines,
+						index_t nb_elements_per_line,
+						const char* elements_names,
+						const char* avl_name,
+						const char* comments,
+						bool create)	// all infos for creation or open
+{
+	OBIDMS_column_p column;
+
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to add a column in a read-only view");
+		return -1;
+	}
+
+	if (view->line_count > nb_lines)
+		nb_lines = view->line_count;
+	else if (nb_lines > view->line_count)
+		obi_view_update_lines(view, nb_lines);
+
+	// 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, avl_name, comments);
+	}
+	else
+	{ // Open column
+		column = obi_open_column(view->dms, column_name, version_number);
+	}
+
+	if (column == NULL)
+	{
+		obidebug(1, "\nError creating or opening a column to add to a view");
+		return -1;
+	}
+
+	// Store column in the view
+	(view->columns)[view->column_count] = column;
+	view->column_count++;
+	if (view->column_count == 1)	// first column in the view
+		view->line_count = (column->header)->lines_used;
+
+	return 0;
+}
+
+
+OBIDMS_column_p obi_view_clone_column(Obiview_p view, const char* column_name)
+{
+	int i;
+	OBIDMS_column_p current_line_selection = NULL;
+	OBIDMS_column_p column;
+	OBIDMS_column_p column_buffer;
+
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to delete a column in a read-only view");
+		return NULL;
+	}
+
+	if (view->new_line_selection != NULL)	// TODO Probably shouldn't happen
+		current_line_selection = view->new_line_selection;
+	else
+		current_line_selection = view->line_selection;
+
+	for (i=0; i<(view->column_count); i++)
+	{
+		if ((current_line_selection != NULL) || (!(strcmp((((view->columns)[i])->header)->name, column_name))))
+		{ // Clone with the right line selection and replace
+			column_buffer = (view->columns)[i];
+			(view->columns)[i] = obi_clone_column(view->dms, current_line_selection, (((view->columns)[i])->header)->name, (((view->columns)[i])->header)->version, 1);
+			if ((view->columns)[i] == NULL)
+			{
+				obi_set_errno(OBIVIEW_ERROR);
+				obidebug(1, "\nError cloning a column to replace in a view");
+				return NULL;
+			}
+			// Found the column to return
+			if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
+				column = (view->columns)[i];
+			else
+				obi_truncate_and_close_column(column_buffer);	// TODO weird closing after cloning but can't think of cleaner yet
+		}
+	}
+
+	if (view->line_selection != NULL)
+	{
+		obi_truncate_and_close_column(view->line_selection);
+		view->line_selection = NULL;
+	}
+	if (view->new_line_selection != NULL)
+	{
+		obi_truncate_and_close_column(view->new_line_selection);
+		view->new_line_selection = NULL;
+	}
+
+	return column;
+}
+
+
+int obi_view_delete_column(Obiview_p view, const char* column_name)
+{
+	int  i;
+	bool found;
+
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to delete a column in a read-only view");
+		return -1;
+	}
+
+	found = 0;
+
+	for (i=0; i<(view->column_count); i++)
+	{
+		if (!strcmp((((view->columns)[i])->header)->name, column_name))
+		{
+			obi_truncate_and_close_column((view->columns)[i]);
+			found = 1;
+		}
+		if (found)
+		{
+			if (i != ((view->column_count) - 1))	// not the last one
+				(view->columns)[i] = (view->columns)[i+1];
+			else  	// Last column
+				(view->columns)[i] = NULL;
+		}
+	}
+
+	if (!found)
+		return -1;
+
+	(view->column_count)--;
+
+	return 0;
+}
+
+
+int obi_select_line(Obiview_p view, index_t line_nb)
+{
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to select a line in a read-only view");
+		return -1;
+	}
+
+	// If column for line selection doesn't already exists, create it and store its informations
+	if ((view->new_line_selection) == NULL)
+	{
+		view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
+		if ((view->new_line_selection) == NULL)
+		{
+			obidebug(1, "\nError creating a column corresponding to a line selection");
+			return -1;
+		}
+	}
+
+	// If we are already working on a line selection, get the pointed line number
+	if (view->line_selection)
+		line_nb = obi_column_get_index(view->line_selection, line_nb);
+
+	if (obi_column_set_index(view->new_line_selection, ((view->new_line_selection)->header)->lines_used, line_nb) < 0)
+		return -1;
+
+	return 0;
+}
+
+
+int obi_select_lines(Obiview_p view, index_t* line_nbs)
+{
+	int i;
+	index_t line_nb;
+
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to select a line in a read-only view");
+		return -1;
+	}
+
+	// If column for line selection doesn't already exists, create it and store its informations
+	if ((view->new_line_selection) == NULL)
+	{
+		view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
+		if ((view->new_line_selection) == NULL)
+		{
+			obidebug(1, "\nError creating a column corresponding to a line selection");
+			return -1;
+		}
+	}
+
+	for (i=0; line_nbs[i] != -1; i++)
+	{
+		line_nb = line_nbs[i];
+
+		// If we are already working on a line selection, get the pointed line number
+		if (view->line_selection)
+			line_nb = obi_column_get_index(view->line_selection, line_nb);
+
+		if (obi_column_set_index(view->new_line_selection, ((view->new_line_selection)->header)->lines_used, line_nb) < 0)
+			return -1;
+	}
+
+	return 0;
+}
+
+
+int obi_view_update_lines(Obiview_p view, index_t line_count)
+{
+	int i;
+
+	for (i=0; i<(view->column_count); i++)
+	{
+		while (line_count > (((view->columns)[i])->header)->line_count)
+		{
+			// Enlarge the column
+			if (obi_enlarge_column((view->columns)[i]) < 0)
+		    	return -1;
+		}
+	}
+
+	view->line_count = line_count;
+
+	return 0;
+}
+
+
+OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name)
+{
+	int i;
+
+	for (i=0; i<(view->column_count); i++)
+	{
+		if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
+			return (view->columns)[i];
+	}
+	return NULL;
+}
+
+
+OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name)
+{
+	int i;
+
+	for (i=0; i<(view->column_count); i++)
+	{
+		if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
+			return ((view->columns)+i);
+	}
+	return NULL;
+}
+
+
+int obi_save_view(Obiview_p view)
+{
+	int i;
+    struct stat 		buffer;
+	char*       		view_file_name;
+	char*  				full_path;
+    int         		check_file;
+	int 				obiview_file_descriptor;
+	size_t  			header_size;
+	size_t				views_size;
+	size_t  			file_size;
+	Obiviews_header_p 	header;
+	Obiview_infos_p 	views;
+	Obiview_infos_p     view_infos;
+	OBIDMS_column_p     current_line_selection;
+
+	// 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;
+	}
+
+	view_file_name = build_obiview_file_name();
+	if (view_file_name == NULL)
+		return -1;
+
+	// Get the full path for the column directory
+	full_path = get_full_path((view->dms)->dir_fd, view_file_name);
+	if (full_path == NULL)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError getting the full path of an obiview file");
+		free(view_file_name);
+		return -1;
+	}
+
+	check_file = stat(full_path, &buffer);
+    if (check_file < 0)
+    { // 1st view: create view file
+    	if (create_obiview_file((view->dms)->dir_fd) < 0)
+    		return -1;
+    }
+
+	// Open view file, read header size and map header and views
+	obiview_file_descriptor = openat((view->dms)->dir_fd, view_file_name, O_RDWR, 0777);
+	if (obiview_file_descriptor < 0)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError opening an obiview file");
+		free(view_file_name);
+		return -1;
+	}
+
+	free(view_file_name);
+
+	// Read the header size
+	if (read(obiview_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError reading the header size of an obiview file");
+		close(obiview_file_descriptor);
+		return -1;
+	}
+
+	// Map the header
+	header = mmap(NULL,
+				  header_size,
+				  PROT_READ | PROT_WRITE,
+				  MAP_SHARED,
+				  obiview_file_descriptor,
+				  0
+ 	 	   	   	 );
+	if (header == MAP_FAILED)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError mmapping an obiview file header");
+		close(obiview_file_descriptor);
+		return -1;
+	}
+
+	// Truncate file to the right size to add a new view // TODO lock for multithreading
+	views_size = get_platform_views_size((header->view_count)+1);
+	file_size = header_size + views_size;
+
+	if (ftruncate(obiview_file_descriptor, file_size) < 0)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError truncating an obiview file to the right size");
+		munmap(header, header_size);
+		close(obiview_file_descriptor);
+		return -1;
+	}
+
+	header->views_size = views_size;
+
+	// Map the views
+	views = mmap(NULL,
+				 header->views_size,
+				 PROT_READ | PROT_WRITE,
+				 MAP_SHARED,
+				 obiview_file_descriptor,
+				 header_size
+ 	 	   	   	);
+	if (views == MAP_FAILED)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError mmapping the views from an obiview file");
+		munmap(header, header_size);
+		close(obiview_file_descriptor);
+		return -1;
+	}
+
+    // Write view infos
+	view_infos = views + (header->view_count);
+	view_infos->view_number = (header->view_count);
+	view_infos->column_count = view->column_count;
+	view_infos->creation_date = time(NULL);
+	strcpy(view_infos->created_from, view->created_from);
+	strcpy(view_infos->name, view->name);
+	// Store reference for the line selection associated with that view
+	if (view->new_line_selection != NULL)
+	{
+		view_infos->line_count = ((view->new_line_selection)->header)->lines_used;
+		current_line_selection = view->new_line_selection;
+	}
+	else
+	{
+		view_infos->line_count = view->line_count;
+		current_line_selection = view->line_selection;
+	}
+	if (current_line_selection != NULL)
+	{
+		view_infos->all_lines = 0;
+		strcpy((view_infos->line_selection).column_name, (current_line_selection->header)->name);
+		(view_infos->line_selection).version = (current_line_selection->header)->version;
+	}
+	else
+	{
+		view_infos->all_lines = 1;
+		((view_infos->line_selection).column_name)[0] = '\0';
+		(view_infos->line_selection).version = -1;
+	}
+	for (i=0; i<view->column_count; i++)
+	{
+		strcpy(((view_infos->column_references)+i)->column_name, (((view->columns)[i])->header)->name);
+		((view_infos->column_references)+i)->version = (((view->columns)[i])->header)->version;
+	}
+
+	// Increment view count
+	(header->view_count)++;
+
+	// Unmap and close file
+	munmap(views, header->views_size);
+	munmap(header, header_size);
+	close(obiview_file_descriptor);
+
+	return 0;
+}
+
+
+int obi_close_view(Obiview_p view)
+{
+	int i;
+
+	for (i=0; i < (view->column_count); i++)
+	{
+		obi_close_column((view->columns)[i]);
+	}
+
+	free(view);
+
+	return 0;
+}
+
+
+int obi_save_and_close_view(Obiview_p view)
+{
+	if (!(view->read_only))	// TODO discuss
+	{
+		if (obi_save_view(view) < 0)
+			return -1;
+	}
+	if (obi_close_view(view) < 0)
+		return -1;
+	return 0;
+}
+

src/obiview.h

@@ -0,0 +1,158 @@
+/********************************************************************
+ * Obiview header file                                              *
+ ********************************************************************/
+
+/**
+ * @file obiview.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date 16 December 2015
+ * @brief Header file for the OBIDMS view functions and structures.
+ */
+
+
+#ifndef OBIVIEW_H_
+#define OBIVIEW_H_
+
+
+#include <stdlib.h>
+#include <errno.h>
+#include <stdio.h>
+#include <stdbool.h>
+#include <time.h>
+#include <math.h>
+
+#include "obidms.h"
+#include "obidmscolumn.h"
+#include "obierrno.h"
+
+
+#define OBIVIEW_NAME_MAX_LENGTH (10239)   /**< The maximum length of an OBIDMS view name.
+                                	 	   */
+#define OBIVIEW_FILE_NAME "obiviews"
+
+#define LINES_COLUMN_NAME "LINES"
+
+
+/**
+ * @brief .
+ */
+typedef struct Column_reference {
+	char 	   	 column_name[OBIDMS_COLUMN_MAX_NAME+1];    /**< Name of the column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	    */
+	obiversion_t version;				   		    	   /**< Version of the column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	    */
+} Column_reference_t, *Column_reference_p;
+
+
+/**
+ * @brief .
+ */
+typedef struct Obiview {
+
+	OBIDMS_p         	dms;
+
+	bool             	read_only;
+
+	OBIDMS_column_p  	line_selection;
+
+	OBIDMS_column_p  	new_line_selection;
+
+	index_t			 	line_count;
+
+	int    			 	column_count;
+
+	OBIDMS_column_p  	columns[MAX_NB_OPENED_COLUMNS];
+
+	char   				name[OBIVIEW_NAME_MAX_LENGTH+1];
+
+	char				created_from[OBIVIEW_NAME_MAX_LENGTH+1];
+
+	int					view_number;
+
+} Obiview_t, *Obiview_p;
+
+
+/**
+ * @brief .
+ */
+typedef struct Obiview_infos {
+	int					view_number;
+
+	int 				column_count;
+
+	index_t             line_count;
+
+	char   				name[OBIVIEW_NAME_MAX_LENGTH+1];
+
+	char				created_from[OBIVIEW_NAME_MAX_LENGTH+1];
+
+	time_t 		 		creation_date;
+
+	bool				all_lines;
+
+	Column_reference_t	line_selection;
+
+	Column_reference_t	column_references[MAX_NB_OPENED_COLUMNS];
+
+} Obiview_infos_t, *Obiview_infos_p;
+
+
+/**
+ * @brief .
+ */
+typedef struct Obiviews_header {
+	size_t header_size;
+	size_t views_size;
+	int    view_count;
+} Obiviews_header_t, *Obiviews_header_p;
+
+
+/**
+ * @brief .
+ */
+typedef struct Obiviews {	// not used
+	Obiviews_header_p	header;
+
+	Obiview_infos_p 	views;
+
+} Obiviews_t, *Obiviews_p;
+
+
+Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection);
+
+Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection);
+
+Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
+
+int obi_view_add_column(Obiview_p view,
+						const char* column_name,
+						obiversion_t version_number,
+						OBIType_t data_type,
+						index_t nb_lines,
+						index_t nb_elements_per_line,
+						const char* elements_names,
+						const char* avl_name,
+						const char* comments,
+						bool create);
+
+int obi_view_delete_column(Obiview_p view, const char* column_name);
+
+int obi_select_line(Obiview_p view, index_t line_nb);
+
+int obi_select_lines(Obiview_p view, index_t* line_nbs);
+
+int obi_view_update_lines(Obiview_p view, index_t line_count);
+
+OBIDMS_column_p obi_view_clone_column(Obiview_p view, const char* column_name);
+
+OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name);
+
+OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name);
+
+int obi_save_view(Obiview_p view);
+
+int obi_close_view(Obiview_p view);
+
+int obi_save_and_close_view(Obiview_p view);
+
+#endif /* OBIVIEW_H_ */