Strong refactoring 1

2016-12-26 13:35:31 +01:00
parent 3cedd00d7f
commit daacd0df76
58 changed files with 732 additions and 1525 deletions
--- a/python/obitools3/obidms/init.py
+++ b/python/obitools3/obidms/init.py
--- a/python/obitools3/obidms/_obidms.cfiles
+++ b/python/obitools3/obidms/_obidms.cfiles
--- a/python/obitools3/obidms/_obidms.pxd
+++ b/python/obitools3/obidms/_obidms.pxd
--- a/python/obitools3/obidms/_obidms.pyx
+++ b/python/obitools3/obidms/_obidms.pyx
@ -10,7 +10,13 @@ from .capi.obidmscolumn cimport obi_close_column, \
                                OBIDMS_column_header_p

 from .capi.obiutils cimport obi_format_date
-                   
+
+from .capi.obiview cimport Obiview_p, \
+                           Obiview_infos_p, \
+                           Alias_column_pair_p, \
+                           obi_view_map_file, \
+                           obi_view_unmap_file
+                                              
 from .capi.obitypes cimport const_char_p, \
                            OBIType_t, \
                            OBI_INT, \
@ -23,11 +29,6 @@ from .capi.obitypes cimport const_char_p, \
                            name_data_type, \
                            only_ATGC    # discuss
                            
-from ._obidms cimport OBIDMS, \
-                      OBIDMS_column, \
-                      OBIView, \
-                      OBIView_line
-
 from ._obitaxo cimport OBI_Taxonomy


--- a/python/obitools3/obidms/_obidmscolumn.cfiles
+++ b/python/obitools3/obidms/_obidmscolumn.cfiles
--- a/python/obitools3/dms/_obidmscolumn.pxd
+++ b/python/obitools3/dms/_obidmscolumn.pxd
@ -0,0 +1,41 @@
+#cython: language_level=3
+
+from .capi.obidmscolumn cimport OBIDMS_column_p, \
+                                OBIDMS_column_header_p, \
+                                obi_close_column, \
+                                obi_column_prepare_to_get_value
+                                
+from .capi.obiview      cimport Obiview_p, \
+                                obi_view_get_pointer_on_column_in_view
+                                
+from .capi.obitypes     cimport obiversion_t, \
+                                OBIType_t, \
+                                index_t, \
+                                name_data_type
+                                
+from .capi.obiutils     cimport obi_format_date
+
+from ._obiview cimport OBIView
+
+cdef class OBIDMS_column:
+
+    cdef  bytes              _alias               # associated property: alias
+    cdef  OBIDMS_column_p*   _pointer
+    cdef  OBIView            _view
+        
+    cpdef close(self)
+    
+    @staticmethod
+    cdef type get_subclass_type(OBIDMS_column_p column_p)
+
+cdef class OBIDMS_column_line:
+
+    cdef OBIDMS_column    _column
+    cdef OBIDMS_column_p  _column_p
+    cdef OBIDMS_column_p* _column_pp
+    cdef index_t          _index
+    cdef int              _len
+
+    cpdef update(self, data)
+    
+cdef register_column_class(OBIType_t obitype,type classe)
--- a/python/obitools3/dms/_obidmscolumn.pyx
+++ b/python/obitools3/dms/_obidmscolumn.pyx
@ -0,0 +1,182 @@
+#cython: language_level=3
+
+cdef dict __OBIDMS_COLUMN_CLASS__ = {}
+
+cdef class Column :
+    """
+    The OBIDMS.Column class 
+    """
+
+    # Note: should only be initialized through a subclass
+    def __init__(self,
+                 View view,
+                 object name):
+        '''
+        Create a new OBDMS column objected referring to a already created column
+        in the context of a view. 
+        
+        This constructor is normally only called by subclass constructor.
+        
+            @param view: The view object containing the column.
+            @type  view: OBIView
+            @param name: The name of the column in the view
+            @type  name: a `str` or a `bytes`
+        '''
+        
+        cdef OBIDMS_column_p* column_pp
+
+        # Check that the class is only created as a subclass instance
+        if type(self)==Column or not isinstance(self, Column):
+            raise RuntimeError('OBIDMS.Column constructor cannot be called directly')
+        
+        column_pp = obi_view_get_pointer_on_column_in_view(view._pointer, 
+                                                           tobytes(column_alias))
+        
+        # Fill structure
+        self._alias    = column_alias
+        self._pointer  = column_pp
+        self._view     = view
+        
+    def __len__(self):
+        '''
+        implements the len() function for the Column class
+        
+            @rtype: `int`
+        '''
+        return self.lines_used
+    
+    def __sizeof__(self):
+        '''
+        returns the size of the C object wrapped by the Column instance
+        '''
+        cdef OBIDMS_column_header_p header = self._pointer[0].header
+        return header.header_size + header.data_size
+    
+    def __iter__(self):
+        cdef index_t line_nb  
+
+        for line_nb in range(self.lines_used):
+            yield self[line_nb]
+                
+    def __str__(self) :
+        cdef str to_print
+        to_print = ''
+        for line in self :
+            to_print = to_print + str(line) + "\n"
+        return to_print
+
+    def __repr__(self) :
+        return b"%s, original name: %s, version %d, data type: %d" % (
+                    self._alias,
+                    self.original_name,
+                    self.version,
+                    self.data_type
+                )
+        
+    cpdef close(self):
+        if obi_close_column((self._pointer)[0]) < 0 :
+            raise Exception("Problem closing a column")
+
+    # Column alias property getter and setter
+    @property
+    def alias(self):
+        return self._alias
+    @alias.setter
+    def alias(self, new_alias):  # @DuplicatedSignature
+        self._view.change_column_alias(self._alias, new_alias)
+
+    # elements_names property getter
+    @property
+    def elements_names(self):
+        return (((self._pointer)[0].header).elements_names).split(b';')
+
+    # nb_elements_per_line property getter
+    @property
+    def nb_elements_per_line(self):
+        return ((self._pointer)[0].header).nb_elements_per_line
+
+    # data_type property getter
+    @property
+    def data_type(self):
+        return name_data_type(((self._pointer)[0].header).returned_data_type)
+
+    # original_name property getter
+    @property
+    def original_name(self):
+        return ((self._pointer)[0].header).name
+
+    # version property getter
+    @property
+    def version(self):
+        return ((self._pointer)[0].header).version
+
+    # lines_used property getter
+    @property
+    def lines_used(self):
+        return (self._pointer)[0].header.lines_used
+
+    # comments property getter
+    @property
+    def comments(self):
+        return (self._pointer)[0].header.comments
+    
+    # creation_date property getter
+    @property
+    def creation_date(self):
+        return obi_format_date((self._pointer)[0].header.creation_date)
+    
+    @staticmethod
+    cdef type get_subclass_type(OBIDMS_column_p column_p) :
+        
+        cdef type                   subclass
+        cdef OBIType_t              col_type
+
+        col_type = column_p.header.returned_data_type         
+        subclass = __OBIDMS_COLUMN_CLASS__[col_type]
+
+        return subclass
+
+    
+
+
+######################################################################################################
+
+
+cdef class OBIDMS_column_line :
+
+    def __init__(self, OBIDMS_column column, index_t line_nb) :
+        self._index = line_nb
+        self._column = column
+        self._column_pp = column._pointer
+        self._column_p  = NULL
+        self._len = self._column_pp[0].header.nb_elements_per_line
+
+        if obi_column_prepare_to_get_value(self._column_pp[0],line_nb) < 0:
+            raise IndexError("Cannot access to the line %d" % line_nb)
+        
+        
+    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))
+    
+    cpdef update(self, data):
+        if isinstance(data, dict):
+            data=data.items()
+        for key,value in data:
+            if key in self:
+                self[key]=value
+
+
+######################################################################################################
+
+
+cdef register_column_class(OBIType_t obitype,type classe):
+    """
+    Each sub class of `OBIDMS_column` needs to be registered after its declaration
+    to declare its relationship with an `OBIType_t`
+    """
+    assert issubclass(classe,OBIDMS_column)
+    
+    __OBIDMS_COLUMN_CLASS__[obitype]=classe
--- a/python/obitools3/obidms/_obidmscolumn_bool.cfiles
+++ b/python/obitools3/obidms/_obidmscolumn_bool.cfiles
--- a/python/obitools3/dms/_obidmscolumn_bool.pxd
+++ b/python/obitools3/dms/_obidmscolumn_bool.pxd
@ -0,0 +1,57 @@
+#cython: language_level=3
+
+from .capi.obiview      cimport obi_get_bool_with_elt_name_and_col_p_in_view, \
+                                obi_get_bool_with_elt_idx_and_col_p_in_view, \
+                                obi_set_bool_with_elt_name_and_col_p_in_view, \
+                                obi_set_bool_with_elt_idx_and_col_p_in_view
+
+from cpython.bool cimport bool, PyBool_FromLong
+from .capi.obitypes cimport index_t, \
+                            const_char_p, \
+                            OBIType_t, \
+                            obibool_t, \
+                            OBI_BOOL, \
+                            OBIBool_NA
+                            
+from .capi.obierrno  cimport obi_errno
+
+from ._obidmscolumn  cimport OBIDMS_column, \
+                             OBIDMS_column_line, \
+                             OBIDMS_column_p, \
+                             register_column_class
+                             
+from .capi.obidmscolumn  cimport  obi_column_get_obibool_with_elt_name, \
+                                  obi_column_get_obibool_with_elt_idx, \
+                                  obi_column_set_obibool_with_elt_name, \
+                                  obi_column_set_obibool_with_elt_idx
+
+
+from obitools3.utils cimport str2bytes, bytes2str
+
+cdef class OBIDMS_column_line_bool(OBIDMS_column_line) :
+    cdef update_pointer(self)
+    
+    @staticmethod
+    cdef bool obibool_t2bool(obibool_t value)
+    
+    @staticmethod
+    cdef bool2obibool_t(bool value)
+    
+    cpdef bool get_bool_item_by_name(self,bytes element_name)
+    cpdef bool get_bool_item_by_idx(self,index_t index)
+    cpdef set_bool_item_by_name(self,bytes element_name,bool value)
+    cpdef set_bool_item_by_idx(self,index_t index,bool value)
+
+      
+#    cdef obibool_t [:]    _data_view
+
+cdef class OBIDMS_column_bool(OBIDMS_column):
+    cdef OBIDMS_column _new(OBIView view,
+                            bytes column_name,
+                            index_t nb_elements_per_line=1,
+                            object elements_names=None,
+                            bytes comments=b""):
+
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+
--- a/python/obitools3/dms/_obidmscolumn_bool.pyx
+++ b/python/obitools3/dms/_obidmscolumn_bool.pyx
@ -0,0 +1,294 @@
+#cython: language_level=3
+ 
+
+cdef class OBIDMS_column_line_bool(OBIDMS_column_line) :
+
+    cdef update_pointer(self):
+        """
+        Checks if the obicolumn address changed since the last call and update
+        if need the `_column_p` and `_data_view` data structure fields.
+        """
+        cdef OBIDMS_column_p column_p = self._column_pp[0]
+        
+        if column_p != self._column_p:
+            self._column_p  = column_p
+#             self._data_view = (<obibool_t*> (column_p.data)) + \
+#                               self._index * column_p.header.nb_elements_per_line
+    
+    @staticmethod                      
+    cdef bool obibool_t2bool(obibool_t value):
+        cdef bool      result
+        
+        if value == OBIBool_NA :
+            result = None
+        else :
+            result = PyBool_FromLong(value)
+            
+        return result
+    
+    @staticmethod                      
+    cdef bool2obibool_t(bool value):
+        cdef obibool_t result
+        
+        if value is None:
+            result=OBIBool_NA 
+        else:
+            result= <obibool_t> <int> value
+            
+        return result
+        
+
+    def __init__(self, OBIDMS_column column, index_t line_nb) :
+        """
+        Creates a new `OBIDMS_column_line_bool`
+        
+            @param column: an OBIDMS_column instance
+            @param line_nb: the line in the column 
+        """
+        
+        OBIDMS_column_line.__init__(self,column,line_nb)
+        self.update_pointer()
+
+        
+        
+    cpdef bool get_bool_item_by_name(self,bytes element_name):
+        """
+        Returns the value associated to the name `element_name` of the current line
+        
+            @param element_name: a `bytes` instance containing the name of the element
+            
+            @return: the `bool` value corresponding to the name
+        """
+        cdef char*     cname = element_name
+        cdef obibool_t value 
+        global obi_errno
+        
+        self.update_pointer()
+        
+        value = obi_column_get_obibool_with_elt_name(self._column_p, 
+                                                     self._index, 
+                                                     cname)
+        
+        if obi_errno > 0 :
+            obi_errno = 0
+            raise KeyError("Cannot access to key %s" % bytes2str(element_name))
+                    
+        return OBIDMS_column_line_bool.obibool_t2bool(value)
+
+    cpdef bool get_bool_item_by_idx(self,index_t index):
+        """
+        Returns the value associated to the name `element_name` of the current line
+        
+            @param index: a `int` instance containing the index of the element
+            
+            @return: the `bool` value corresponding to the name
+        """
+        cdef obibool_t value  # @DuplicatedSignature
+        global obi_errno
+
+        
+        self.update_pointer()
+        
+        value = obi_column_get_obibool_with_elt_idx(self._column_p, 
+                                                    self._index, 
+                                                    index)
+        
+        if obi_errno > 0 :
+            obi_errno = 0
+            raise IndexError("Cannot access to element %d" % index)
+                    
+        return OBIDMS_column_line_bool.obibool_t2bool(value)
+
+        
+    def __getitem__(self, object element_name) :
+        cdef bytes     name
+        cdef int   cindex
+        cdef obibool_t value        
+        cdef type      typearg = type(element_name)
+        cdef bool      result
+        
+
+        if typearg == int:
+            cindex=element_name
+            if cindex < 0:
+                cindex = self._len - cindex
+            result=self.get_bool_item_by_idx(cindex)
+        elif typearg == bytes:
+            result=self.get_bool_item_by_name(element_name)
+        elif typearg == str:
+            name = str2bytes(element_name)
+            result=self.get_bool_item_by_name(name)
+        
+        return result
+    
+    cpdef set_bool_item_by_name(self,bytes element_name,bool value):
+        """
+        Sets the value associated to the name `element_name` of the current line
+        
+            @param element_name: a `bytes` instance containing the name of the element
+            @param value: a `bool` instance of the new value
+            
+            @return: the `bool` value corresponding to the name
+        """
+        cdef char*     cname = element_name
+        cdef obibool_t cvalue 
+        
+        self.update_pointer()
+        cvalue = OBIDMS_column_line_bool.bool2obibool_t(value)
+
+        if ( obi_column_set_obibool_with_elt_name(self._column_p, 
+                                                  self._index, 
+                                                  cname,
+                                                  cvalue) < 0 ):
+            raise KeyError("Cannot access to key %s" % bytes2str(element_name))
+                    
+    cpdef set_bool_item_by_idx(self,index_t index,bool value):
+        """
+        Sets the value associated to the name `element_name` of the current line
+        
+            @param index: a `int` instance containing the index of the element
+            @param value: a `bool` instance of the new value
+            
+            @return: the `bool` value corresponding to the name
+        """
+        cdef obibool_t cvalue  # @DuplicatedSignature
+        
+        self.update_pointer()
+        cvalue = OBIDMS_column_line_bool.bool2obibool_t(value)
+
+        if ( obi_column_set_obibool_with_elt_idx(self._column_p, 
+                                                 self._index, 
+                                                 index,
+                                                 cvalue) < 0 ):
+            raise IndexError("Cannot access to item index %d" % index)
+                    
+
+             
+    def __setitem__(self, object element_name, object value):
+        cdef bytes     name
+        cdef int   cindex
+        cdef type      typearg = type(element_name)
+        cdef bool      result
+        
+
+        if typearg == int:
+            cindex=element_name
+            if cindex < 0:
+                cindex = self._len - cindex
+            self.set_bool_item_by_idx(cindex,value)
+        elif typearg == bytes:
+            self.set_bool_item_by_name(element_name,value)
+        elif typearg == str:
+            name = str2bytes(element_name)
+            self.set_bool_item_by_name(name,value)
+
+    def __repr__(self) :
+        return str(self._column.get_line(self._index))
+    
+    def __len__(self):
+        return self._len
+
+
+
+cdef class OBIDMS_column_bool(OBIDMS_column):
+
+    @staticmethod
+    cdef OBIDMS_column _new(OBIView view,
+                            bytes column_name,
+                            index_t nb_elements_per_line=1,
+                            object elements_names=None,
+                            bytes comments=b""):
+                            
+        cdef bytes elements_names_b
+        cdef char* elements_names_p
+        cdef OBIDMS_column new_column
+        
+        if elements_names is not None:
+            elements_names_b = b''.join([tobytes(x) for x in elements_names])
+            elements_names_p = elements_names_b
+        else:
+            elements_names_p = NULL
+                            
+        if (obi_view_add_column(view                      = view._pointer,
+                                column_name               = column_name,
+                                version_number            = -1,
+                                alias                     = NULL,
+                                data_type                 = OBI_BOOL,
+                                nb_lines                  = len(view),
+                                nb_elements_per_line      = nb_elements_per_line,
+                                elements_names            = elements_names_p,
+                                indexer_name              = NULL,
+                                associated_column_name    = NULL,
+                                associated_column_version = -1,
+                                comments                  = comments,
+                                create                    = True)<0):
+            raise RuntimeError("Cannot create column %s in view %s" % (bytes2str(column_name),
+                                                                       bytes2str(view.name)))
+        
+        view.__init_columns__()
+        new_column = self._columns[column_name]
+        
+        return new_column
+        
+    @staticmethod
+    def new(OBIView view,
+            object column_name,
+            index_t nb_elements_per_line=1,
+            object elements_names=None,
+            object comments=b""):
+        
+        return OBIDMS_column_bool._new(view,
+                                       tobytes(column_name),
+                                       nb_elements_per_line,
+                                       elements_names,
+                                       tobytes(comments))
+        
+    cpdef add_to_view(self,
+                      OBIView view,
+                      object column_name=None,
+                      object comments=b""):
+                      
+        cdef OBIDMS_column_p column_p = self._column_pp[0]
+        cdef bytes alias
+        
+        if (column_name is None):
+            alias = self._alias
+        else:
+            alias = tobytes(column_name)
+                      
+        obi_view_add_column(view                      = view._ponter,
+                            column_name               = column_p.header.name,
+                            version_number            = column_p.header.version,
+                            alias                     = alias,
+                            data_type                 = OBI_BOOL,
+                            nb_lines                  = column_p.header.lines_used,
+                            nb_elements_per_line      = column_p.header.nb_elements_per_line,
+                            elements_names            = column_p.header.elements_names,
+                            indexer_name              = NULL,
+                            associated_column_name    = NULL,
+                            associated_column_version = NULL,
+                            comments                  = tobytes(comments),
+                            create                    = False)
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef obibool_t value
+        cdef object result
+        global obi_errno
+
+        value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIBool_NA :
+            result = None
+        else :
+            result = PyBool_FromLong(value)
+        return result
+    
+    cpdef set_line(self, index_t line_nb, object value):
+        if value is None :
+            value = OBIBool_NA
+        if obi_set_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, <obibool_t> value) < 0:
+            raise Exception("Problem setting a value in a column")
+
+
+register_column_class(OBI_BOOL,OBIDMS_column_bool)
--- a/python/obitools3/obidms/_obiseq.cfiles
+++ b/python/obitools3/obidms/_obiseq.cfiles
--- a/python/obitools3/obidms/_obiseq.pxd
+++ b/python/obitools3/obidms/_obiseq.pxd
@ -1,6 +1,6 @@
 #cython: language_level=3

-from ._obidms cimport OBIView_line
+from ._obiview cimport OBIView_line


 cdef class OBI_Seq(dict) :
--- a/python/obitools3/obidms/_obiseq.pyx
+++ b/python/obitools3/obidms/_obiseq.pyx
--- a/python/obitools3/obidms/_obitaxo.cfiles
+++ b/python/obitools3/obidms/_obitaxo.cfiles
--- a/python/obitools3/obidms/_obitaxo.pxd
+++ b/python/obitools3/obidms/_obitaxo.pxd
--- a/python/obitools3/obidms/_obitaxo.pyx
+++ b/python/obitools3/obidms/_obitaxo.pyx
--- a/python/obitools3/obidms/_obiview.pxd
+++ b/python/obitools3/obidms/_obiview.pxd
@ -1,5 +1,9 @@
 #cython: language_level=3

+from .capi.obitypes cimport obiversion_t, \
+                            index_t, \
+                            only_ATGC
+
 from .capi.obiview cimport Obiview_p, \
                           Obiview_infos_p, \
                           Alias_column_pair_p, \
@ -21,45 +25,55 @@ from .capi.obiview cimport Obiview_p, \
                           ID_COLUMN, \
                           DEFINITION_COLUMN, \
                           QUALITY_COLUMN
+                           
+from ._obidmscolumn cimport OBIDMS_column_p, \
+                            OBIDMS_column
+                           
+from ._obidms cimport OBIDMS
+from obitools3.utils cimport tobytes, \
+                             bytes2str, \
+                             tostr

 cdef class OBIView:
    
+    cdef OBIDMS    _dms
    cdef Obiview_p _pointer
    cdef dict      _columns
    
-    cdef __init_columns__(self):
+    cdef __init_columns__(self)

    cpdef OBIView clone(self, 
-                        str view_name, 
-                        OBIView_line_selection line_selection=*, 
-                        str comments=*)
+                        view_name, 
+                        comments=*)
    
    @staticmethod
-    cpdef OBIView new(OBIDMS dms, 
-                      str view_name, 
-                      str comments=*)
+    cdef OBIView _new(OBIDMS dms, 
+                      bytes view_name, 
+                      bytes comments=*)

    @staticmethod
-    cpdef OBIView open(OBIDMS dms, 
-                       str view_name)
+    cdef OBIView _open(OBIDMS dms, 
+                       bytes view_name)
    
-    cpdef delete_column(self, str column_name)
+    cpdef delete_column(self, column_name)
    cpdef add_column(self, 
                     str column_name, 
                     obiversion_t version_number=*, 
-                     str alias=*,
-                     str type=*,
+                     object alias=*,
+                     object type=*,
                     index_t nb_lines=*, 
                     index_t nb_elements_per_line=*,
                     list elements_names=*,
-                     str indexer_name=*,
-                     str associated_column_name=*,
+                     object indexer_name=*,
+                     object associated_column_name=*,
                     obiversion_t associated_column_version=*,
-                     str comments=*,
+                     object comments=*,
                     bint create=*
-                    )
-    cpdef change_column_alias(self, str current_alias, str new_alias)
-    cpdef update_column_pointers(self)
+                     )
+    
+    
+    cpdef change_column_alias(self, bytes current_alias, bytes new_alias)
+    cdef update_column_pointers(self)
    
    cpdef OBIView_line_selection new_selection(self,
                                               list lines=*)
--- a/python/obitools3/obidms/_obiview.pyx
+++ b/python/obitools3/obidms/_obiview.pyx
@ -3,84 +3,100 @@

 cdef class OBIView :
    
-    def __init__(self,int __internalCall__):
+    def __init__(self,dms,int __internalCall__):
        if __internalCall__!=987654:
            raise RuntimeError('OBIView constructor cannot be called directly')
+        self._dms     = dms
        self._pointer = NULL
        self._columns = {}
            
    cdef __init_columns__(self):
        cdef size_t          i
-        cdef str             col_alias
+        cdef bytes           col_alias
        cdef OBIDMS_column_p column_p
        cdef Obiview_p       pointer = self._pointer
        
        self._columns = {}
        
        for i in range(pointer.infos.column_count) :
-            col_alias                = bytes2str(pointer.infos.column_references[i].alias)
+            col_alias                = pointer.infos.column_references[i].alias
            column_p                 = <OBIDMS_column_p> (pointer.columns)[i]
            subclass                 = OBIDMS_column.get_subclass_type(column_p)
            self._columns[col_alias] = subclass(self, col_alias)
    
    
    cpdef OBIView clone(self, 
-                          str view_name,
-                          str comments=""):
+                        view_name,
+                        comments=b""):
                          
-        cdef OBIView view = OBIView(987654)
+        cdef OBIView view = OBIView(self._dms,
+                                    987654)
                                
        view._pointer = obi_new_view(self._pointer.dms, 
-                                     str2bytes(view_name), 
+                                     tobytes(view_name), 
                                     self._pointer, 
                                     NULL, 
-                                     str2bytes(comments))
+                                     tobytes(comments))
        
        if view._pointer == NULL :
            raise RuntimeError("Error : Cannot clone view %s into view %s" 
                               % (str(self.name),
-                                  view_name)
+                                  tobytes(view_name))
                              )
        
-        view.__init_columns__(self)
+        view.__init_columns__()
        
        return view
    
    @staticmethod
-    cpdef OBIView new(OBIDMS dms, 
-                      str view_name, 
-                      str comments=""):
+    cdef OBIView _new(OBIDMS dms, 
+                      bytes view_name, 
+                      bytes comments=b""):

-        cdef OBIView view = OBIView(987654)  # @DuplicatedSignature
+        cdef OBIView view = OBIView(dms,
+                                    987654)  # @DuplicatedSignature
                                
        view._pointer = obi_new_view(dms._pointer, 
-                                     str2bytes(view_name), 
+                                     view_name, 
                                     NULL, 
                                     NULL, 
-                                     str2bytes(comments))
+                                     comments)
        
        if view._pointer == NULL :
            raise RuntimeError("Error : Cannot create view %s" % view_name)
        
-        view.__init_columns__(self)
+        view.__init_columns__()
        
        return view
-
+    
    @staticmethod
-    cpdef OBIView open(OBIDMS dms, 
-                       str view_name):
+    def new(OBIDMS dms, 
+            view_name, 
+            comments=b""):
+        return OBIView._new(dms,tobytes(view_name),tobytes(comments))
+    
+    
+    @staticmethod
+    cdef OBIView _open(OBIDMS dms, 
+                       bytes view_name):

-        cdef OBIView view = OBIView(987654)  # @DuplicatedSignature
+        cdef OBIView view = OBIView(dms,
+                                    987654)  # @DuplicatedSignature
                
        view._pointer = obi_open_view(dms._pointer, 
-                                      str2bytes(view_name))                
+                                      view_name)                

        if view._pointer == NULL :
-            raise RuntimeError("Error : Cannot open view %s" % view_name)
+            raise RuntimeError("Error : Cannot open view %s" % bytes2str(view_name))
        
-        view.__init_columns__(self)
+        view.__init_columns__()

        return view
+    
+    @staticmethod
+    def open(OBIDMS dms,                                        # @ReservedAssignment
+             view_name):
+        return OBIView._open(dms,tobytes(view_name))

    def __dealloc__(self):
        if (obi_save_and_close_view(self._pointer) < 0) :
@ -95,46 +111,45 @@ cdef class OBIView :
        return s
        
    
-    cpdef delete_column(self, str column_name) :
-        cdef str column_n
-        if obi_view_delete_column(self._pointer, str2bytes(column_name)) < 0 :
-            raise Exception("Problem deleting a column from a view")
+    cpdef delete_column(self, column_name) :
+        if obi_view_delete_column(self._pointer, tobytes(column_name)) < 0 :
+            raise Exception("Problem deleting column %s from a view",
+                            tostr(column_name))
        # Update the dictionary of column objects:
        (self._columns).pop(column_name)
        self.update_column_pointers()
-    
-    
+            
    cpdef add_column(self, 
                     str column_name, 
                     obiversion_t version_number=-1, 
-                     str alias='',
-                     str type='',
+                     object alias=None,
+                     object type=b'',
                     index_t nb_lines=0, 
                     index_t nb_elements_per_line=1,
                     list elements_names=None,
-                     str indexer_name="",
-                     str associated_column_name="",
+                     object indexer_name=b"",
+                     object associated_column_name=b"",
                     obiversion_t associated_column_version=-1,
-                     str comments="",
+                     object comments=b"",
                     bint create=True
                     ) :
        
        cdef bytes           column_name_b
        cdef bytes           elements_names_b
+        cdef bytes           alias_b
        cdef object          subclass
        cdef OBIDMS_column_p column_p
        
-        column_name_b = str2bytes(column_name)
-        if alias == '' :
-            alias = column_name
+        column_name_b = tobytes(column_name)
+        if alias is None :
            alias_b = column_name_b
        else :
-            alias_b = str2bytes(alias)
+            alias_b = tobytes(alias)
        
        if elements_names is None :
-            elements_names_b = str2bytes("")
+            elements_names_b = b""
        else :
-            elements_names_b = str2bytes(';'.join(elements_names))
+            elements_names_b = b';'.join([tobytes(i) for i in elements_names])
    
        if type :                       # TODO make C function that does that
            if type == 'OBI_INT' :
@ -169,9 +184,9 @@ cdef class OBIView :
        (self._columns)[alias] = subclass(self, alias)


-    cpdef change_column_alias(self, str current_alias, str new_alias):
+    cpdef change_column_alias(self, bytes current_alias, bytes new_alias):
        cdef OBIDMS_column column
-        if (obi_view_create_column_alias(self._pointer, str2bytes(current_alias), str2bytes(new_alias)) < 0) :
+        if (obi_view_create_column_alias(self._pointer, current_alias, new_alias) < 0) :
            raise Exception("Problem changing a column alias")
        # Update the dictionaries of column objects
        self._columns[new_alias] = self._columns[current_alias]
@ -180,7 +195,7 @@ cdef class OBIView :
        (self._columns).pop(current_alias)
    
    
-    cpdef update_column_pointers(self):
+    cdef update_column_pointers(self):
        cdef str              column_n
        cdef OBIDMS_column    column
        for column_n in self._columns :
@ -227,6 +242,10 @@ cdef class OBIView :
        return to_print
    
    
+    @property
+    def dms(self):
+        return self._dms
+    
    # line_count property getter
    @property
    def line_count(self):
@ -317,7 +336,7 @@ cdef class OBIView_line_selection(list):
                                  view_name)
                              )
        
-        view.__init_columns__(self)
+        view.__init_columns__()
        
        return view

--- a/python/obitools3/obidms/_obiview_nuc_seq.pxd
+++ b/python/obitools3/obidms/_obiview_nuc_seq.pxd
--- a/python/obitools3/obidms/_obiview_nuc_seq.pyx
+++ b/python/obitools3/obidms/_obiview_nuc_seq.pyx
--- a/python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
+++ b/python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
--- a/python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
+++ b/python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
--- a/python/obitools3/obidms/capi/init.py
+++ b/python/obitools3/obidms/capi/init.py
--- a/python/obitools3/obidms/capi/obialign.pxd
+++ b/python/obitools3/obidms/capi/obialign.pxd
--- a/python/obitools3/obidms/capi/obidms.pxd
+++ b/python/obitools3/obidms/capi/obidms.pxd
--- a/python/obitools3/obidms/capi/obidmscolumn.pxd
+++ b/python/obitools3/obidms/capi/obidmscolumn.pxd
@ -62,9 +62,7 @@ cdef extern from "obidmscolumn.h" nogil:
    OBIDMS_column_p obi_open_column(OBIDMS_p dms, 
                                    const_char_p column_name, 
                                    obiversion_t version_number)
-        
-    int obi_close_column(OBIDMS_column_p column)
-        
+                
    OBIDMS_column_p obi_clone_column(OBIDMS_p dms, 
                                     OBIDMS_column_p line_selection,
                                     const_char_p column_name, 
@ -83,6 +81,8 @@ cdef extern from "obidmscolumn.h" nogil:
    int obi_close_header(OBIDMS_column_header_p header)

    int obi_select(OBIDMS_column_p line_selection_column, index_t line_to_grep)
+    
+    int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb)


 cdef extern from "obidmscolumn_int.h" nogil:
--- a/python/obitools3/dms/capi/obierrno.pxd
+++ b/python/obitools3/dms/capi/obierrno.pxd
@ -0,0 +1,5 @@
+#cython: language_level=3
+
+
+cdef extern from "obierrno.h":
+    int obi_errno
--- a/python/obitools3/obidms/capi/obitaxonomy.pxd
+++ b/python/obitools3/obidms/capi/obitaxonomy.pxd
--- a/python/obitools3/obidms/capi/obitypes.pxd
+++ b/python/obitools3/obidms/capi/obitypes.pxd
--- a/python/obitools3/obidms/capi/obiutils.pxd
+++ b/python/obitools3/obidms/capi/obiutils.pxd
--- a/python/obitools3/obidms/capi/obiview.pxd
+++ b/python/obitools3/obidms/capi/obiview.pxd
--- a/python/obitools3/obidms/_obidmscolumn.pxd
+++ b/python/obitools3/obidms/_obidmscolumn.pxd
@ -1,54 +0,0 @@
-#cython: language_level=3
-
-from .capi.obidmscolumn cimport OBIDMS_column_p
-from .capi.obiview      cimport Obiview_p
-from .capi.obitypes     cimport obiversion_t, OBIType_t, index_t
-
-
-from ._obidmscolumn_int cimport OBIDMS_column_int, \
-                                OBIDMS_column_multi_elts_int
-                                
-from ._obidmscolumn_float cimport OBIDMS_column_float, \
-                                  OBIDMS_column_multi_elts_float
-
-from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
-                                 OBIDMS_column_multi_elts_bool
-
-from ._obidmscolumn_char cimport OBIDMS_column_char, \
-                                 OBIDMS_column_multi_elts_char
-
-from ._obidmscolumn_qual cimport OBIDMS_column_qual, \
-                                 OBIDMS_column_multi_elts_qual
-
-from ._obidmscolumn_str cimport OBIDMS_column_str, \
-                                OBIDMS_column_multi_elts_str
-
-from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
-                                OBIDMS_column_multi_elts_seq
-
-
-from ._obiview cimport OBIView
-
-cdef class OBIDMS_column:
-
-    cdef  str                _alias               # associated property: alias
-    cdef  OBIDMS_column_p*   _pointer
-    cdef  OBIView            _view
-        
-    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 register_column_class(OBIType_t obitype,type classe)
--- a/python/obitools3/obidms/_obidmscolumn.pyx
+++ b/python/obitools3/obidms/_obidmscolumn.pyx
@ -1,200 +0,0 @@
-#cython: language_level=3
-
-cdef dict __OBIDMS_COLUMN_CLASS__ = {}
-
-cdef class OBIDMS_column :
-
-    # Note: should only be initialized through a subclass
-    def __init__(self, OBIView view, str column_alias):
-        
-        cdef OBIDMS_column_p  column_p
-        cdef OBIDMS_column_p* column_pp
-        
-        column_pp = obi_view_get_pointer_on_column_in_view(view._pointer, str2bytes(column_alias))
-        column_p = column_pp[0]     # TODO ugly cython dereferencing but can't find better
-        
-        # Fill structure
-        self._alias   = column_alias
-        self._pointer = column_pp
-        self._view     = view
-        
-    cpdef getitem(self,index_t line_nb, str element_name):
-
-    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.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 line_nb  
-        # Yield each line
-        for line_nb in range(self.lines_used):
-            yield self.get_line(line_nb)
-                
-    def __str__(self) :
-        cdef str to_print
-        to_print = ''
-        for line in self :
-            to_print = to_print + str(line) + "\n"
-        return to_print
-
-    def __repr__(self) :
-        return (self._alias + ", original name: " + self.original_name + ", version " + str(self.version) + ", data type: " + self.data_type)
-        
-    cpdef close(self):
-        if obi_close_column((self._pointer)[0]) < 0 :
-            raise Exception("Problem closing a column")
-
-    # Column alias property getter and setter
-    @property
-    def alias(self):
-        return self._alias
-    @alias.setter
-    def alias(self, new_alias):  # @DuplicatedSignature
-        self._view.change_column_alias(self._alias, new_alias)
-
-    # elements_names property getter
-    @property
-    def elements_names(self):
-        return (bytes2str(((self._pointer)[0].header).elements_names)).split(';')
-
-    # nb_elements_per_line property getter
-    @property
-    def nb_elements_per_line(self):
-        return ((self._pointer)[0].header).nb_elements_per_line
-
-    # data_type property getter
-    @property
-    def data_type(self):
-        return bytes2str(name_data_type(((self._pointer)[0].header).returned_data_type))
-
-    # original_name property getter
-    @property
-    def original_name(self):
-        return bytes2str(((self._pointer)[0].header).name)
-
-    # version property getter
-    @property
-    def version(self):
-        return ((self._pointer)[0].header).version
-
-    # lines_used property getter
-    @property
-    def lines_used(self):
-        return (self._pointer)[0].header.lines_used
-
-    # comments property getter
-    @property
-    def comments(self):
-        return bytes2str((self._pointer)[0].header.comments)
-    
-    # creation_date property getter
-    @property
-    def creation_date(self):
-        return bytes2str(obi_format_date((self._pointer)[0].header.creation_date))
-    
-    @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_QUAL :
-            if col_one_element_per_line :
-                subclass = OBIDMS_column_qual
-            else :
-                subclass = OBIDMS_column_multi_elts_qual
-        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 register_column_class(OBIType_t obitype,type classe):
-    assert issubclass(classe,OBIDMS_column)
-    
-    __OBIDMS_COLUMN_CLASS__[obitype]=classe
--- a/python/obitools3/obidms/_obidmscolumn_bool.pxd
+++ b/python/obitools3/obidms/_obidmscolumn_bool.pxd
@ -1,14 +0,0 @@
-#cython: language_level=3
-
-from .capi.obitypes cimport index_t
-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)
-
-cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
-    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, object value)
--- a/python/obitools3/obidms/_obidmscolumn_bool.pyx
+++ b/python/obitools3/obidms/_obidmscolumn_bool.pyx
@ -1,77 +0,0 @@
-#cython: language_level=3
- 
-from .capi.obiview      cimport obi_get_bool_with_elt_name_and_col_p_in_view, \
-                                obi_get_bool_with_elt_idx_and_col_p_in_view, \
-                                obi_set_bool_with_elt_name_and_col_p_in_view, \
-                                obi_set_bool_with_elt_idx_and_col_p_in_view
-from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIBool_NA, obibool_t
-
-from obitools3.utils cimport str2bytes
-
-from cpython.bool cimport PyBool_FromLong
-
-
-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_get_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
-        if obi_errno > 0 :
-            raise IndexError(line_nb)
-        if value == OBIBool_NA :
-            result = None
-        else :
-            result = PyBool_FromLong(value)
-        return result
-    
-    cpdef set_line(self, index_t line_nb, object value):
-        if value is None :
-            value = OBIBool_NA
-        if obi_set_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, <obibool_t> value) < 0:
-            raise Exception("Problem setting a value in a column")
-
-
-cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
-
-    cpdef object get_item(self, index_t line_nb, str element_name):
-        cdef obibool_t value
-        cdef object result
-        value = obi_get_bool_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        if value == OBIBool_NA :
-            result = None
-        else :
-            result = PyBool_FromLong(value)
-        return result
-    
-    cpdef object get_line(self, index_t line_nb) :
-        cdef obibool_t value
-        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_get_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
-            if obi_errno > 0 :
-                raise IndexError(line_nb)
-            if 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, object value):
-        if value is None :
-            value = OBIBool_NA
-        if obi_set_bool_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
-            raise Exception("Problem setting a value in a column")
--- a/python/obitools3/obidms/_obidmscolumn_char.cfiles
+++ b/python/obitools3/obidms/_obidmscolumn_char.cfiles
@ -1,65 +0,0 @@
-../../../src/bloom.h
-../../../src/bloom.c
-../../../src/char_str_indexer.h
-../../../src/char_str_indexer.c
-../../../src/crc64.h
-../../../src/crc64.c
-../../../src/dna_seq_indexer.h
-../../../src/dna_seq_indexer.c
-../../../src/encode.h
-../../../src/encode.c
-../../../src/hashtable.h
-../../../src/hashtable.c
-../../../src/murmurhash2.h
-../../../src/murmurhash2.c
-../../../src/obi_align.h
-../../../src/obi_align.c
-../../../src/obiavl.h
-../../../src/obiavl.c
-../../../src/obiblob_indexer.h
-../../../src/obiblob_indexer.c
-../../../src/obiblob.h
-../../../src/obiblob.c
-../../../src/obidebug.h
-../../../src/obidms_taxonomy.h
-../../../src/obidms_taxonomy.c
-../../../src/obidms.h
-../../../src/obidms.c
-../../../src/obidmscolumn_blob.c
-../../../src/obidmscolumn_blob.h
-../../../src/obidmscolumn_bool.c
-../../../src/obidmscolumn_bool.h
-../../../src/obidmscolumn_char.c
-../../../src/obidmscolumn_char.h
-../../../src/obidmscolumn_float.c
-../../../src/obidmscolumn_float.h
-../../../src/obidmscolumn_idx.h
-../../../src/obidmscolumn_idx.c
-../../../src/obidmscolumn_int.c
-../../../src/obidmscolumn_int.h
-../../../src/obidmscolumn_qual.h
-../../../src/obidmscolumn_qual.c
-../../../src/obidmscolumn_seq.c
-../../../src/obidmscolumn_seq.h
-../../../src/obidmscolumn_str.c
-../../../src/obidmscolumn_str.h
-../../../src/obidmscolumn.h
-../../../src/obidmscolumn.c
-../../../src/obidmscolumndir.h
-../../../src/obidmscolumndir.c
-../../../src/obierrno.h
-../../../src/obierrno.c
-../../../src/obilittlebigman.h
-../../../src/obilittlebigman.c
-../../../src/obitypes.h
-../../../src/obitypes.c
-../../../src/obiview.h
-../../../src/obiview.c
-../../../src/sse_banded_LCS_alignment.h
-../../../src/sse_banded_LCS_alignment.c
-../../../src/uint8_indexer.h
-../../../src/uint8_indexer.c
-../../../src/upperband.h
-../../../src/upperband.c
-../../../src/utils.h
-../../../src/utils.c
--- a/python/obitools3/obidms/_obidmscolumn_char.pxd
+++ b/python/obitools3/obidms/_obidmscolumn_char.pxd
@ -1,14 +0,0 @@
-#cython: language_level=3
-
-from .capi.obitypes cimport index_t
-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)
-
-cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
-    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, object value)
--- a/python/obitools3/obidms/_obidmscolumn_char.pyx
+++ b/python/obitools3/obidms/_obidmscolumn_char.pyx
@ -1,76 +0,0 @@
-#cython: language_level=3
- 
-from .capi.obiview      cimport obi_get_char_with_elt_name_and_col_p_in_view, \
-                                obi_get_char_with_elt_idx_and_col_p_in_view, \
-                                obi_set_char_with_elt_name_and_col_p_in_view, \
-                                obi_set_char_with_elt_idx_and_col_p_in_view
-from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIChar_NA, obichar_t
-
-from obitools3.utils cimport str2bytes, bytes2str
-
-
-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_get_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
-        if obi_errno > 0 :
-            raise IndexError(line_nb)
-        if value == OBIChar_NA :
-            result = None
-        else :
-            result = bytes2str(value)
-        return result
-
-    cpdef set_line(self, index_t line_nb, object value):
-        if value is None :
-            value = OBIChar_NA
-        if obi_set_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, str2bytes(value)[0]) < 0:
-            raise Exception("Problem setting a value in a column")
-
-
-cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
-
-    cpdef object get_item(self, index_t line_nb, str element_name):
-        cdef obichar_t value
-        cdef object result
-        value = obi_get_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        if value == OBIChar_NA :
-            result = None
-        else :
-            result = bytes2str(value)
-        return result
-
-    cpdef object get_line(self, index_t line_nb) :
-        cdef obichar_t value
-        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_get_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
-            if obi_errno > 0 :
-                raise IndexError(line_nb)
-            if 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, object value):
-        if value is None :
-            value = OBIChar_NA
-        if obi_set_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
-            raise Exception("Problem setting a value in a column")
-
--- a/python/obitools3/obidms/_obidmscolumn_float.cfiles
+++ b/python/obitools3/obidms/_obidmscolumn_float.cfiles
@ -1,65 +0,0 @@
-../../../src/bloom.h
-../../../src/bloom.c
-../../../src/char_str_indexer.h
-../../../src/char_str_indexer.c
-../../../src/crc64.h
-../../../src/crc64.c
-../../../src/dna_seq_indexer.h
-../../../src/dna_seq_indexer.c
-../../../src/encode.h
-../../../src/encode.c
-../../../src/hashtable.h
-../../../src/hashtable.c
-../../../src/murmurhash2.h
-../../../src/murmurhash2.c
-../../../src/obi_align.h
-../../../src/obi_align.c
-../../../src/obiavl.h
-../../../src/obiavl.c
-../../../src/obiblob_indexer.h
-../../../src/obiblob_indexer.c
-../../../src/obiblob.h
-../../../src/obiblob.c
-../../../src/obidebug.h
-../../../src/obidms_taxonomy.h
-../../../src/obidms_taxonomy.c
-../../../src/obidms.h
-../../../src/obidms.c
-../../../src/obidmscolumn_blob.c
-../../../src/obidmscolumn_blob.h
-../../../src/obidmscolumn_bool.c
-../../../src/obidmscolumn_bool.h
-../../../src/obidmscolumn_char.c
-../../../src/obidmscolumn_char.h
-../../../src/obidmscolumn_float.c
-../../../src/obidmscolumn_float.h
-../../../src/obidmscolumn_idx.h
-../../../src/obidmscolumn_idx.c
-../../../src/obidmscolumn_int.c
-../../../src/obidmscolumn_int.h
-../../../src/obidmscolumn_qual.h
-../../../src/obidmscolumn_qual.c
-../../../src/obidmscolumn_seq.c
-../../../src/obidmscolumn_seq.h
-../../../src/obidmscolumn_str.c
-../../../src/obidmscolumn_str.h
-../../../src/obidmscolumn.h
-../../../src/obidmscolumn.c
-../../../src/obidmscolumndir.h
-../../../src/obidmscolumndir.c
-../../../src/obierrno.h
-../../../src/obierrno.c
-../../../src/obilittlebigman.h
-../../../src/obilittlebigman.c
-../../../src/obitypes.h
-../../../src/obitypes.c
-../../../src/obiview.h
-../../../src/obiview.c
-../../../src/sse_banded_LCS_alignment.h
-../../../src/sse_banded_LCS_alignment.c
-../../../src/uint8_indexer.h
-../../../src/uint8_indexer.c
-../../../src/upperband.h
-../../../src/upperband.c
-../../../src/utils.h
-../../../src/utils.c
--- a/python/obitools3/obidms/_obidmscolumn_float.pxd
+++ b/python/obitools3/obidms/_obidmscolumn_float.pxd
@ -1,14 +0,0 @@
-#cython: language_level=3
-
-from .capi.obitypes cimport index_t
-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)
-
-cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
-    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, object value)
--- a/python/obitools3/obidms/_obidmscolumn_float.pyx
+++ b/python/obitools3/obidms/_obidmscolumn_float.pyx
@ -1,76 +0,0 @@
-#cython: language_level=3
-
-from .capi.obiview      cimport obi_get_float_with_elt_name_and_col_p_in_view, \
-                                obi_get_float_with_elt_idx_and_col_p_in_view, \
-                                obi_set_float_with_elt_name_and_col_p_in_view, \
-                                obi_set_float_with_elt_idx_and_col_p_in_view
-from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIFloat_NA, obifloat_t
-
-from obitools3.utils cimport str2bytes
-
-
-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_get_float_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
-        if obi_errno > 0 :
-            raise IndexError(line_nb)
-        if value == OBIFloat_NA :
-            result = None
-        else :
-            result = <double> value
-        return result
-
-    cpdef set_line(self, index_t line_nb, object value):
-        if value is None :
-            value = OBIFloat_NA
-        if obi_set_float_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, <obifloat_t> value) < 0:
-            raise Exception("Problem setting a value in a column")
-
-
-cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
-
-    cpdef object get_item(self, index_t line_nb, str element_name):
-        cdef obifloat_t value
-        cdef object result
-        value = obi_get_float_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        if value == OBIFloat_NA :
-            result = None
-        else :
-            result = <double> value
-        return result
-
-    cpdef object get_line(self, index_t line_nb) :
-        cdef obifloat_t value
-        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_get_float_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
-            if obi_errno > 0 :
-                raise IndexError(line_nb)
-            if 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, object value):
-        if value is None :
-            value = OBIFloat_NA
-        if obi_set_float_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), <obifloat_t> value) < 0:
-            raise Exception("Problem setting a value in a column")
- 
--- a/python/obitools3/obidms/_obidmscolumn_int.cfiles
+++ b/python/obitools3/obidms/_obidmscolumn_int.cfiles
@ -1,65 +0,0 @@
-../../../src/bloom.h
-../../../src/bloom.c
-../../../src/char_str_indexer.h
-../../../src/char_str_indexer.c
-../../../src/crc64.h
-../../../src/crc64.c
-../../../src/dna_seq_indexer.h
-../../../src/dna_seq_indexer.c
-../../../src/encode.h
-../../../src/encode.c
-../../../src/hashtable.h
-../../../src/hashtable.c
-../../../src/murmurhash2.h
-../../../src/murmurhash2.c
-../../../src/obi_align.h
-../../../src/obi_align.c
-../../../src/obiavl.h
-../../../src/obiavl.c
-../../../src/obiblob_indexer.h
-../../../src/obiblob_indexer.c
-../../../src/obiblob.h
-../../../src/obiblob.c
-../../../src/obidebug.h
-../../../src/obidms_taxonomy.h
-../../../src/obidms_taxonomy.c
-../../../src/obidms.h
-../../../src/obidms.c
-../../../src/obidmscolumn_blob.c
-../../../src/obidmscolumn_blob.h
-../../../src/obidmscolumn_bool.c
-../../../src/obidmscolumn_bool.h
-../../../src/obidmscolumn_char.c
-../../../src/obidmscolumn_char.h
-../../../src/obidmscolumn_float.c
-../../../src/obidmscolumn_float.h
-../../../src/obidmscolumn_idx.h
-../../../src/obidmscolumn_idx.c
-../../../src/obidmscolumn_int.c
-../../../src/obidmscolumn_int.h
-../../../src/obidmscolumn_qual.h
-../../../src/obidmscolumn_qual.c
-../../../src/obidmscolumn_seq.c
-../../../src/obidmscolumn_seq.h
-../../../src/obidmscolumn_str.c
-../../../src/obidmscolumn_str.h
-../../../src/obidmscolumn.h
-../../../src/obidmscolumn.c
-../../../src/obidmscolumndir.h
-../../../src/obidmscolumndir.c
-../../../src/obierrno.h
-../../../src/obierrno.c
-../../../src/obilittlebigman.h
-../../../src/obilittlebigman.c
-../../../src/obitypes.h
-../../../src/obitypes.c
-../../../src/obiview.h
-../../../src/obiview.c
-../../../src/sse_banded_LCS_alignment.h
-../../../src/sse_banded_LCS_alignment.c
-../../../src/uint8_indexer.h
-../../../src/uint8_indexer.c
-../../../src/upperband.h
-../../../src/upperband.c
-../../../src/utils.h
-../../../src/utils.c
--- a/python/obitools3/obidms/_obidmscolumn_int.pxd
+++ b/python/obitools3/obidms/_obidmscolumn_int.pxd
@ -1,14 +0,0 @@
-#cython: language_level=3
-
-from .capi.obitypes cimport index_t
-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)
-
-cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
-    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, object value)
--- a/python/obitools3/obidms/_obidmscolumn_int.pyx
+++ b/python/obitools3/obidms/_obidmscolumn_int.pyx
@ -1,78 +0,0 @@
-#cython: language_level=3
-
-from .capi.obiview      cimport obi_get_int_with_elt_name_and_col_p_in_view, \
-                                obi_get_int_with_elt_idx_and_col_p_in_view, \
-                                obi_set_int_with_elt_name_and_col_p_in_view, \
-                                obi_set_int_with_elt_idx_and_col_p_in_view
-from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIInt_NA, obiint_t
-
-from obitools3.utils cimport str2bytes
-
-from cpython.int cimport PyInt_FromLong
-
-
-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_get_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
-        if obi_errno > 0 :
-            raise IndexError(line_nb)
-        if value == OBIInt_NA :
-            result = None
-        else :
-            result = PyInt_FromLong(value)
-        return result
-            
-    cpdef set_line(self, index_t line_nb, object value):
-        if value is None :
-            value = OBIInt_NA
-        if obi_set_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, <obiint_t> value) < 0:
-            raise Exception("Problem setting a value in a column")
-
-
-cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
-
-    cpdef object get_item(self, index_t line_nb, str element_name):
-        cdef obiint_t value
-        cdef object result
-        value = obi_get_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        if value == OBIInt_NA :
-            result = None
-        else :
-            result = PyInt_FromLong(value)
-        return result
-    
-    cpdef object get_line(self, index_t line_nb) :
-        cdef obiint_t value
-        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_get_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
-            if obi_errno > 0 :
-                raise IndexError(line_nb)
-            if 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   # TODO discuss
-        return result
-
-    cpdef set_item(self, index_t line_nb, str element_name, object value):
-        if value is None :
-            value = OBIInt_NA
-        if obi_set_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), <obiint_t> value) < 0:
-            raise Exception("Problem setting a value in a column")
-
--- a/python/obitools3/obidms/_obidmscolumn_qual.cfiles
+++ b/python/obitools3/obidms/_obidmscolumn_qual.cfiles
@ -1,65 +0,0 @@
-../../../src/bloom.h
-../../../src/bloom.c
-../../../src/char_str_indexer.h
-../../../src/char_str_indexer.c
-../../../src/crc64.h
-../../../src/crc64.c
-../../../src/dna_seq_indexer.h
-../../../src/dna_seq_indexer.c
-../../../src/encode.h
-../../../src/encode.c
-../../../src/hashtable.h
-../../../src/hashtable.c
-../../../src/murmurhash2.h
-../../../src/murmurhash2.c
-../../../src/obi_align.h
-../../../src/obi_align.c
-../../../src/obiavl.h
-../../../src/obiavl.c
-../../../src/obiblob_indexer.h
-../../../src/obiblob_indexer.c
-../../../src/obiblob.h
-../../../src/obiblob.c
-../../../src/obidebug.h
-../../../src/obidms_taxonomy.h
-../../../src/obidms_taxonomy.c
-../../../src/obidms.h
-../../../src/obidms.c
-../../../src/obidmscolumn_blob.c
-../../../src/obidmscolumn_blob.h
-../../../src/obidmscolumn_bool.c
-../../../src/obidmscolumn_bool.h
-../../../src/obidmscolumn_char.c
-../../../src/obidmscolumn_char.h
-../../../src/obidmscolumn_float.c
-../../../src/obidmscolumn_float.h
-../../../src/obidmscolumn_idx.h
-../../../src/obidmscolumn_idx.c
-../../../src/obidmscolumn_int.c
-../../../src/obidmscolumn_int.h
-../../../src/obidmscolumn_qual.h
-../../../src/obidmscolumn_qual.c
-../../../src/obidmscolumn_seq.c
-../../../src/obidmscolumn_seq.h
-../../../src/obidmscolumn_str.c
-../../../src/obidmscolumn_str.h
-../../../src/obidmscolumn.h
-../../../src/obidmscolumn.c
-../../../src/obidmscolumndir.h
-../../../src/obidmscolumndir.c
-../../../src/obierrno.h
-../../../src/obierrno.c
-../../../src/obilittlebigman.h
-../../../src/obilittlebigman.c
-../../../src/obitypes.h
-../../../src/obitypes.c
-../../../src/obiview.h
-../../../src/obiview.c
-../../../src/sse_banded_LCS_alignment.h
-../../../src/sse_banded_LCS_alignment.c
-../../../src/uint8_indexer.h
-../../../src/uint8_indexer.c
-../../../src/upperband.h
-../../../src/upperband.c
-../../../src/utils.h
-../../../src/utils.c
--- a/python/obitools3/obidms/_obidmscolumn_qual.pxd
+++ b/python/obitools3/obidms/_obidmscolumn_qual.pxd
@ -1,20 +0,0 @@
-#cython: language_level=3
-
-from .capi.obitypes cimport index_t
-from ._obidms       cimport OBIDMS_column , OBIDMS_column_multi_elts
-
-
-cdef class OBIDMS_column_qual(OBIDMS_column):
-    cpdef object get_line(self, index_t line_nb)
-    cpdef object get_str_line(self, index_t line_nb)
-    cpdef set_line(self, index_t line_nb, object value)
-    cpdef set_str_line(self, index_t line_nb, object value)
-
-
-cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
-    cpdef object get_item(self, index_t line_nb, str element_name)
-    cpdef object get_str_item(self, index_t line_nb, str element_name)
-    cpdef object get_line(self, index_t line_nb)
-    cpdef object get_str_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, object value)
-    cpdef set_str_item(self, index_t line_nb, str element_name, object value)
--- a/python/obitools3/obidms/_obidmscolumn_qual.pyx
+++ b/python/obitools3/obidms/_obidmscolumn_qual.pyx
@ -1,189 +0,0 @@
-#cython: language_level=3
- 
-from .capi.obiview      cimport obi_get_qual_char_with_elt_name_and_col_p_in_view, \
-                                obi_get_qual_char_with_elt_idx_and_col_p_in_view, \
-                                obi_set_qual_char_with_elt_name_and_col_p_in_view, \
-                                obi_set_qual_char_with_elt_idx_and_col_p_in_view, \
-                                obi_get_qual_int_with_elt_name_and_col_p_in_view, \
-                                obi_get_qual_int_with_elt_idx_and_col_p_in_view, \
-                                obi_set_qual_int_with_elt_name_and_col_p_in_view, \
-                                obi_set_qual_int_with_elt_idx_and_col_p_in_view
-                                
-from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIQual_char_NA, OBIQual_int_NA, const_char_p
-
-from ._obidms           cimport OBIView
-
-from obitools3.utils cimport str2bytes, bytes2str
-
-from libc.stdlib cimport free
-from libc.string cimport strcmp
-from libc.stdint cimport uint8_t
-from libc.stdlib cimport malloc
-
-
-cdef class OBIDMS_column_qual(OBIDMS_column):
-
-    cpdef object get_line(self, index_t line_nb):
-        cdef const uint8_t*  value
-        cdef int             value_length
-        cdef object          result
-        cdef int             i
-        value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, &value_length)
-        if obi_errno > 0 :
-            raise IndexError(line_nb)
-        if value == OBIQual_int_NA :
-            result = None
-        else :
-            result = []
-            for i in range(value_length) :
-                result.append(<int>value[i])            
-        return result
-    
-    cpdef object get_str_line(self, index_t line_nb):
-        cdef char*  value
-        cdef object result
-        cdef int    i
-        value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
-        if obi_errno > 0 :
-            raise IndexError(line_nb)
-        if value == OBIQual_char_NA :
-            result = None
-        else :
-            result = bytes2str(value)
-            free(value)
-        return result
-
-    cpdef set_line(self, index_t line_nb, object value):
-        cdef uint8_t* value_b
-        cdef int      value_length
-        if value is None :
-            if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, OBIQual_int_NA, 0) < 0:
-                raise Exception("Problem setting a value in a column")
-        else :
-            value_length = len(value)
-            value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
-            for i in range(value_length) :
-                value_b[i] = <uint8_t>value[i]
-            if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value_b, value_length) < 0:
-                raise Exception("Problem setting a value in a column")
-            free(value_b)
-
-    cpdef set_str_line(self, index_t line_nb, object value):
-        cdef bytes value_b        
-        if value is None :
-            if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, OBIQual_char_NA) < 0:
-                raise Exception("Problem setting a value in a column")
-        else :
-            if type(value) == str:
-                value_b = str2bytes(value)
-            else :
-                value_b = value
-            if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value_b) < 0:
-                raise Exception("Problem setting a value in a column")
-
-
-cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
- 
-    cpdef object get_item(self, index_t line_nb, str element_name):
-        cdef const uint8_t*  value
-        cdef int             value_length
-        cdef object          result
-        cdef int             i
-        value = obi_get_qual_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), &value_length)
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        if value == OBIQual_int_NA :
-            result = None
-        else :
-            result = []
-            for i in range(value_length) :
-                result.append(<int>value[i])            
-        return result
- 
-    cpdef object get_str_item(self, index_t line_nb, str element_name):
-        cdef char*  value
-        cdef object result
-        value = obi_get_qual_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        if value == OBIQual_char_NA :
-            result = None
-        else :
-            result = bytes2str(value)
-            free(value)
-        return result
-
-    cpdef object get_line(self, index_t line_nb) :
-        cdef const uint8_t*  value
-        cdef int             value_length
-        cdef object          value_in_result
-        cdef dict            result
-        cdef index_t         i
-        cdef int             j
-        cdef bint            all_NA
-        result = {}
-        all_NA = True
-        for i in range(self.nb_elements_per_line) :
-            value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i, &value_length)
-            if obi_errno > 0 :
-                raise IndexError(line_nb)
-            if value == OBIQual_int_NA :
-                value_in_result = None
-            else :
-                value_in_result = []
-                for j in range(value_length) :
-                    value_in_result.append(<int>value[j])            
-            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 object get_str_line(self, index_t line_nb) :
-        cdef char*   value
-        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_get_qual_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
-            if obi_errno > 0 :
-                raise IndexError(line_nb)
-            if value == OBIQual_char_NA :
-                value_in_result = None
-            else :
-                value_in_result = bytes2str(value)
-                free(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, object value):
-        cdef uint8_t* value_b
-        cdef int      value_length
-        if value is None :
-            if obi_set_qual_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), OBIQual_int_NA, 0) < 0:
-                raise Exception("Problem setting a value in a column")
-        else :
-            value_length = len(value)
-            value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
-            for i in range(value_length) :
-                value_b[i] = <uint8_t>value[i]
-            if obi_set_qual_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), value_b, value_length) < 0:
-                raise Exception("Problem setting a value in a column")
-            free(value_b)
-
-    cpdef set_str_item(self, index_t line_nb, str element_name, object value):
-        if value is None :
-            if obi_set_qual_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), OBIQual_char_NA) < 0:
-                raise Exception("Problem setting a value in a column")
-        else :
-            if obi_set_qual_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)) < 0:
-                raise Exception("Problem setting a value in a column")
--- a/python/obitools3/obidms/_obidmscolumn_seq.cfiles
+++ b/python/obitools3/obidms/_obidmscolumn_seq.cfiles
@ -1,65 +0,0 @@
-../../../src/bloom.h
-../../../src/bloom.c
-../../../src/char_str_indexer.h
-../../../src/char_str_indexer.c
-../../../src/crc64.h
-../../../src/crc64.c
-../../../src/dna_seq_indexer.h
-../../../src/dna_seq_indexer.c
-../../../src/encode.h
-../../../src/encode.c
-../../../src/hashtable.h
-../../../src/hashtable.c
-../../../src/murmurhash2.h
-../../../src/murmurhash2.c
-../../../src/obi_align.h
-../../../src/obi_align.c
-../../../src/obiavl.h
-../../../src/obiavl.c
-../../../src/obiblob_indexer.h
-../../../src/obiblob_indexer.c
-../../../src/obiblob.h
-../../../src/obiblob.c
-../../../src/obidebug.h
-../../../src/obidms_taxonomy.h
-../../../src/obidms_taxonomy.c
-../../../src/obidms.h
-../../../src/obidms.c
-../../../src/obidmscolumn_blob.c
-../../../src/obidmscolumn_blob.h
-../../../src/obidmscolumn_bool.c
-../../../src/obidmscolumn_bool.h
-../../../src/obidmscolumn_char.c
-../../../src/obidmscolumn_char.h
-../../../src/obidmscolumn_float.c
-../../../src/obidmscolumn_float.h
-../../../src/obidmscolumn_idx.h
-../../../src/obidmscolumn_idx.c
-../../../src/obidmscolumn_int.c
-../../../src/obidmscolumn_int.h
-../../../src/obidmscolumn_qual.h
-../../../src/obidmscolumn_qual.c
-../../../src/obidmscolumn_seq.c
-../../../src/obidmscolumn_seq.h
-../../../src/obidmscolumn_str.c
-../../../src/obidmscolumn_str.h
-../../../src/obidmscolumn.h
-../../../src/obidmscolumn.c
-../../../src/obidmscolumndir.h
-../../../src/obidmscolumndir.c
-../../../src/obierrno.h
-../../../src/obierrno.c
-../../../src/obilittlebigman.h
-../../../src/obilittlebigman.c
-../../../src/obitypes.h
-../../../src/obitypes.c
-../../../src/obiview.h
-../../../src/obiview.c
-../../../src/sse_banded_LCS_alignment.h
-../../../src/sse_banded_LCS_alignment.c
-../../../src/uint8_indexer.h
-../../../src/uint8_indexer.c
-../../../src/upperband.h
-../../../src/upperband.c
-../../../src/utils.h
-../../../src/utils.c
--- a/python/obitools3/obidms/_obidmscolumn_seq.pxd
+++ b/python/obitools3/obidms/_obidmscolumn_seq.pxd
@ -1,15 +0,0 @@
-#cython: language_level=3
-
-from .capi.obitypes cimport index_t
-from ._obidms       cimport OBIView, 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)
-    
-
-cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
-    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, object value)
--- a/python/obitools3/obidms/_obidmscolumn_seq.pyx
+++ b/python/obitools3/obidms/_obidmscolumn_seq.pyx
@ -1,108 +0,0 @@
-#cython: language_level=3
- 
-from .capi.obiview      cimport obi_get_seq_with_elt_name_and_col_p_in_view, \
-                                obi_get_seq_with_elt_idx_and_col_p_in_view, \
-                                obi_set_seq_with_elt_name_and_col_p_in_view, \
-                                obi_set_seq_with_elt_idx_and_col_p_in_view
-from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBISeq_NA, const_char_p
-
-from ._obidms           cimport OBIView
-
-from obitools3.utils cimport str2bytes, bytes2str
-
-from libc.stdlib cimport free
-
-
-cdef class OBIDMS_column_seq(OBIDMS_column):
-
-    cpdef object get_line(self, index_t line_nb):
-        cdef char*  value
-        cdef object result
-        value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
-        if obi_errno > 0 :
-            raise IndexError(line_nb)
-        if value == OBISeq_NA :
-            result = None
-        else :
-            try:
-                result = <bytes> value
-            finally:
-                free(value)
-        return result
-
-    cpdef set_line(self, index_t line_nb, object value):
-        cdef bytes value_b
-
-        if value is None :
-            value_b = OBISeq_NA
-        elif isinstance(value, bytes) :
-            value_b = value
-        elif isinstance(value, str) :
-            value_b = str2bytes(value)
-        else:
-            raise TypeError('Sequence value must be of type Bytes, Str or None')
-
-        if obi_set_seq_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value_b) < 0:
-            raise Exception("Problem setting a value in a column")
-        
-
-cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
-
-    cpdef object get_item(self, index_t line_nb, str element_name):
-        cdef char*  value
-        cdef object result
-        value = obi_get_seq_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        if value == OBISeq_NA :
-            result = None
-        else :
-            try:
-                result = <bytes> value
-            finally:
-                free(value)
-        return result
-
-    
-    cpdef object get_line(self, index_t line_nb) :
-        cdef char*   value
-        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_get_seq_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
-            if obi_errno > 0 :
-                raise IndexError(line_nb)
-            if value == OBISeq_NA :
-                value_in_result = None
-            else :
-                try:
-                    value_in_result = <bytes> value
-                finally:
-                    free(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, object value):
-        cdef bytes value_b
-        
-        if value is None :
-            value_b = OBISeq_NA
-        elif isinstance(value, bytes) :
-            value_b = value
-        elif isinstance(value, str) :
-            value_b = str2bytes(value)
-        else:
-            raise TypeError('Sequence value must be of type Bytes, Str or None')
-        
-        if obi_set_seq_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
-            raise Exception("Problem setting a value in a column")
-
--- a/python/obitools3/obidms/_obidmscolumn_str.cfiles
+++ b/python/obitools3/obidms/_obidmscolumn_str.cfiles
@ -1,65 +0,0 @@
-../../../src/bloom.h
-../../../src/bloom.c
-../../../src/char_str_indexer.h
-../../../src/char_str_indexer.c
-../../../src/crc64.h
-../../../src/crc64.c
-../../../src/dna_seq_indexer.h
-../../../src/dna_seq_indexer.c
-../../../src/encode.h
-../../../src/encode.c
-../../../src/hashtable.h
-../../../src/hashtable.c
-../../../src/murmurhash2.h
-../../../src/murmurhash2.c
-../../../src/obi_align.h
-../../../src/obi_align.c
-../../../src/obiavl.h
-../../../src/obiavl.c
-../../../src/obiblob_indexer.h
-../../../src/obiblob_indexer.c
-../../../src/obiblob.h
-../../../src/obiblob.c
-../../../src/obidebug.h
-../../../src/obidms_taxonomy.h
-../../../src/obidms_taxonomy.c
-../../../src/obidms.h
-../../../src/obidms.c
-../../../src/obidmscolumn_blob.c
-../../../src/obidmscolumn_blob.h
-../../../src/obidmscolumn_bool.c
-../../../src/obidmscolumn_bool.h
-../../../src/obidmscolumn_char.c
-../../../src/obidmscolumn_char.h
-../../../src/obidmscolumn_float.c
-../../../src/obidmscolumn_float.h
-../../../src/obidmscolumn_idx.h
-../../../src/obidmscolumn_idx.c
-../../../src/obidmscolumn_int.c
-../../../src/obidmscolumn_int.h
-../../../src/obidmscolumn_qual.h
-../../../src/obidmscolumn_qual.c
-../../../src/obidmscolumn_seq.c
-../../../src/obidmscolumn_seq.h
-../../../src/obidmscolumn_str.c
-../../../src/obidmscolumn_str.h
-../../../src/obidmscolumn.h
-../../../src/obidmscolumn.c
-../../../src/obidmscolumndir.h
-../../../src/obidmscolumndir.c
-../../../src/obierrno.h
-../../../src/obierrno.c
-../../../src/obilittlebigman.h
-../../../src/obilittlebigman.c
-../../../src/obitypes.h
-../../../src/obitypes.c
-../../../src/obiview.h
-../../../src/obiview.c
-../../../src/sse_banded_LCS_alignment.h
-../../../src/sse_banded_LCS_alignment.c
-../../../src/uint8_indexer.h
-../../../src/uint8_indexer.c
-../../../src/upperband.h
-../../../src/upperband.c
-../../../src/utils.h
-../../../src/utils.c
--- a/python/obitools3/obidms/_obidmscolumn_str.pxd
+++ b/python/obitools3/obidms/_obidmscolumn_str.pxd
@ -1,14 +0,0 @@
-#cython: language_level=3
-
-from .capi.obitypes cimport index_t
-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)
-
-cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
-    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, object value)
--- a/python/obitools3/obidms/_obidmscolumn_str.pyx
+++ b/python/obitools3/obidms/_obidmscolumn_str.pyx
@ -1,84 +0,0 @@
-#cython: language_level=3
- 
-from .capi.obiview      cimport obi_get_str_with_elt_name_and_col_p_in_view, \
-                                obi_get_str_with_elt_idx_and_col_p_in_view, \
-                                obi_set_str_with_elt_name_and_col_p_in_view, \
-                                obi_set_str_with_elt_idx_and_col_p_in_view
-from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIStr_NA, const_char_p
-
-from obitools3.utils cimport str2bytes, bytes2str
-
-
-cdef class OBIDMS_column_str(OBIDMS_column):
-
-    cpdef object get_line(self, index_t line_nb):
-        cdef const_char_p value
-        cdef object       result
-        value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
-        if obi_errno > 0 :
-            raise IndexError(line_nb)
-        if value == OBIStr_NA :
-            result = None
-        else :
-            result = bytes2str(value)
-        # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
-        return result
-
-    cpdef set_line(self, index_t line_nb, object value):
-        if value is None :
-            if obi_set_str_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, OBIStr_NA) < 0:
-                raise Exception("Problem setting a value in a column")
-        else :
-            if obi_set_str_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, str2bytes(value)) < 0:
-                raise Exception("Problem setting a value in a column")
-
-
-cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
-
-    cpdef object get_item(self, index_t line_nb, str element_name):
-        cdef const_char_p value
-        cdef object       result
-        value = obi_get_str_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        if value == OBIStr_NA :
-            result = None
-        else :
-            result = bytes2str(value)
-        # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
-        return result
-
-    cpdef object get_line(self, index_t line_nb) :
-        cdef const_char_p value  # @DuplicatedSignature
-        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_get_str_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
-            if obi_errno > 0 :
-                raise IndexError(line_nb)
-            if value == OBIStr_NA :
-                value_in_result = None
-            else :
-                value_in_result = bytes2str(value)
-            # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
-            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, object value):
-        cdef bytes value_b
-        if value is None :
-            value_b = OBIStr_NA
-        else :
-            value_b = str2bytes(value)
-        if obi_set_str_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
-            raise Exception("Problem setting a value in a column")
-    
--- a/python/obitools3/obidms/capi/obierrno.pxd
+++ b/python/obitools3/obidms/capi/obierrno.pxd
@ -1,5 +0,0 @@
-#cython: language_level=3
-
-
-cdef extern from "obierrno.h" nogil:
-    extern int obi_errno
--- a/python/obitools3/utils.pxd
+++ b/python/obitools3/utils.pxd
@ -2,5 +2,6 @@


 cdef bytes str2bytes(str string)
-
-cdef str bytes2str(bytes string)
+cdef str bytes2str(bytes string)
+cdef bytes tobytes(object string)
+cdef str tostr(object string)
--- a/python/obitools3/utils.pyx
+++ b/python/obitools3/utils.pyx
@ -1,4 +1,5 @@
 #cython: language_level=3
+from IPython.utils._tokenize_py2 import String


 cdef bytes str2bytes(str string):
@ -24,3 +25,32 @@ cdef str bytes2str(bytes string):
    """
    return string.decode('ascii')

+cdef bytes tobytes(object string):
+    """
+    Short cut to convert ascii encoded string (str or bytes) to bytes 
+    which can be easily converted to C-strings. 
+    
+        @param string: the python string to be converted.
+        @type string: bytes or str
+        @return a transcoded string
+        @rtype: bytes 
+    """
+    if isinstance(string, bytes):
+        return string
+    return str2bytes(string)
+
+
+cdef str tostr(object string):
+    """
+    Short cut to convert ascii encoded string (str or bytes) to bytes 
+    which can be easily converted to C-strings. 
+    
+        @param string: the python string to be converted.
+        @type string: bytes or str
+        @return a transcoded string
+        @rtype: bytes 
+    """
+    if isinstance(string, str):
+        return string
+    return bytes2str(string)
+
--- a/src/obidmscolumn.c
+++ b/src/obidmscolumn.c
@ -639,7 +639,7 @@ 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 > 8))		// TODO check in more robust way
+	if ((data_type < 1) || (data_type > 8))		// TODO check in more robust way and use macro define somewhere
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
 		obidebug(1, "\nCan't create column because of invalid data type");
@ -665,7 +665,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 	// Build the indexer name if needed
 	if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || (data_type == OBI_QUAL))
 	{
-		if ((indexer_name == NULL) || (strcmp(indexer_name, "") == 0))
+		if ((indexer_name == NULL) || (*indexer_name == 0))
 		{
 			final_indexer_name = obi_build_indexer_name(column_name, version_number);
 			if (final_indexer_name == NULL)
--- a/src/obidmscolumn.h
+++ b/src/obidmscolumn.h
@ -102,18 +102,22 @@ typedef struct OBIDMS_column_header {
 * creating, opening or cloning an OBIDMS column.
 */
 typedef struct OBIDMS_column {
-	OBIDMS_p                	dms;			 	/**< A pointer to the OBIDMS structure to which the column belongs.
+	OBIDMS_p                	dms;			 	/**< A pointer to the OBIDMS structure to
+	                                                 *   which the column belongs.
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	OBIDMS_column_directory_p   column_directory;	/**< A pointer to the OBIDMS column directory structure to which the column belongs.
+	OBIDMS_column_directory_p   column_directory;	/**< A pointer to the OBIDMS column directory
+	                                                 *   structure to which the column belongs.
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	OBIDMS_column_header_p		header; 		 	/**< A pointer to the header of the column.
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	Obi_indexer_p    			indexer;		    /**< A pointer to the blob indexer associated with the column if there is one.
+	Obi_indexer_p    			indexer;		    /**< A pointer to the blob indexer associated
+	                                                 *   with the column if there is one.
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	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.
+													 *   @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.
 													 *       - `true` the column is writable
@ -122,7 +126,8 @@ typedef struct OBIDMS_column {
 													 * A column is writable only by its creator
 													 * until it closes it.
 													 */
-	size_t						counter;			/**< Indicates by how many threads/programs (TODO) the column is used.
+	size_t						counter;			/**< Indicates by how many threads/programs
+	                                                 *   (TODO) the column is used.
 													 */
 } OBIDMS_column_t, *OBIDMS_column_p;