Removed a list of column pointers kept in the OBIView class that was not

really needed

python/obitools3/obidms/_obidms.pxd

@@ -45,7 +45,6 @@ cdef class OBIView:
     cdef str       name
     cdef str       comments
     cdef dict      columns
-    cdef dict      columns_pp    # TODO this dict might be unnecessary
     cdef OBIDMS    dms
     
     cpdef delete_column(self, str column_name)

python/obitools3/obidms/_obidms.pyx

@@ -84,7 +84,7 @@ cdef class OBIDMS_column :
         cdef OBIDMS_column_p  column_p
         cdef OBIDMS_column_p* column_pp
         
-        column_pp = <OBIDMS_column_p*> PyCapsule_GetPointer(((view.columns_pp)[column_name]), NULL) # or use C function
+        column_pp = obi_view_get_pointer_on_column_in_view(view.pointer, str2bytes(column_name))
         column_p = column_pp[0]     # TODO ugly cython dereferencing but can't find better
         
         # Fill structure
@@ -243,10 +243,8 @@ cdef class OBIView :
         cdef str col_name
         cdef OBIDMS_column column
         cdef OBIDMS_column_p column_p
-        cdef OBIDMS_column_p* column_pp
         cdef OBIDMS_column_header_p header
         cdef index_t* line_selection_p
-        cdef object col_capsule
         
         self.dms = dms
         
@@ -280,18 +278,13 @@ cdef class OBIView :
         
         # go through columns to build list and open python object (TODO make separate function?)
         self.columns = {}
-        self.columns_pp = {}
-                
+
         i = 0
         while i < view.column_count :
-            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
             column_p = <OBIDMS_column_p> (view.columns)[i]
             header = (column_p).header
             
-            col_name = bytes2str(header.name)
-            col_capsule = PyCapsule_New(column_pp, NULL, NULL)   # TODO discuss
-            (self.columns_pp)[col_name] = col_capsule
-            
+            col_name = bytes2str(header.name)         
             subclass = OBIDMS_column.get_subclass_type(column_p)
             self.columns[col_name] = subclass(self, col_name)
             
@@ -319,7 +312,6 @@ cdef class OBIView :
         cdef Obiview_p view
         cdef OBIDMS_column column
         cdef OBIDMS_column_p column_p
-        cdef OBIDMS_column_p* column_pp
         cdef OBIDMS_column_header_p header
         cdef str column_n
  
@@ -330,18 +322,7 @@ cdef class OBIView :
         
         # Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
         (self.columns).pop(column_name)
-        (self.columns_pp).pop(column_name)
         
-        i = 0
-        while i < view.column_count :
-            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
-            column_p = <OBIDMS_column_p> (view.columns)[i]
-            header = (column_p).header
-            col_name = bytes2str(header.name)
-            col_capsule = PyCapsule_New(column_pp, NULL, NULL)
-            (self.columns_pp)[col_name] = col_capsule
-            i+=1
-
         for column_n in self.columns :
             (self.columns[column_n]).update_pointer()
 
@@ -393,13 +374,8 @@ cdef class OBIView :
                                 str2bytes(comments), create) < 0) :
             raise Exception("Problem adding a column in a view")
         
-        # Store the column pointer
+        # Get the column pointer
         column_pp = obi_view_get_pointer_on_column_in_view(self.pointer, column_name_b)
-        if column_pp == NULL :
-            raise Exception("Problem getting a column in a view")
-        
-        col_capsule = PyCapsule_New(column_pp, NULL, NULL)   # TODO
-        (self.columns_pp)[column_name] = col_capsule
         
         # Open and store the subclass
         column_p = column_pp[0]     # TODO ugly cython dereferencing
@@ -474,7 +450,6 @@ cdef class OBIView_NUC_SEQS(OBIView):
         cdef str col_name
         cdef OBIDMS_column column
         cdef OBIDMS_column_p column_p
-        cdef OBIDMS_column_p* column_pp
         cdef OBIDMS_column_header_p header
         cdef index_t* line_selection_p
                 
@@ -511,18 +486,14 @@ cdef class OBIView_NUC_SEQS(OBIView):
         
         # go through columns to build list and open python object (TODO make separate function?)
         self.columns = {}
-        self.columns_pp = {}
                 
         i = 0
         while i < view.column_count :
-            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
             column_p = <OBIDMS_column_p> (view.columns)[i]
             header = (column_p).header
             
             col_name = bytes2str(header.name)
-            col_capsule = PyCapsule_New(column_pp, NULL, NULL)   # TODO discuss
-            (self.columns_pp)[col_name] = col_capsule
-            
+
             subclass = OBIDMS_column.get_subclass_type(column_p)
             self.columns[col_name] = subclass(self, col_name)
             
@@ -539,7 +510,6 @@ cdef class OBIView_NUC_SEQS(OBIView):
         cdef Obiview_p view
         cdef OBIDMS_column column
         cdef OBIDMS_column_p column_p
-        cdef OBIDMS_column_p* column_pp
         cdef OBIDMS_column_header_p header
         cdef str column_n
  
@@ -553,18 +523,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
         
         # Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
         (self.columns).pop(column_name)
-        (self.columns_pp).pop(column_name)
         
-        i = 0
-        while i < view.column_count :
-            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
-            column_p = <OBIDMS_column_p> (view.columns)[i]
-            header = (column_p).header
-            col_name = bytes2str(header.name)
-            col_capsule = PyCapsule_New(column_pp, NULL, NULL)
-            (self.columns_pp)[col_name] = col_capsule
-            i+=1
-
         for column_n in self.columns :
             (self.columns[column_n]).update_pointer()
 
@@ -572,7 +531,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
     def __getitem__(self, object item) :
         if type(item) == str :
             return (self.columns)[item]
-        elif type(item) == int :     # TODO int?
+        elif type(item) == int :     # TODO int? (range problem)
             return OBI_Nuc_Seq_Stored(self, item)