Some change in the way to manage access to special items of the

dictionary like sequence or quality

python/obitools3/obidms/_obiseq.pxd

@@ -11,9 +11,11 @@ cdef class OBI_Seq(dict) :
 
 cdef class OBI_Nuc_Seq(OBI_Seq) :
     cdef object _quality   
-    #cpdef object reverse_complement(self)    
+    cpdef object get_str_quality(self)
     
+    #cpdef object reverse_complement(self)    
 
 cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
     cpdef object get_str_quality(self)
+    
     #cpdef object reverse_complement(self)

python/obitools3/obidms/_obiseq.pyx

@@ -8,14 +8,31 @@ from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
                            QUALITY_COLUMN
 
 
+cdef str __str__ID_COLUMN__ = bytes2str(ID_COLUMN)
+cdef str __str__DEFINITION_COLUMN__ = bytes2str(DEFINITION_COLUMN)
+cdef str __str__QUALITY_COLUMN__ = bytes2str(QUALITY_COLUMN)
+cdef str __str__NUC_SEQUENCE_COLUMN__ = bytes2str(NUC_SEQUENCE_COLUMN)
+
+
 cdef class OBI_Seq(dict) :
 
-    def __init__(self, str id, object seq, object definition=None) :
+    def __init__(self, str id, 
+                       object seq, 
+                       str definition=None,
+                       dict attributes=None) :
         self.id = id
         self.seq = seq
         if definition is not None :
             self.definition = definition
             
+    def __getitem__(self,str key):
+        if key == __str__ID_COLUMN__:
+            return self._id
+        elif key == __str__DEFINITION_COLUMN__:
+            return self._definition
+        else:
+            return dict.__getitem__(self,key)
+        
     # sequence id property getter and setter
     @property
     def id(self):  # @ReservedAssignment
@@ -23,7 +40,6 @@ cdef class OBI_Seq(dict) :
     @id.setter
     def id(self, str new_id):  # @ReservedAssignment @DuplicatedSignature
         self._id = new_id
-        self[bytes2str(ID_COLUMN)] = new_id
 
     # sequence property getter and setter
     @property
@@ -32,7 +48,7 @@ cdef class OBI_Seq(dict) :
     @seq.setter
     def seq(self, object new_seq):  # @DuplicatedSignature
         self._seq = new_seq
-        self["SEQ"] = new_seq   # TODO discuss
+    #    self["SEQ"] = new_seq   # TODO discuss
 
     # sequence definition property getter and setter
     @property
@@ -41,11 +57,21 @@ cdef class OBI_Seq(dict) :
     @definition.setter
     def definition(self, object new_definition):  # @DuplicatedSignature
         self._definition = new_definition
-        self[bytes2str(DEFINITION_COLUMN)] = new_definition
 
 
 cdef class OBI_Nuc_Seq(OBI_Seq) :
     
+    def __getitem__(self,str key):
+        if key == __str__NUC_SEQUENCE_COLUMN__:
+            return self._id
+        elif key == __str__QUALITY_COLUMN__:
+            return self._quality
+        else:
+            return OBI_Seq.__getitem__(self,key)
+        
+    cpdef object get_str_quality(self) :    # TODO not ideal. Make quality_int and quality_str properties
+        return self._quality
+    
     # nuc sequence property getter and setter
     @property
     def seq(self):
@@ -53,7 +79,7 @@ cdef class OBI_Nuc_Seq(OBI_Seq) :
     @seq.setter
     def seq(self, object new_seq):  # @DuplicatedSignature
         self._seq = new_seq
-        self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq
+#        self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq
 
     # sequence quality property getter and setter
     @property
@@ -62,7 +88,7 @@ cdef class OBI_Nuc_Seq(OBI_Seq) :
     @quality.setter
     def quality(self, object new_quality):  # @DuplicatedSignature
         self._quality = new_quality
-        self[bytes2str(QUALITY_COLUMN)] = new_quality
+#        self[bytes2str(QUALITY_COLUMN)] = new_quality
 
 #    cpdef str reverse_complement(self) :    TODO in C ?
 #        pass
@@ -75,40 +101,44 @@ cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
     # sequence id property getter and setter
     @property
     def id(self):               # @ReservedAssignment @DuplicatedSignature
-        return self[bytes2str(ID_COLUMN)]
+        return self[__str__ID_COLUMN__]
+    
     @id.setter
     def id(self, str new_id):   # @ReservedAssignment @DuplicatedSignature
-        self[bytes2str(ID_COLUMN)] = new_id
+        self[__str__ID_COLUMN__] = new_id
 
     # sequence definition property getter and setter
     @property
     def definition(self):
-        return self[bytes2str(DEFINITION_COLUMN)]
+        return self[__str__DEFINITION_COLUMN__]
+    
     @definition.setter
     def definition(self, str new_def): # @DuplicatedSignature
-        self[bytes2str(DEFINITION_COLUMN)] = new_def
+        self[__str__DEFINITION_COLUMN__] = new_def
 
     # nuc_seq property getter and setter
     @property
     def nuc_seq(self):
-        return self[bytes2str(NUC_SEQUENCE_COLUMN)]
+        return self[__str__NUC_SEQUENCE_COLUMN__]
+    
     @nuc_seq.setter
     def nuc_seq(self, object new_seq): # @DuplicatedSignature
-        self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq
+        self[__str__NUC_SEQUENCE_COLUMN__] = new_seq
 
     # quality property getter and setter
     @property
     def quality(self):
-        return self[bytes2str(QUALITY_COLUMN)]
+        return self[__str__QUALITY_COLUMN__]
+    
     @quality.setter
     def quality(self, object new_qual): # @DuplicatedSignature
         if (type(new_qual) == list) or (new_qual is None) : # TODO check that quality column exists
-            self[bytes2str(QUALITY_COLUMN)] = new_qual
+            self[__str__QUALITY_COLUMN__] = new_qual
         else :  # Quality is in str form
-            (((self._view).columns)[bytes2str(QUALITY_COLUMN)]).set_str_line(self._index, new_qual)
+            (((self._view).columns)[__str__QUALITY_COLUMN__]).set_str_line(self._index, new_qual)
 
     cpdef object get_str_quality(self) :    # TODO not ideal. Make quality_int and quality_str properties
-        return ((self._view).columns)[bytes2str(QUALITY_COLUMN)].get_str_line(self._index)
+        return ((self._view).columns)[__str__QUALITY_COLUMN__].get_str_line(self._index)
     
 #    cpdef str reverse_complement(self) :    TODO in C ?
 #        pass