Cython view API: added NUC_SEQS views and sequence classes + changed

cloning API

python/obitools3/dms/capi/obiview.pxd

@@ -66,8 +66,12 @@ cdef extern from "obiview.h" nogil:
     
     Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments)
 
-    Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments, bint quality_column)
+    Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments)
-              
+    
+    Obiview_p obi_clone_view(OBIDMS_p dms, Obiview_p view_to_clone, const char* view_name, index_t* line_selection, const char* comments)
+
+    Obiview_p obi_clone_view_from_name(OBIDMS_p dms, const char* view_to_clone_name, const char* view_name, index_t* line_selection, const char* comments)
+    
     Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name, bint finished)
 
     int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos)

python/obitools3/dms/obiseq.pxd

@@ -0,0 +1,22 @@
+#cython: language_level=3
+
+from .view.view cimport Line
+
+
+cdef class Seq(dict) :
+
+    cdef str    _id
+    cdef object _seq
+    cdef str    _definition
+    
+    
+cdef class Nuc_Seq(Seq) :
+
+    cdef object _quality   
+    #cpdef object reverse_complement(self)    
+    
+    
+cdef class Nuc_Seq_Stored(Line) :
+
+    cpdef object get_str_quality(self)
+    #cpdef object reverse_complement(self)

python/obitools3/dms/obiseq.pyx

@@ -0,0 +1,126 @@
+#cython: language_level=3
+
+from obitools3.utils cimport bytes2str, str2bytes
+
+from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
+                            ID_COLUMN, \
+                            DEFINITION_COLUMN, \
+                            QUALITY_COLUMN
+
+
+cdef class Seq(dict) :
+    def __init__(self, str id, object seq, object definition=None) :
+        self.id = id
+        self.seq = seq
+        if definition is not None :
+            self.definition = definition
+            
+    # sequence id property getter and setter
+    @property
+    def id(self):  # @ReservedAssignment
+        return self._id
+    
+    @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
+    def seq(self):
+        return self._seq
+    
+    @seq.setter
+    def seq(self, object new_seq):  # @DuplicatedSignature
+        self._seq = new_seq
+        self["SEQ"] = new_seq   # TODO discuss
+        
+    # sequence definition property getter and setter
+    @property
+    def definition(self):
+        return self._definition
+    
+    @definition.setter
+    def definition(self, object new_definition):  # @DuplicatedSignature
+        self._definition = new_definition
+        self[bytes2str(DEFINITION_COLUMN)] = new_definition
+        
+        
+cdef class Nuc_Seq(Seq) :
+    
+    # nuc sequence property getter and setter
+    @property
+    def seq(self):
+        return self._seq
+    
+    @seq.setter
+    def seq(self, object new_seq):  # @DuplicatedSignature
+        self._seq = new_seq
+        self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq
+        
+    # sequence quality property getter and setter
+    @property
+    def quality(self):
+        return self._quality
+    
+    @quality.setter
+    def quality(self, object new_quality):  # @DuplicatedSignature
+        self._quality = new_quality
+        self[bytes2str(QUALITY_COLUMN)] = new_quality
+        
+#    cpdef str reverse_complement(self) :    TODO in C ?
+#        pass
+
+
+cdef class Nuc_Seq_Stored(Line) :
+
+    # TODO store the str version of column name macros?
+    
+    # sequence id property getter and setter
+    @property
+    def id(self):               # @ReservedAssignment @DuplicatedSignature
+        return self[bytes2str(ID_COLUMN)]
+    
+    @id.setter
+    def id(self, str new_id):   # @ReservedAssignment @DuplicatedSignature
+        self[bytes2str(ID_COLUMN)] = new_id
+        
+    # sequence definition property getter and setter
+    @property
+    def definition(self):
+        return self[bytes2str(DEFINITION_COLUMN)]
+    
+    @definition.setter
+    def definition(self, str new_def): # @DuplicatedSignature
+        self[bytes2str(DEFINITION_COLUMN)] = new_def
+        
+    # nuc_seq property getter and setter
+    @property
+    def nuc_seq(self):
+        return self[bytes2str(NUC_SEQUENCE_COLUMN)]
+    
+    @nuc_seq.setter
+    def nuc_seq(self, object new_seq): # @DuplicatedSignature
+        self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq
+        
+    # quality property getter and setter
+    @property
+    def quality(self):
+        return self[bytes2str(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
+        else :  # Quality is in str form
+            (((self._view).columns)[bytes2str(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)
+    
+#    cpdef str reverse_complement(self) :    TODO in C ?
+#        pass
+
+    # TODO static method to import OBI_Nuc_Seq to OBI_Nuc_Seq_Stored ?
+    
+    

python/obitools3/dms/view/view.pxd

@@ -30,11 +30,7 @@ cdef class View(OBIWrapper):
                                        list lines=*)
 
     @staticmethod
-    cdef type get_view_class(bytes viewtype)
+    cdef type get_view_class(bytes view_type)
-
-    @staticmethod
-    cdef register_view_class(bytes viewtype,
-                            type classe)
 
 
 cdef class Line_selection(list):
@@ -55,3 +51,7 @@ cdef class Line :
     cdef View    _view
     
 
+cdef register_view_class(bytes view_type_name,
+                         type view_class)
+
+cdef register_all_view_classes()

python/obitools3/dms/view/view.pyx

@@ -9,6 +9,7 @@ from libc.stdlib  cimport malloc
 from ..capi.obiview cimport Alias_column_pair_p, \
                             obi_new_view, \
                             obi_open_view, \
+                            obi_clone_view, \
                             obi_save_and_close_view, \
                             obi_view_get_pointer_on_column_in_view, \
                             obi_view_delete_column, \
@@ -26,6 +27,8 @@ from ..object cimport OBIObjectClosedInstance
           
 from ..column.column cimport Column
 
+from obitools3.dms.view import typed_view
+
 from ..capi.obitypes cimport only_ATGC, \
                              OBI_BOOL, \
                              OBI_CHAR, \
@@ -34,27 +37,16 @@ from ..capi.obitypes cimport only_ATGC, \
                              OBI_QUAL, \
                              OBI_SEQ, \
                              OBI_STR
-          
+
+import importlib
+import inspect
+import pkgutil
+  
 
 cdef class View(OBIWrapper) :
 
     cdef inline Obiview_p pointer(self) :
-        return <Obiview_p>(self._pointer)
+        return <Obiview_p>(self._pointer)        
-
-
-    @staticmethod
-    cdef register_view_class(bytes view_type_name,
-                             type view_class):
-        '''
-        Each sub class of `dms.View` needs to be registered after its declaration
-        to declare its relationship with an `OBIType_t`
-        '''
-        global __VIEW_CLASS__
-    
-        assert issubclass(view_class, View)
-        
-        __VIEW_CLASS__[view_type_name] = view_class
-        
     
     @staticmethod
     cdef type get_view_class(bytes view_type):
@@ -65,8 +57,7 @@ cdef class View(OBIWrapper) :
     @staticmethod
     def new(DMS dms, 
             object view_name, 
-            object comments=None,
+            object comments=None):
-            type view_class=View):
 
         cdef bytes view_name_b = tobytes(view_name)
         cdef bytes comments_b
@@ -74,7 +65,7 @@ cdef class View(OBIWrapper) :
         cdef void* pointer
 
         cdef View view  # @DuplicatedSignature
-                                
+
         if comments is not None:
             comments_b  = tobytes(comments)
         else:
@@ -90,7 +81,7 @@ cdef class View(OBIWrapper) :
             message = "Error : Cannot create view %s" % bytes2str(view_name_b)
             raise RuntimeError(message)
         
-        view = OBIWrapper.new(view_class, pointer)
+        view = OBIWrapper.new(View, pointer)
         view._dms = dms
         dms.register(view)
 
@@ -115,11 +106,11 @@ cdef class View(OBIWrapper) :
         else:
             comments_b  = b''
                                 
-        pointer = <void*> obi_new_view(self._dms.pointer(), 
+        pointer = <void*> obi_clone_view(self._dms.pointer(), 
-                                       view_name_b, 
+                                         self.pointer(), 
-                                       self.pointer(), 
+                                         view_name_b, 
-                                       NULL, 
+                                         NULL, 
-                                       comments_b)
+                                         comments_b)
         
         if pointer == NULL :
             raise RuntimeError("Error : Cannot clone view %s into view %s" 
@@ -485,13 +476,13 @@ cdef class Line_selection(list):
             comments_b  = tobytes(comments)
         else:
             comments_b  = b''
-        
+    
-        pointer = obi_new_view(self._view._dms.pointer(), 
+        pointer = obi_clone_view(self._view._dms.pointer(), 
-                                       view_name_b, 
+                                 self._view.pointer(), 
-                                       self._view.pointer(), 
+                                 view_name_b, 
-                                       self.__build_binary_list__(), 
+                                 self.__build_binary_list__(), 
-                                       comments_b)
+                                 comments_b)
-        
+
         if pointer == NULL :
             raise RuntimeError("Error : Cannot clone view %s into view %s with new line selection" 
                                % (str(self._view.name),
@@ -504,3 +495,28 @@ cdef class Line_selection(list):
                 
         return view
 
+
+#############################################################
+
+
+cdef register_view_class(bytes view_type_name,
+                         type view_class):
+    '''
+    Each subclass of `dms.view` needs to be registered after its declaration
+    '''
+    global __VIEW_CLASS__
+
+    assert issubclass(view_class, View)
+    
+    __VIEW_CLASS__[view_type_name] = view_class
+
+
+cdef register_all_view_classes() :
+    
+    x = list(pkgutil.walk_packages(typed_view.__path__, prefix="obitools3.dms.view.typed_view."))
+    all_modules = [importlib.import_module(a[1]) for a in x]
+    for mod in all_modules :
+        getattr(mod, 'register_class')()
+
+
+register_all_view_classes()