Added OBIView_line_selection class to make new line selections

associated with the view to clone, and improved and renamed method
closing a view

python/obi.py

@@ -21,7 +21,9 @@ default_config = { 'software'       : "The OBITools",
                    'log'            : False,
                    'loglevel'       : 'INFO',
                    'progress'       : True,
-                   'defaultdms'     : None
+                   'defaultdms'     : None,
+                   'inputview'      : None,
+                   'outputview'     : None
                   }
 
 root_config_name='obi'

python/obitools3/commands/align.pyx

@@ -108,10 +108,10 @@ def run(config):
     # Call cython alignment function
     iview.align(oview)
     
-    print(oview.__repr__())
+    repr(oview)
     
-    iview.save_and_close()
+    iview.close()
-    oview.save_and_close()
+    oview.close()
     d.close()
      
     print("Done.")
@@ -120,6 +120,3 @@ def run(config):
     
     
         
-    
-    
-        

python/obitools3/commands/export.pyx

@@ -85,7 +85,7 @@ def run(config):
         print(toprint)
         i+=1
         
-    iview.save_and_close()
+    iview.close()
     d.close()
     
     print("Done.")

python/obitools3/commands/grep.pyx

@@ -75,10 +75,10 @@ def run(config):
     # Create output view with the line selection
     oview = d.new_view(config['obi']['outputview'], view_to_clone=iview, line_selection=selection, comments="obi grep: "+config['grep']['predicate']+"\n")
 
-    print(oview.__repr__())
+    repr(oview)
 
-    iview.save_and_close()
+    iview.close()
-    oview.save_and_close()
+    oview.close()
     d.close()
     
     print("Done.")

python/obitools3/commands/import.pyx

@@ -4,9 +4,9 @@ from obitools3.parsers.fasta import fastaIterator
 from obitools3.parsers.fastq import fastqIterator
 from obitools3.obidms._obidms import OBIDMS
 
-
 import time
 
+
 __title__="Counts sequences in a sequence set"
 
 
@@ -90,7 +90,7 @@ def addOptions(parser):
 
 # TODO: Handling of NA values
 def run(config):
-    #pb = ProgressBar(35000000, config, seconde=5)
+    pb = ProgressBar(35000000, config, seconde=5)
       
     inputs = uopen(config['import']['filename'])
     
@@ -113,7 +113,7 @@ def run(config):
     
     i = 0
     for seq in iseq:
-        #pb(i)
+        pb(i)
         view[i].set_id(seq['id'])
         view[i].set_definition(seq['definition'])
         view[i].set_sequence(seq['sequence'])
@@ -125,7 +125,7 @@ def run(config):
 
     print(view.__repr__())
 
-    view.save_and_close()    
+    view.close()
     d.close()
     
     print("Done.")

python/obitools3/commands/test.pyx

@@ -1,5 +1,6 @@
 from obitools3.apps.progress cimport ProgressBar  # TODO I absolutely don't understand why it doesn't work without that line
 from obitools3.obidms._obidms import OBIDMS       # TODO cimport doesn't work
+from obitools3.obidms._obidms import OBIView_line_selection
 from obitools3.utils cimport str2bytes
 
 import shutil
@@ -120,7 +121,7 @@ def test_add_col(config, infos):
     #    else :
     #        alias = ''
     #    infos['view'].add_column(random_column_refs['name'], version_number=random_column_refs['version'], alias=alias, create=False)
-    #    random_view.save_and_close()
+    #    random_view.close()
     #else :
     create_random_column(config, infos)
     print_test(config, ">>> Add column test OK")
@@ -215,7 +216,7 @@ def random_new_view(config, infos, first=False):
     quality_col = False     # TODO
     if not first:
         infos['view_names'].append(infos['view'].name)
-        infos['view'].save_and_close()
+        infos['view'].close()
         v_to_clone = infos['dms'].open_view(random.choice(infos["view_names"]))
         v_type = None
         print_test(config, "View to clone: ")
@@ -223,7 +224,7 @@ def random_new_view(config, infos, first=False):
         create_line_selection = random_bool(config)
         if create_line_selection and v_to_clone.line_count > 0:
             print_test(config, "New view with new line selection.")
-            line_selection = []
+            line_selection = OBIView_line_selection(v_to_clone)
             for i in range(random.randint(1, v_to_clone.line_count)) :
                 line_selection.append(random.randint(0, v_to_clone.line_count-1))
             #print_test(config, "New line selection: "+str(line_selection))
@@ -241,7 +242,7 @@ def random_new_view(config, infos, first=False):
             assert v_to_clone.line_count == infos['view'].line_count, "New view and cloned view don't have the same line count"
         else :
             assert len(line_selection) == infos['view'].line_count, "New view with new line selection does not have the right line count"
-        v_to_clone.save_and_close()
+        v_to_clone.close()
     if first :
         fill_view(config, infos)
 
@@ -370,7 +371,7 @@ def run(config):
 
     #print(infos)
     
-    infos['view'].save_and_close()
+    infos['view'].close()
     infos['dms'].close()
     shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
     

python/obitools3/format/fasta.pyx

@@ -1,6 +1,4 @@
 cimport cython
-from libc.stdlib cimport malloc, free, realloc
-from libc.string cimport strncpy
 
 cdef class FastaFormat:
 	

python/obitools3/obidms/_obidms.pxd

@@ -52,7 +52,7 @@ cdef class OBIView:
                     )
     cpdef change_column_alias(self, str current_alias, str new_alias)
     cpdef update_column_pointers(self)
-    cpdef save_and_close(self)
+    cpdef close(self)
     
 
 cdef class OBIView_NUC_SEQS(OBIView):
@@ -73,6 +73,12 @@ cdef class OBIView_line :
     cdef OBIView _view
 
 
+cdef class OBIView_line_selection(list):
+    
+    cdef OBIView _view
+    cdef str     _view_name
+    
+        
 cdef class OBIDMS:
 
     cdef OBIDMS_p _pointer
@@ -80,7 +86,7 @@ cdef class OBIDMS:
     cpdef close(self)
     cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name)
     cpdef OBIView open_view(self, str view_name)
-    cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*, str view_type=*, str comments=*, bint quality_column=*)
+    cpdef OBIView new_view(self, str view_name, object view_to_clone=*, OBIView_line_selection line_selection=*, str view_type=*, str comments=*, bint quality_column=*)
     cpdef dict read_view_infos(self, str view_name)
 #    cpdef dict read_views(self)    TODO
 

python/obitools3/obidms/_obidms.pyx

@@ -273,7 +273,7 @@ cdef class OBIDMS_column_line :
 
 cdef class OBIView :
     
-    def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None, str comments="", bint quality_column=False):     
+    def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, OBIView_line_selection line_selection=None, str comments="", bint quality_column=False):     
         # TODO quality_column is only here because it's needed for OBIView_NUC_SEQS views, not clean?
                 
         cdef Obiview_p       view = NULL
@@ -420,9 +420,11 @@ cdef class OBIView :
             column._pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self._pointer, str2bytes(column_n))
 
     
-    cpdef save_and_close(self) :
+    cpdef close(self) :
         if (obi_save_and_close_view(self._pointer) < 0) :
             raise Exception("Problem closing a view")
+        self._pointer = NULL
+        self._columns = {}
     
 
     def __iter__(self):
@@ -483,11 +485,13 @@ cdef class OBIView :
         return bytes2str(self._pointer.infos.comments)
     # TODO setter that concatenates new comments?
 
-#############################################
+
+######################################################################################################
+
 
 cdef class OBIView_NUC_SEQS(OBIView):
     
-    def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None, str comments="", bint quality_column=False): 
+    def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, OBIView_line_selection line_selection=None, str comments="", bint quality_column=False): 
         
         cdef Obiview_p       view = NULL
         cdef index_t*        line_selection_p
@@ -497,10 +501,20 @@ cdef class OBIView_NUC_SEQS(OBIView):
         cdef object          subclass
                 
         if line_selection is not None :
-            line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
+            # Check that the line selection is associated with the view to clone
+            if view_to_clone is None :
+                raise Exception("Error creating a view: there is a new line selection but no associated view to clone")
+            if type(view_to_clone) == str :
+                if line_selection._view_name != view_to_clone :
+                    raise Exception("Error creating a view: the new line selection isn't associated with the view to clone")
+            elif line_selection._view != view_to_clone :
+                raise Exception("Error creating a view: the new line selection isn't associated with the view to clone")
+            
+            # Build the C array corresponding to the line selection
+            line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))   # +1 for the -1 flagging the end of the array
             for i in range(len(line_selection)) :
                 line_selection_p[i] = line_selection[i]
-            line_selection_p[len(line_selection)] = -1
+            line_selection_p[len(line_selection)] = -1      # flagging the end of the array
         else :
             line_selection_p = NULL
        
@@ -602,7 +616,8 @@ cdef class OBIView_NUC_SEQS(OBIView):
             raise Exception("Error aligning sequences")
         
 
-#############################################
+######################################################################################################
+
 
 cdef class OBIView_line :
 
@@ -656,7 +671,29 @@ cdef class OBIView_line :
             line[column_name] = self[column_name]
         return str(line)
 
-##########################################
+
+######################################################################################################
+
+
+cdef class OBIView_line_selection(list):
+    
+    def __init__(self, OBIView view) :
+        if view._pointer == NULL:
+            raise Exception("Error: trying to create a line selection with an invalidated view")
+        self._view = view
+        self._view_name = view.name
+        
+    def append(self, index_t idx) :
+        if idx >= self._view.line_count :
+            raise Exception("Error: trying to select a line beyond the line count of a view")
+ #       if idx in self :    # TODO discuss. Discuss order too
+ #           pass    
+ #       else :
+        super(OBIView_line_selection, self).append(idx)
+
+
+######################################################################################################
+
 
 cdef class OBIDMS :
     
@@ -704,7 +741,7 @@ cdef class OBIDMS :
         return view_class(self, view_name)
     
 
-    cpdef OBIView new_view(self, str view_name, object view_to_clone=None, list line_selection=None, str view_type=None, str comments="", bint quality_column=False) :
+    cpdef OBIView new_view(self, str view_name, object view_to_clone=None, OBIView_line_selection line_selection=None, str view_type=None, str comments="", bint quality_column=False) :
         
         cdef object view_class
         

src/obiview.c

@@ -1132,6 +1132,22 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 	int 			i;
 	index_t 		line_nb;
 
+	// Check that the DMS is a valid pointer
+	if (dms == NULL)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError creating a view: DMS pointer is NULL");
+		return NULL;
+	}
+
+	// Check that the view name pointer is valid
+	if (view_name == NULL)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError creating a view: view name is NULL");
+		return NULL;
+	}
+
 	// Check uniqueness of name
 	if (view_exists(dms, view_name))
 	{