Reworked a bit alignment API

python/obitools3/commands/align.pyx

@@ -8,10 +8,6 @@ __title__="Aligns one sequence column with itself or two sequence columns"
 
 
 default_config = {   'inputview'    : None,
-                     'skip'         : 0,
-                     'only'         : None,
-                     'skiperror'    : False,
-                     'moltype'      : 'nuc',
                  }
 
 def addOptions(parser):
@@ -31,8 +27,7 @@ def addOptions(parser):
                        metavar='<INPUT VIEW NAME>',
                        default=None,
                        type=str,
-                       help="Name of the input view, either raw if the view is in the default DMS,"
-                            " or in the form 'dms:view' if it is in another DMS.")
+                       help="Name of the input view.")
 
     # TODO eventually 2nd view, or 2nd column?
 
@@ -41,8 +36,7 @@ def addOptions(parser):
                        metavar='<OUTPUT VIEW NAME>',
                        default=None,
                        type=str,
-                       help="Name of the output view, either raw if the view is in the default DMS,"
-                            " or in the form 'dms:view' if it is in another DMS.")
+                       help="Name of the output view.")
 
 
     group=parser.add_argument_group('obi align specific options')
@@ -106,16 +100,17 @@ def run(config):
 
     # TODO Open input view 2 if there is one
 
-    # Create output view if necessary
-    if config['obi']['outputview'] is not None :
-        oview = d.new_view(config['obi']['outputview'])
-    else :
-        oview = None
+    # Create output view
+    oview = d.new_view(config['obi']['outputview'])
     
     # TODO Take other alignment types into account when they'll be implemented
     
     # Call cython alignment function
-    iview.align(output_view=oview)
+    iview.align(oview)
+    
+    iview.save_and_close()
+    oview.save_and_close()
+    d.close()
      
     print("Done.")
     

python/obitools3/obidms/_obidms.pxd

@@ -78,8 +78,8 @@ cdef class OBIView_NUC_SEQS(OBIView):
     
     cpdef delete_column(self, str column_name)
     cpdef align(self,
+                OBIView oview, 
                 OBIView iview2=*, 
-                object output_view=*, 
                 double threshold=*, 
                 bint normalize=*, 
                 int reference=*, 

python/obitools3/obidms/_obidms.pyx

@@ -534,11 +534,10 @@ cdef class OBIView_NUC_SEQS(OBIView):
 
 
     # TODO
-    cpdef align(self, OBIView iview2=None, object output_view=None,
+    cpdef align(self, OBIView oview, OBIView iview2=None,
                 double threshold=0.0, bint normalize=True, int reference=0, bint similarity_mode=True) :
                 
         cdef OBIView iview1
-        cdef OBIView oview
 
         cdef Obiview_p iview1_p
         cdef Obiview_p iview2_p
@@ -574,14 +573,6 @@ cdef class OBIView_NUC_SEQS(OBIView):
         icol1_pp = icol1.pointer
         icol1_p = icol1_pp[0]
 
-        # Create the output view if needed
-        if output_view is None :
-            oview = self.dms.new_view("alignment_score_view")    # TODO discuss
-        elif type(output_view) == str :
-            oview = self.dms.new_view(output_view)
-        else :
-            oview = output_view
-
         oview.add_column(id1_col_name, type='OBI_STR', create=True)
         oview.add_column(id2_col_name, type='OBI_STR', create=True)       
         oview.add_column(score_col_name, type='OBI_FLOAT', create=True)