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/obitools3/commands/align.pyx

@@ -108,18 +108,15 @@ def run(config):
     # Call cython alignment function
     iview.align(oview)
     
-    print(oview.__repr__())
+    repr(oview)
     
-    iview.save_and_close()
-    oview.save_and_close()
+    iview.close()
+    oview.close()
     d.close()
      
     print("Done.")
-    
-    
 
     
     
     
-    
         

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()
-    oview.save_and_close()
+    iview.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)