From 2d65db4ebc3faff85aa0b8ba9bba69711b66d8f8 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Fri, 21 Apr 2017 15:15:12 +0200
Subject: [PATCH] Goes with c2af955b : forgotten files for NUC_SEQS views

---
 .../obitools3/dms/view/typed_view/__init__.py |  0
 .../dms/view/typed_view/view_NUC_SEQS.pxd     |  8 ++
 .../dms/view/typed_view/view_NUC_SEQS.pyx     | 76 +++++++++++++++++++
 3 files changed, 84 insertions(+)
 create mode 100644 python/obitools3/dms/view/typed_view/__init__.py
 create mode 100644 python/obitools3/dms/view/typed_view/view_NUC_SEQS.pxd
 create mode 100644 python/obitools3/dms/view/typed_view/view_NUC_SEQS.pyx

diff --git a/python/obitools3/dms/view/typed_view/__init__.py b/python/obitools3/dms/view/typed_view/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/python/obitools3/dms/view/typed_view/view_NUC_SEQS.pxd b/python/obitools3/dms/view/typed_view/view_NUC_SEQS.pxd
new file mode 100644
index 0000000..a5ec324
--- /dev/null
+++ b/python/obitools3/dms/view/typed_view/view_NUC_SEQS.pxd
@@ -0,0 +1,8 @@
+#cython: language_level=3
+
+
+from ..view cimport View
+
+
+cdef class View_NUC_SEQS(View):
+    pass
diff --git a/python/obitools3/dms/view/typed_view/view_NUC_SEQS.pyx b/python/obitools3/dms/view/typed_view/view_NUC_SEQS.pyx
new file mode 100644
index 0000000..693b43e
--- /dev/null
+++ b/python/obitools3/dms/view/typed_view/view_NUC_SEQS.pyx
@@ -0,0 +1,76 @@
+#cython: language_level=3
+
+from obitools3.dms.capi.obiview cimport obi_new_view_nuc_seqs, \
+                             obi_new_view_nuc_seqs_cloned_from_name, \
+                             VIEW_TYPE_NUC_SEQS
+
+from ..view cimport register_view_class
+
+from obitools3.dms.obiseq cimport Nuc_Seq, Nuc_Seq_Stored
+
+from obitools3.dms.dms cimport DMS
+
+from obitools3.dms.capi.obitypes cimport index_t
+
+from obitools3.utils cimport tobytes, bytes2str
+
+from obitools3.dms.capi.obidms cimport OBIDMS_p
+
+from obitools3.dms.object cimport OBIWrapper                          
+
+
+
+cdef class View_NUC_SEQS(View):
+    
+    @staticmethod
+    def new(DMS dms, 
+            object view_name, 
+            object comments=None,
+            bint quality=False):
+
+        cdef bytes view_name_b = tobytes(view_name)
+        cdef bytes comments_b
+        cdef str message
+        cdef void* pointer
+
+        cdef View_NUC_SEQS view
+
+        if comments is not None:
+            comments_b = tobytes(comments)
+        else:
+            comments_b = b''
+
+        pointer = <void*>obi_new_view_nuc_seqs(<OBIDMS_p>dms._pointer, 
+                                               view_name_b, 
+                                               NULL, 
+                                               NULL, 
+                                               comments_b,
+                                               quality)
+        
+        if pointer == NULL :
+            message = "Error : Cannot create view %s" % bytes2str(view_name_b)
+            raise RuntimeError(message)
+        
+        view = OBIWrapper.new(View_NUC_SEQS, pointer)
+        view._dms = dms
+        dms.register(view)
+
+        return view
+
+    
+    def __getitem__(self, object item) :
+        if type(item) == str :
+            return self.get_column(item)    # TODO hyper lent dans la pratique
+        elif type(item) == int :
+            return Nuc_Seq_Stored(self, item)
+    
+    
+    def __setitem__(self, index_t line_idx, Nuc_Seq sequence_obj) :
+        for key in sequence_obj :
+            self[line_idx][key] = sequence_obj[key]
+
+
+
+def register_class() :
+    register_view_class(VIEW_TYPE_NUC_SEQS, View_NUC_SEQS)
+