From 8f189075663eef1cacbcb3dbfe8852c10ec0eb44 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 6 Feb 2019 18:09:11 +0100
Subject: [PATCH] Cython API: changed revcomp attribute of Nuc_Seq class to
 is_revcomp to be more explicit

---
 python/obitools3/dms/obiseq.pxd |  2 +-
 python/obitools3/dms/obiseq.pyx | 18 +++++++++---------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/python/obitools3/dms/obiseq.pxd b/python/obitools3/dms/obiseq.pxd
index 8c04f1c..c096649 100755
--- a/python/obitools3/dms/obiseq.pxd
+++ b/python/obitools3/dms/obiseq.pxd
@@ -15,7 +15,7 @@ cdef class Nuc_Seq(Seq) :
     
     cdef  Nuc_Seq _reverse_complement
     cdef  object  _quality_array
-    cdef  bint    _revcomp
+    cdef  bint    _is_revcomp
     cpdef set_quality(self, object new_quality, int offset=*)  
     cpdef object build_quality_array(self, list quality)
     cpdef bytes  build_reverse_complement(self)
diff --git a/python/obitools3/dms/obiseq.pyx b/python/obitools3/dms/obiseq.pyx
index efa1b30..1669ca4 100755
--- a/python/obitools3/dms/obiseq.pyx
+++ b/python/obitools3/dms/obiseq.pyx
@@ -144,7 +144,7 @@ cdef class Nuc_Seq(Seq) :
         if quality is not None:
             self.set_quality(quality, offset=offset)
         
-        self._revcomp = False
+        self._is_revcomp = False
         
         if tags is not None:
             for k in tags:
@@ -162,14 +162,14 @@ cdef class Nuc_Seq(Seq) :
         new_seq = Nuc_Seq(seq_to_clone.id, seq_to_clone.seq, definition=seq_to_clone.definition, quality=seq_to_clone.quality, tags=seq_to_clone)
         return new_seq
 
-    # revcomp property getter and setter (boolean indicating whether the sequence was created by reverse complementing another sequence)
+    # is_revcomp property getter and setter (boolean indicating whether the sequence was created by reverse complementing another sequence)
     @property
-    def revcomp(self):
-        return self._revcomp
+    def is_revcomp(self):
+        return self._is_revcomp
 
-    @revcomp.setter
-    def revcomp(self, bint revcomp):  # @DuplicatedSignature
-        self._revcomp = revcomp
+    @is_revcomp.setter
+    def is_revcomp(self, bint is_revcomp):  # @DuplicatedSignature
+        self._is_revcomp = is_revcomp
 
     # nuc sequence property getter and setter
     @property
@@ -227,7 +227,7 @@ cdef class Nuc_Seq(Seq) :
             else:
                 reversed_quality = None
             seq = Nuc_Seq(self.id+b"_CMP", rev_comp, definition=self.definition, quality=reversed_quality, tags=self)
-            seq.revcomp = True
+            seq.is_revcomp = True
             self._reverse_complement = seq
         return self._reverse_complement
     
@@ -400,7 +400,7 @@ cdef class Nuc_Seq_Stored(Seq_Stored) :
             else:
                 reversed_quality = None
             seq = Nuc_Seq(self.id+b"_CMP", rev_comp, definition=self.definition, quality=reversed_quality, tags=self)
-            seq.revcomp = True
+            seq.is_revcomp = True
             self._reverse_complement = seq
         return self._reverse_complement