Changed sequence 'description' to 'definition' everywhere

python/obitools3/obidms/_obidms.pxd

@@ -69,7 +69,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
 
     cdef OBIDMS_column ids
     cdef OBIDMS_column sequences
-    cdef OBIDMS_column descriptions
+    cdef OBIDMS_column definitions
     
     cpdef delete_column(self, str column_name)
     

python/obitools3/obidms/_obidms.pyx

@@ -69,7 +69,7 @@ from .capi.obiview cimport Obiview_p, \
                            VIEW_TYPE_NUC_SEQS, \
                            NUC_SEQUENCE_COLUMN, \
                            ID_COLUMN, \
-                           DESCRIPTION_COLUMN
+                           DEFINITION_COLUMN
                            
 from libc.stdlib cimport malloc
 from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
@@ -529,7 +529,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
         
         self.ids = self.columns[bytes2str(ID_COLUMN)]
         self.sequences = self.columns[bytes2str(NUC_SEQUENCE_COLUMN)]
-        self.descriptions = self.columns[bytes2str(DESCRIPTION_COLUMN)]
+        self.definitions = self.columns[bytes2str(DEFINITION_COLUMN)]
 
 
     cpdef delete_column(self, str column_name) :
@@ -542,7 +542,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
         cdef OBIDMS_column_header_p header
         cdef str column_n
  
-        if ((column_name == bytes2str(ID_COLUMN)) or (column_name == bytes2str(NUC_SEQUENCE_COLUMN)) or (column_name == bytes2str(DESCRIPTION_COLUMN))) :
+        if ((column_name == bytes2str(ID_COLUMN)) or (column_name == bytes2str(NUC_SEQUENCE_COLUMN)) or (column_name == bytes2str(DEFINITION_COLUMN))) :
             raise Exception("Can't delete an obligatory column from a NUC_SEQS view")
         
         view = self.pointer

python/obitools3/obidms/_obiseq.pxd

@@ -5,13 +5,13 @@ from ._obidms cimport OBIView_line
 
 cdef class OBI_Seq(dict) :
     cdef str id
-    cdef str description
+    cdef str definition
     cdef str sequence
 
     cpdef set_id(self, str id)
     cpdef get_id(self)
-    cpdef set_description(self, str description)
-    cpdef get_description(self)
+    cpdef set_definition(self, str definition)
+    cpdef get_definition(self)
     cpdef get_sequence(self)
 
 
@@ -23,8 +23,8 @@ cdef class OBI_Nuc_Seq(OBI_Seq) :
 cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
     cpdef set_id(self, str id)
     cpdef get_id(self)
-    cpdef set_description(self, str description)
-    cpdef get_description(self)
+    cpdef set_definition(self, str definition)
+    cpdef get_definition(self)
     cpdef set_sequence(self, str sequence)
     cpdef get_sequence(self)
    # cpdef str reverse_complement(self)

python/obitools3/obidms/_obiseq.pyx

@@ -4,15 +4,15 @@ from obitools3.utils cimport bytes2str, str2bytes
 
 from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
                            ID_COLUMN, \
-                           DESCRIPTION_COLUMN
+                           DEFINITION_COLUMN
 
 cdef class OBI_Seq(dict) :
 
-    def __init__(self, str id, str seq, str description=None) :
+    def __init__(self, str id, str seq, str definition=None) :
         self.set_id(id)
         self.set_sequence(seq)
-        if description is not None :
-            self.set_description(description)
+        if definition is not None :
+            self.set_definition(definition)
         
     cpdef set_id(self, str id) :
         self.id = id
@@ -21,12 +21,12 @@ cdef class OBI_Seq(dict) :
     cpdef get_id(self) :
         return self.id
             
-    cpdef set_description(self, str description) :
-        self.description = description
-        self[bytes2str(DESCRIPTION_COLUMN)] = description
+    cpdef set_definition(self, str definition) :
+        self.definition = definition
+        self[bytes2str(DEFINITION_COLUMN)] = definition
         
-    cpdef get_description(self) :
-        return self.description     # TODO no
+    cpdef get_definition(self) :
+        return self.definition
         
     cpdef get_sequence(self) :
         return self.sequence
@@ -53,11 +53,11 @@ cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
     cpdef get_id(self) :
         return self[bytes2str(ID_COLUMN)]
             
-    cpdef set_description(self, str description) :
-        self[bytes2str(DESCRIPTION_COLUMN)] = description
+    cpdef set_definition(self, str definition) :
+        self[bytes2str(DEFINITION_COLUMN)] = definition
 
-    cpdef get_description(self) :
-        return self[bytes2str(DESCRIPTION_COLUMN)]
+    cpdef get_definition(self) :
+        return self[bytes2str(DEFINITION_COLUMN)]
 
     cpdef set_sequence(self, str sequence) :
         self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence

python/obitools3/obidms/capi/obiview.pxd

@@ -18,7 +18,7 @@ cdef extern from "obiview.h" nogil:
     extern const_char_p VIEW_TYPE_NUC_SEQS
     extern const_char_p NUC_SEQUENCE_COLUMN
     extern const_char_p ID_COLUMN
-    extern const_char_p DESCRIPTION_COLUMN
+    extern const_char_p DEFINITION_COLUMN
 
     struct Column_reference_t :
         const_char_p  column_name